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  • 8/10/2019 Siezen, 1997, Subtilase

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    Protein

    Science

    (1997 ), 6301 -523. Cambridge University Press. Printed in the USA.

    Copyright

    0

    1997

    The

    Protein Society

    REVIEW

    Subtilases:

    The superfamily of subtilisin-like serine proteases

    ROLAND J. SIEZEN

    A N D

    JACK A.M. LEUNISSEN2

    Department of Biophysical Chemistry, NIZO, P.O. Box 20, 6710BA Ede, The Netherlands

    CAOSKAMM Center, University of Nijmegen, Toernooiveld, 525ED, Nijmegen, The Netherlands

    (RECEIV ED ugust 22, 1996; ACC EPTE Dovember

    5 ,

    1996)

    Abstract

    Subtila ses are memb ers of the clan (or superfamily) of subtilisin-like serine proteases. Over 200 subtilases are presently

    known, more than 170 of which with their complete amino acid sequence. In this update of our previous overview

    (Siezen RJ, de Vos WM, Leunissen JAM, Dijkstra BW, 1991,

    Protein

    Eng 4719-731), details of more than

    100

    new

    subtilases discovered in the past five years are summarized, and amino acid sequences of their catalytic domains are

    compared in a multiple sequence alignment. Based on sequence homology, a subdivision into six families is proposed.

    Highly con served residues of the catalytic domain are identified, as are large or unusual deletions and insertions.

    Predictions have been updated for Ca*+-bindingsites, disulfide bond s, and substrate specificity, based on both sequence

    alignment and three-dimensional homology modeling.

    Keywords:

    homology modeling; sequence alignment; serine protease; subtilase; subtilisin family

    Serine endo- and exo-peptidases are of extremely widespread oc-

    currence and diverse function. Many distinct families of serine

    proteases exist; they have been grouped into six clans (Rawlings

    and Barrett, 1994; Barrett and Rawlings, 1995), of which the two

    largest are the (chymo)trypsin-like and subtilisin-like clans. These

    two clans are distinguished by a highly similar arrangement of

    catalytic His, Asp, and S er residues in radically different PIP (chy-

    motrypsin) and a @ (subtilisin) protein scaffolds.

    In 1991, we presented a review of over 40 members of the

    subtilisin-like serine proteases, termed sub tilases, which occur in

    Archaea, Bacteria, fungi, yeasts, and higher eukaryotes (Siezen

    et al., 1991). The mature enzymes were found to contain up to

    1775 residues, with N-terminal catalytic domains ranging from

    268 to

    5 1

    1 residues, and signal and/or activation-peptides ranging

    from 27 to 280 residues. Several members contain C-terminal

    extensions, relative to the subtilisins, which display additional prop-

    erties such as sequence repeats, Cys-rich domains,

    or

    transmem-

    brane segm ents. From four known crystal structures and a multiple

    alignment of 40 known amino acid sequences, a core structure was

    predicted for the catalytic domain of all subtilases, together with

    the variations that are allowed in the main-chain length as a result

    of insertions and deletions (Fig.

    1).

    Nineteen of these core residues

    were found to be highly conserved, 10 of which are glycines.

    Predictionswerealsomade for subtilases of unknown three-

    dimensional structure concerning essential conserved residues, al-

    Reprint requests to: Dr. Roland J. Siezen, Department of Biophysical

    Chemistry, NIZO, P.O. Box 20, 6710BA Ede, The Netherlands; e-mail:

    [email protected].

    lowable substitutions, disulfide bonds, Ca2+-bind ingsites, substrate-

    binding site residues, ionic and aromatic interactions, and surface

    loops. Based on these predictions, strategies for homology mod-

    eling and protein engineering were developed and implemented,

    aimed at modulating either stability, catalytic activity, or substrate

    specificity (Siezen et al., 1991, 1993, 1994, 1995a).

    Since 1991, more than 100 new subtilases have been discovered,

    and these are now included in this updated review. In addition to

    many new enzymes from micro-organisms, numerous members of

    the subtilase superfamily have now also been identified in various

    eukaryotes such as slime molds, plants, insects, nematodes, mol-

    luscs, amphibia, fish, mammals, and even in a catfish virus.

    Structure-based alignment

    The coordinates of subtilisin BPN, subtilisin Carlsberg, thermi-

    tase, and proteinase K were used previously (Siezen et al., 1991)

    to determine the core of structurally conserved regions (scrs;

    Greer, 1990) and the common secondary structure elements, as

    analyzed with the DSSP program (Kabsch and Sander, 1983). This

    core of about 190 residues contains virtually all of the common

    a-h elix and &strand elements, including the active site residues

    D32, H64, and S221 (Siezen et al., 1991). Slight adjustments to

    thesecore regions have now been incorporated (core ABC in

    Fig. 2) based on a recent spatial superpositioning of seven struc-

    tures that also included mesentericopeptidase, Savinase, and

    Es-

    perase (Heringaetal., 1995); topologically equivalent residues

    were defined as those that have Ca-atom distances of less than

    2.0 A . The variable regions (or vrs) nearly always correspond to

    501

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    502

    R.J. Siezen and J.A.M. Leunissen

    A

    connecting loops between helices and strands and generally lien

    the external surface of the protein (Fig. 1).

    When only the subtilisin BPN', subtilisin Carlsberg, and ther-

    mitase structures were superimposed the number of structurally

    equivalent Ca atoms increased to over 230or about 85% of allCa

    atoms), which we refer o as the extended core (core AB n

    Fig. 2). This distinction between core and extended core scrs is f

    relevance

    for

    homology modeling, because the superfamilyf sub-

    tilases can be subdivided into several families (see below).

    Identification of subtilase supetfamily members

    An extensive search of scientific literature and databases (EMBL,

    Genbank, Swiss-Rot) was performed o dentify new subtilisin-

    like serine proteases, using the programs BLAST (Altschul et al.,

    1990), TFASTA, and FASTA (Pearson and Lipman, 1988). Con-

    sensus sequence segmentsf 20-40 residues around he active site

    residues D32, H64, and S221 were used or this purpose; different

    consensus segments were obtained or different subtilase families

    (see Fig. 2). Sequences from patent literature and databases are not

    included because they represent synthetic or mutated genes encod-

    ing engineered subtilases. The main results of these searches are

    summarized n Tables 1 and 2. Further details, including reference

    to 10 crystal structures, can be found in the EMBLlGenbank and

    PDB databases using codes listed in the tables.

    At present, over 170 complete and several partial amino acid

    sequences of subtilases are known; most are derived from he

    B

    n

    Fig.

    1.

    A:

    Schematic representation

    of

    the secondary structure topology

    f

    subtilases, with a-he lices shown as cylinders and p-sh eet strands as ar-

    rows. Solid lines indicate he conserved regions (scrs) o al l subtilases, and

    dashed lines the variable regions (vrs ). Approximate location is indicated

    of

    the main Ca2+-b inding sites (by Ca l and CaZ), catalytic triad residues

    D32,H64,

    nd S221 (by

    *)

    and substrate-binding region (between strands

    e1 and em ). B: Ribbon-plot representation

    of

    the secondary and tertiary

    structure

    of

    subtilisin

    (PDB

    ode

    2SNI),

    made with MOLSCRET (Krau-

    lis, 1991).Side chains of the catalytic residues are shown in ball-and-stick

    representation.

    corresponding geneor cDNA sequences. We caution that in many

    cases it has not been established whether these genes encode func-

    tional proteinsor whether the encoded protein is actually a prote-

    ase. Examplesof the latter are the outer-membrane antigenhssal

    of

    Pasteurella haemolytica

    (Lo et al., 1991), and the anti-freeze

    protein af70 of Picea abies (EMBL D86598), which were not

    described as proteases by the authors.

    Themajority of the subtilases are synthesized as pre-pro-

    enzymes, subsequently translocated over cell membrane via the

    pre-peptide (or signal peptide), and finally activatedy cleavage of

    the pro-peptide. A detailed comparison of the pre-pro sequences

    and the putative processing sites f these subtilases has identified

    two main types of pro-peptide (Siezen et

    al.,

    1995b). However,

    there

    are

    numerous exceptions n which the pro-peptides appear o

    be completely unrelatedor even absent. A small number of subti-

    lases is intracellular (Table 1).

    Table 1 shows that the (putative) mature enzymes range in size

    from 266 o 1775 residues. The catalytic domain or module s

    defined as the segment with sequence homology to subtilisins; it is

    always located at the N-terminal end of the amino acid sequence

    directly after the pre-pro region.This review is focussed

    only

    on

    the catalytic domains.

    Alignment of primary sequences

    The multiple sequence alignment f the catalytic domains of over

    120 subtilases is shownn Figure 2. Additional variants with 10%

  • 8/10/2019 Siezen, 1997, Subtilase

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  • 8/10/2019 Siezen, 1997, Subtilase

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    ~ ~ N Y D P D I S y D F ~ N D D D p Q P R Y ~ ~ ~ ~ ~ ~ ~ ~ ~ T N ~ N ~ G ~ c A G E ~ A M A A ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ c ~ ~ ~ ~ ~ A ~ N ~ ~ A R ~ G G ~ R M L D~ ~ - G Y V T D I Y E I S S I G F N I Q - - - - - - - H V D I Y S R S W C P N D D - E G P E K L A

    ~ - N y D S y A S y D V N G N D Y D p ~ P R Y ~ ~ ~ ~ ~ ~ ~ D A ~ N E N ~ ~ ~ c A G E V A A S A - ~ ~ ~ . ~ . ~ ~ y c ~ . v ~ I A Y N ~ ~ A K ~ G G I R M L D - - - - - G D ~ ~ V V E A K S L G ~ R P N - - - - - - - ~ - ~ ~ ~ ~ ~ ~ ~ ~ Y ~ D

    - -NYD LI SCDVNGNDLDPMPRY~-~-...As NEN~G=cACEVAAAA---....

    S ~ ~ T . ~ G ~ A ~ ~ - - ~ K I ~ ~ ~ R ~ ~ ~ - - - - - ~ D V ~ M V E A K S V S F N P Q ~ ~ ~ ~ ~ ~ ~ ~ - ~ ~ ~ ~ ~ ~ ~ ~ H

    ~ . N Y D P I I I \ S Y D V N S I I D D D ~ M ~ H ~ . . . . . . . ~ ~ ~ ~ ~ ~ ~ ~ A G E " ~ T ~ . . . . . . . ~ ~ F ~ A . ~ G ~ ~ ~ ~ . . ~ ~ " G ~ V ~ L D . ~ ~ ~ ~ G D V T D A V E A R S L S L N P Q ~ ~ ~ ~ ~ ~ - - - - ~ - - - - -

    - - NYDPI ( I I SYDYNGNDGDpMPHC ...L T O s ~ G= CA G E V ~ T A--....~ K C A . ~ G I A Y ~ - - A R V G C V ~ L D - - - - - G D V T D V V E A K S L G L N S Q ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ H ~ D ~ Y S A S W G P D D D ~

    ..

    ~ o p K ~ s y ~ v N mo ~ ~p Q p n y...... I I NS~G=CAG~VAAI A

    ......

    ~ ~ ~ A . v ~ ~ A F H . . A G I G G V ~ L D ~ ~ ~ ~ ~ G D V ~ A V E A R S L S L N S Q ~ ~ ~ ~ ~ ~ ~ ~ - ~ - - - - - - - Y ~ D l Y S A S W G P D

    ~ . N ~ ~ ~ R ~ ~ ~ ~ V ~ ~ ~ ~ ~ ~ ~ R ~ . . . . . . . ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ G ~ V ~ ~ F . . . . . . . ~ ~ L ~ I . ~ ~ I A Y N . . A N I G G ~ ~ L D ~ . ~ ~ ~ G D V T D A V E A A S V G ~ N A D ~ ~ - - - - - - ~ - - - -

    ..

    YDPYI \ SYDLNDHDNDPM~R~

    ...... ASNE*G~CAGE SAEA ..~...~-~ ~ ~ ~ ~ I A p D ~ ~ ~ ~ I ~ ~ ~ ~ ~ L D ~ ~ ~ ~ ~ ~ ~ V Y ~ A ~ ~ A A S L S F ~ ~ - ~ ~ ~ ~ ~ ~ ~

    .. YDEI ( ASYD NGHD~DP~PRY...... y~E~G=c AGVV- QA.......

    v ~ ~ . v ~ V A Y N . . AR I G G V ~ L D ~ ~ ~ ~ -G D V ~ S V E A Q S L G LN S Q - - - - - - - - - -- - - ~ ~ ~ - H I H I Y SA T W G P D D D " " - " " "G R F J D G P A T L A

    : : ~ : ~ ~ : : ~ : ~ ; i ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ : : : ~ : : ~ ~ N D ~ ~ ~ ~ ~ : ~ ~ ~ ~ : ~ : ~ ~ ~ ~ : ~ ~ ~ ~ ~ : ~

    : ~ ~ ~ ~ ~ a : ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ g ~ ~ ~ : ~ ~ : : ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ : : ~ : : ~ : : : : : ~ ~ ~ ~ ~ : ~ ~

    : : ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ : : : : ~ : : : : : ~ ~ ~ ~ ~ ~ ~ ~ : ~ ~ ~ : : ~

    : : ~ F ~ ~ ~ ~ ~ : ~ ~ ~ ~ ~ ~ ~ ~ ~ : : : : : : ~ : : : ~ ~ ~ ~ ~ ~ ~ ~ : ~ ~ ~

    ~~N~D~EASF DI NGNDSOPTP Q~~~~. . . .N~DN*G=cAGEVAAVA ..... ~ ~ ~ ~ ~ ~ . ~ ~ v A y N ~ ~ A s I G G v R M L D ~ ~ ~ ~ ~ G K ~ N D ~ E A Q A L S L N P S ~ ~ ~ ~ ~ ~ ~ ~ - ~

    ~~N~DPL AST DI NDHDDD~TP Q~ ~ ~ ~ . ~ . .GDN* G~=A~EVAALA .......

    ~ ~ ~ . ~ ~ v A F K ~ ~ A K ~ ~ ~ v ~ ~ L D ~ ~ ~ ~ ~ G A V S D S V E A A S L ~ ~ N Q D - . . ~ ~ ~ ~ ~

    KTFDGPGPLA

    ~ ~ N ~ D Q T A S I V L N D N D N D ~ ~ ~ R ~ ~ ~ ~ ~ ~ ~ ~ D ~ D A D N ~ ~ ~ = ~ A G E A A A I A

    ...... ~ ~ c ~ . ~ ~ v A y N ~ ~ A K l G G v R M L D ~ ~ ~ ~ ~ G Q A T D A L E A S A L G F R G D

    . . . ~ ~ ~ . - -

    ~ ~ ~ ~ ~ ~ " I D l Y l ~ C W G P K D D ~ - - - ~ ~ ~ ~ ~ ~ ~ G K

    ~ ~ N ~ S ~ ~ G S ~ D L N S N D ~ D ~ ~ P H P - - " - - D V E N G ~ ~ ~ ~ A G E ~ A A V P - - - . ~ ~ ~ ~ ~ F ~ A ~ ~ G V A Y G ~ - S R ~ A C I R V L D ~ - ~ ~ ~ G P L T D S M E A V A F N ~ Y Q ~ ~ ~ ~ ~ ~

    ~~SCKI APRD TRKRI FPTP .~..~......- ~ G T A C A G V A C G ~ ~ ~ ~ ~ ~ ~ ~ . N G ~ G * . S G V A ? G. K = ~~ I ~ F v......L G S Q D E A D S ~ " ~ A ~ Q ~ - - - - ~ - - . - ~ ~ ~ ~ ~ ~ ~ C A D V I S C S W G P P D G ~ - T W W D D R D P L H K Q K V P

    rSYAVVSESWGCVDD-----------GAAFCDTTGNF

    ~~WRP ~CSKWVTGCS DP~p ~ ~ ~ ~ ~ ~ . T ~ D ~ ~ ~ ~ . .V ~G I I A A V~ ~ ~ ~ ~ ~ ~ D N ~ I ~ ~ . L G V A ~ R . . ~ Q L Q ~ ~ N ~ ~ D ~ . . . N I Q Q L Q K D ~ L Y A L C Q R R ~ ~ ~ Q P G - - - . ~ - ~ ~ ~ ~ ~ ~ L Q P E L R M S L V D P E G ~ - - - ~

    ~ ~ V N C V A C K P D T A D C A W R P S ~ ~ ~ ~ ~ - - - - - I \ I E S P ~ G ~ ~ G E I A A A K ~ - ~ ~ - - - - N G V G ~ - T C V A ~ G - - ~ K V A ~ I K V S N P - - - D G F F Y T E A ~ C G F M W A A E H - - ~ - ~ - ~ - ~ ~ ~ ~ ~ ~ ~ - C ~ D V ~ S Y Y T

    : ~ ~ ~ , " ~ ~ ~ ~ ~ , " ~ ~ ~ ~ ~ ~ ~

    : ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~

    y F ? r . , ~ ~ ~ y ~ F ~ ~ ~ ~ ~ ~ ~ : : : : . : : : : ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ : : : : ~ ~ ~ ~ ~ ~

    ~ ~ I P Y ~ K G D A F R y D G T p S Y D S D " - - - - - - - - C T L G S ~ G ~ v A A S P P A A E ~ ~ ~ - - - - - D G G ~ . H G V A F N ~ ~ A Q I l S A E N G D P ~ 6 ] I L ~ N D ~ A V Y Q A G W D A L V A S ~ ~ ~ ~ ~ ~ - ~ - - - - - - - ~ G A R I ~ ~ S W G I G ~ T ~ ~ D ~ Q K

    ~ - ~ Q W L G S T N L N I \ H T G I L P I T Y V ~ N V P ~ ~ ~ D S S S G E G ~ A G F J G G T G A - - - - - - M S G G K Y ~ E G V A P G - - E N L ~ G Y G S G A . . . . . ~ V V A M L D T L G G F D Y A L ~ Q Q E Y ~ ~ ~ - ~ ~ - - - - - - N I R I l ~ S W G A T S D " - - - - - ~ ~ ~ ~ A G T

    - - V Q N V L G S T N L Q G I T G I L P I T Y T ~ N V P ~ ~ ~ D ~ S ~ G ~ A G ~ G G T G A - - - - - ~ M S G G K Y - ~ G A A P G - - A D L I G Y G ~ G G . . . . . ~ A L F ~ L D G ~ G G F D Y A ~ ~ ~ E Y ~ ~ ~ - - - - - - - - - D ~ R V ~ ~ S W G S S

    ~~NEP ENEMNWYDAVAGEASP......... Y D D ~ ~ G ~ ~ G T M V G S E - - - - - - - P D G ~ Q . l G V A P G - - A K ~ l A V ~ A F S E - - - - D G G T D ~ I L E A G E W V L A P ~ A E G ~ H P E M " - - - A P D V ~ S W G C G S G " " " - ~ ~ ~ ~ ~ ~ "

    ~~NFGQYKGYDFVDNDYDPI ( ET... TGDpRGEA~nG- ~~~AANGTl

    ...........

    GVAPD~~ATLLAY RVLGP.. G 5 G T T E W I A G V E R A V Q D - - - - - ~ ~ - ~ ~ - - - - - - G A D V M N L S L G N S L N " - - - - - ~ ~ ~ ~ ~ ~ ~ " N P D

    W V N D K V A Y Y H D y S I ( D G K T " - - A V D Q E B G T W S G I L S G N A P S E T ~ - - K E P Y R L . E G A M P E - - A Q L L L M R V E I V N - - G L A D Y ~ Y A Q A I R D A V ~ - - - - - - - - - - ~ ~ ~ ~ ~ - G A K V I N E I S F G N A A L - ~ ~ ~ " " " - ~ ~ A Y A N L P D E T

    S C N G K I V G A Q Y F R H G A I A V ~ E ~ - N R T R D Y R S P F D ~ G E G S ~ T A S T ~ G N ~ ~ A ~ ~ ~ N G Y N F G Y A S G M A P G - - A W I A ~ Y ~ L ~ ~ - - - - F G G ~ S D V V A A Y D ~ ~ E ~ ~ ~ ~ ~ ~ ~ - - - - - - - - - - G V D I I S L S V

    H C N S ~ L I C I R Y F ~ C I H A A I P - N A T F S M N S R R D T L G E G ~ T A ~ T ~ ~ N ~ N G A S ~ F G Y G K G T A R G I A P ~ - - R R ~ ~ ~ ~ ~ ~ T ~ P - ~ ~ ~ E G R Y T S ~ V L ~ G ~ ~ ~ I A D ~ ~ - ~ ~ - - ~ - - - - - - - ~ G V D V I

    R C N R K I I G A R S Y H I G R P I S P G - - - - - - D ~ G P ~ D ~ G E G ~ T ~ S T ~ G G L V ~ ~ ~ L Y G L G L G ~ A R G G V P L - - ~ R I A A Y K V C W N . ~ ~ ~ D G C S D ~ I L A A Y D D A I A D ~ ~ ~ - - - - ~ - - - ~ ~ ~ ~ ~ G V D I I S L S V

    K C ~ K L I G A R S Y Q L G H C . ~ ~ ~ ~ ~ ~ ~ ~ ~ - - - S P I D D D G ~ G ~ ~ A S T ~ G A F V N G ~ F G N ~ G T A A G V A P F - - A H I A V Y K V C N S ~ ~ - - D G C ~ ~ V L ~ M D ~ I D D - - - - - - - - ~ ~ ~ ~ ~ - ~ - G V

    L C N R K L I G A R F F R R G Y E S M G p ~ D E S K E S R S ~ ~ D D G E G ~ T 5 S T A A G S V V E G A ~ L L ~ Y A ~ G T A R C M L - - ~ - H A L A V Y K V C ~ L - - - - G G C F S S D l L ~ l D ~ l A D - ~ ~ ~ ~ " ~ " " " " W W L S U S L G G G M S ~ ~ ~ " "

    KNVKERRI WRTL

    .............

    DDG~GEGT~VAGVI ASMRE~

    ...........QF A p D . . A ~ L H ~ F RV F ~ . ~ ~ N Q v S Y T SW F L D A F N Y A l L K -- - - - - - - - - ~ ~ ~ -~ - ~ I D V L N L S l G GP D F " " - ~ ~ ~ ~ ~ " "" U D H P F V

    N C N R I ( I I C R R Y ~ S ~ ~ E D D D L K ~ ~ ~ I W P E S R T ~ ) Y Q G ~ C ~ Y T ~ T A A ~ S F ~ N ~ N G L ~ ~ ~ ~ ~ G ~ ~ A S S S ~ ~ A ~ ~ V C G L - - - ~ ~ G ~ P G ~ Q ~ L A A F D D A ~ ~ ~ - - - - ~ ~ ~ -

    .~~~

    ~~~~ . - ~ ~ ~ f y ' : ~ ~ ~ ~ , , I ~ ~ ~ ~ : : ~ ~ ~ : ~ ~ . ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ : ~ ~ ~ ~ ~ ~ : : : : ~

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    D V I A ~ D N G T ~ ~ ~ ~ ~ ~ N G ~ T . ~ ~ ~ ~ ~ ~ S D F H G ~ G T S V ~ ~ I A S R G R V L Y D L Y G D G ~ L ( ~ ~ G V ~ P G - - A K I A G G D A W L L - - - C N I L V L E A N L A G F N I V T E E E D G W Y L S L D P F G P H - ~ D I ~ S N S W G S ~ Y

    ~~~

    ~~~~

    Fig. 2. Continues.

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    Q N A H R N F y Q Q " " . G H L L ~ ~ c N ~ c ~ ~ . ~ . . . . . . . . . ~ . ~ . . . ~ . . ~ . c ~ ~ y p ~ s y ~ ~ ~ ~ . ~ ~ ~ ~ " ~ " ~ ~ . . . . . . . ~ ~ . . . . . . . . s ~ ~ ~ ~ ~ . . . . . ~ Q ~ ~ ~ Q ~ ~ ~ ~ ~ ~ ~ . . . . . . ~ E~~

    RDASyWAqQQ . ~ ~ . .AVQI-I\QTsGDc~pL ~.. . . . .~. . . .~~..~ ~ C y p A K y S...V I ~ - V D Q

    . . . .~~~~.... . . . .

    c S V p T~ . . ~ .S S D G p E~ ~ - ~ . . . . . . . ~ .D T A A P G V - - - - - - - ~ ~

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    - - ~~~~~

    T N A V D Y A Y D K - ~ ~ ~ - G Y L I I ~ A I \ G I ( S G P K P G - - - - - - - - - - - - - ~ ~ ~ ~ - - - S I ~ Y ~ ~ A L V - - - - N ~ ~ ~ ~ A ~ ~ ~ N ~ ~ ~ ~ ~ ~ ~ ~ ~ - - - ~ I Q ~ ~ T ~ ~ ~ ~ ~ F ~ ~ ~ ~ ~ S S ~ ~~~~~

    E A K ~ ~ S . Q I L W ~ - ~ ~ c ~ ~ D~ ~ ~ ~ ~ . . . . . . . ~ . . . . . . ~ ~ ~ ~ ~ ~ ~ ~ . ~ . .V I S V G A I N F ~ ~ ~ ~ ~ ~ ~ ~ ~ . . . . . . . .~ A S E F ~ ~ ~ ~ ~ S N S ~ E~ ~ ~ ~ ~ ~ ~ ~ V D L V A p G E . . . . . .

    .

    ~ ~~~

    ~ ~ ~ ~ N I \ V ~ N . G V L V V C ~ C ~ ~ D C D E R T E~~..............

    L ~ y p A A~ . . .E V I A V G S V S V~ ~ ~ ~ ~ ~ ~ ~ ~ . . . . . . . .R E ~ S ~ F ~ ~ ~ ~ ~ S N A N K E.......... ~ ~ ~ L V A ~ G ~ . . . . . . . ~

    .

    ~~~~~

    I ( ~ R V X y A V S N " " " 1 S v v ~ ~ ~ ~ c D c ~ ~ D~~~. . . . . . . .~ . . . . .~ A y p A A y N V I A V G A V D F ~ ~ ~ ~ ~ ~ ~ ~ ~ . . . . . . . .L R L s D F . ~ ~ ~ ~ p - E E ~ ~ ~ . ~ .D I V A P G . ~ . .

    H Q ~ I R W \ ~ ~ E . ~ ~ " D I L V ~ ~ ~ ~ ~ ~ ~ c ~ ~ ~ ~ ~ . . . . . . . . ~ . . . . . ~ y ~ y p c ~ y p . . . . ~ ~ ~ Q ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ . .

    WDRIKEAVAS"".GRLVV=-G~cDcNEE ~~~~... . . . .~ ~ ~ ~ ~ ~ ~ F A y p G A yE VVQVGSVSL . . . ~ . . ~ ~ ~ . . . . . . . . ~ ~ ~ ~ ~ ~ ~ . . . . .N S N C K ~ ~ ~ ~ ~ ~ ~ ~ ~ ~D L V I \ * G E . ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ .

    Fig. 2.

    Continues.

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    - - - - - - - - - - - - N Y A R I I I - S G T S H R S P H I A C L L A Y F V S L Q P S S D S A ~ A V ~ ~ ~ ~ ~ ~ E E L T P A K L K K D I I A I A T E ~ A ~ ~ - - - - - - - ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~6 1

    ~~N I L S T Y I GS - ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ - - ~ - - - - - - - O D I T A T L - S G T S H I S P R Y I C L L T Y F L S L Q ~ C S D S E F F E L G Q ~ ~ ~ D S L T P Q Q L K K ~ ~ ~ ~ ~ ~ T ~ ~ ~ ~ ~ - - - -5 1

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    ~ ~ - - - ~ - I \ A S I I S E V X D A I I K M G I H D V L L ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ S I P V G S S

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    ~ - E I I T T I G T D A I W I D F Q F I E N V P R G F I l n - I G T S L I T G L F ~ I ~ - - - - - - - - - - - - - - - - - -- - - S L QR F KS A NF Y

    K Q S V L S T S S ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ - - - ~ - ~ ~ - - - - N G R Y I Y Q - S G T S L R ~ P I Y S G I \ L R L E I D I ( Y Q - - ~ ~ - - ~ ~ ~ - - -L ~ O Q P E T A I E L F r K r c l E K E r Y H D R X B Y G N C r L D V Y K L L K E

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    ~ ~ E " L A l D K ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ . ~ " " " " " " " . Q S E I T I Q . S G T S F I \ T P ~ " ~ ~ " ~ ~ L y l E D C E " ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ S I D L D F L R S I ( S E D L G " " " " ~ ~ ~ ~ ~ ~ ~ ~ ~ ~

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    E K ~ I L T T D L H ~ ~ ~ ~ ~ ~ ~ ~ - - - - - - - - - - - - - - - - - - H A C ~ H - T G T S A S A P L A A G I V A L A L E A N P ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ N L T W R D L Q H ~ V I R T A K P I N L ~ G D - - - - - - - - ~ - - - - - W T T N G V G R

    E K Q I V T ~ L H ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ - - - - - - - - - - - - - - - ~ ~ ~ ~ ~ ~ - ~ ~ T ~ A S A P I V ~ ~ L L A L A L E A N P ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ S L T W R D L Q ~ I I ~ E T A K ~ D ~ L ~ ~ D ~ - - - -

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    E K C I A S T D L H ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ - ~ ~ ~ - - - - - - - - - - - - E K C T ~ - T G T S I \ S I ~ ~ ~ ~ ~ ~ ~ E - - - - - - - - - - ~ ~ - ~ W V T N C V G R Q V S L R Y G Y

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    E K Q I V T T D L R - - - - - - - - - - - - - - - " - Q I [ C T E S H T C T E S H ~ T G T S A S A P L A A G I I A L T L E A N K - ~ ~ ~ - ~ ~ ~ ~ ~ - - - - - N L T W R D M Q H L V V Q T S K ~ A H L N A ~ ~ ~ ~ - ~ ~ ~ ~ ~ - ~ ~ - - W A T N G V G R K V S H S Y G Y G L L D

    Q P A I V N D V P - - - - - - - - - - - - - - - - - - - - ~ ~ ~ - ~ ~ G G C ~ K H ~ T G T S A S A P L A A C I I A L A L E A N P ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ E L T W R D M Q H L V L R T A N ~ K P L E ~ G - - - - - - - - - - - - - W S R N G V G R M V S N

    D K S V A N D H D G S L R P D - - - - - - - - " - H I C ? 1 I E H T C T E R S A P L A A G I C A L A L E A N P ~ ~ ~ ~ ~ ~ ~ ~ - - ~ ~ - ~ ~ E L T W R D M Q Y L V V Y T S R P A P L E ~ E N C ~ ~ ~ - ~ ~ ~ - - - - - - ~ T L N ~ V K R K Y S N K F G Y G L M D A G A

    E N ~ H Y ~ L Y - - - - - - - - - - - - - - - - - - - - - - - - ~ - H ~ T E E F ~ K G T S A S A P L A A G I ~ A L T L E A N P ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ L L T ~ R D V Q A L I V H T A Q I T S P V D E ~ - - - - - - - - - - - - - - W ~ R N C R C F H F ~

    L R S I V T T D W D L Q K G - - - - ~ ~ - - ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ T ~ C T E C H ~ T ~ T S A A A P L A A ~ M I A L M L Q V ~ P ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ - C L T W R D V Q H I I V F T A T R Y E D R R A E - ~ ~ ~ ~ ~ ~ - - - -

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    - - Y I I T T D L D - - - ~ - ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ - - - E K C S K I 1 ( - G C T s l U \ R P L A A G I Y T L V L E R N P - - - - - - - - - - - - - - - N L T W R D V Q Y L S I L S S E E I N P H D G K ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ - W Q D T ~ G

    - - Y ~ H S S D I N ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ - ~ ~ - - ~ ~ ~ - - - G R C S N S H - G G T S ~ A P L A A G ~ Y T L ~ L E A N ~ - - - - - - - - - - - - - - - N L ~ W R O Y Q Y L S I L S A V G L E I W A D G D ~ ~ ~

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    ~ ~ P N E ? V U Y D ~ - - - - - - - - - - - - - - - - - - - - - - - - - G K C G F I P - S S S S A R P P I L G ~ L L A L I R A H P - - - - - - - - - - - - - - ~ T L T L ~ I Q R I L ~ R A A ~ ~ V ~ T ~ ~ G R G W ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ W L M l V ~ R ~ ~ R N F

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    81

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    TLFNII-SGTSMSCPHITGIAT~KTY~P ...~ T W S P A A l K S A L M ~ A S P M N ~ - - - ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ - - - - - - - - - F N P Q A E F A Y C S G H V N P L K A V R ? G l

    - ~ N I I A A W N P P N Q S D E D T W S E H T - - - - - - - - - - - - P S T F M L L ~ ~ ~ - ~ - - -- - - - T N ~ S D ~ P G T P F D F G A G W N P I C R L P P C o

    ~ ~ N ~ L A A U T G A R G P T G L A S D S R - - - - - - - - - - - - - - R V E F N I I ~ S G T S M S C P H V S G L A A L L K S V H P - - - - - - - - - - - - - - - ~ ~ ~ P ~ ~ R S A L M ~ A Y K T Y K D G K ~ ~ - - - - - ~ ~ ~ ~ ~ ~ - - L D ~ A T G K P S T P F D H G A G H V S P T T A

    - - GVRGSGV~ - ~ - - - ~ ~ ~ ~ ~ ~ ~ ~ - ~ - ~ ~ ~ . ~ ~ ~ - ~ -GGCRAL. ~ G T ~ ~ A ~ ~ ~ A ~ A ~ T L L ~ ~ ~ Q . . . . . . . . . . . . ~ E L ~ N ~ A ~ ~ K Q A L I A ~ ~ ~ ~ ~ ~ ~ . . . ~ ~ ~ ~ ~ ~ - - - - - -

    - - Y ~ ? . ~ ~ ~ ~ N ~ E N S T o Q C G D G S L P N - - - - - - - - - - - R N ~ ~ ~ ~ ~ - ~ ~ T S ~ A T P L A T A A T T l L R Q Y L V D G Y F P T G E S V E E N K L ~ P ~ ~ ~ ~ ~ ~ ~ L ~ l M I A Q L L N G T Y F W S A S S - - ~ - ~ ~ T N P S N A ~ F E Q l N C A N

    - - Y I T S ~ S N G ~ ~ Q C GD G S L P N - - - - - - - - - - -~ A L L A l - S G T S M A T S F AA A A ~ l L R Q Y L V D G Y Y P TG S l V E S ~ L Q P T G S L L K AL M l M I A Q L L N G T F Q L lT S S S l ~ ~ ~ - T Y P S N Q V FE N F A G A S L V ~ W G A I ~ S NW L H V l l O ~ 2 l

    ~~A I A S V P QF T ~ ~ ~ ~ . ~ ~ ~ ~ ~ ~ ~ ~ . ~ . ~ . . . ~ . . .S K S Q L M . N G T ~ M - ~ ~ A = A " * ~ ~ I S = L K...

    ~ ~ ~ ~ ~ ~ ~ ~ N I E ~ ~ ~ ~ S I K R ~ ~ ~ V T A T K L G ~ V

    . ~ . . . . . . . . ~ . ~ ~ ~ ~ ~ ~ - - - - - - -

    ~ ~ A ~ H G L L ~ ~ = ~ ~ ~ H L 1 2

    ~~AI ASVPNWT ~ ~ ~ ~ ~ ~ ~ ~ . ~ ~~ ~ ~ Q ~ H . N ~ ~ ~ ~ ~ S ~ N A C ~ ~ ~ A L ~ L S ~ L K

    . . . . ~ ~ ~ ~ ~ ~ -D ~- ~ V R R A L E ~ A V ~A D N ] ~ . . . . . . . . . . . ~ ~ ~ ~ ~ ~ ~ - - - - - -V F A Q G ~ G l ~ Q V D K A Y D Y L 1 7 3 ~ 1

    .. FAGYPQYC......................... R Q ~ M - ~ . N ~ T S ~ S ~ ~ N - G - A C M L ~ G L K. . . . . . . . . .Q ~TPY? VRMALE~AYMLP I . . . ~ ~ ~ ~ ~ ~ ~ - - - - - - - - - - -~ ~ ~ E S F S Q G ~ U l K l A T A Y E K L i ~ l 3 l

    . F E U A S ~ T I D C R G Y ~ ~ ~ . . . . . . . . . . . . . . ~ . ~ ~ ~ A Q p D V F - ~ ~ T ~ ~ A T P y T S ~ T ~ A L ~ ~ Q A Y K E - - - - - ~ ~ ~ - ~ V y ~ T p D p ~ T A ~ ~ ~ L K S S A K D I W Y ~ ~ - - - - - - - - - ~ - - ~ ~ ~ ~ ~ ~ - - - - - - ~ P A F S Q C S G R M A L K A R

    .. YSSLPMW

    .........................

    1 G ~ ~ F M . s G T s M ~ T p ~ V S G ~ A L L I s G p K.......... ~ ~ ~ y ~ p D ~ ~ ~ ~ v L E s ~ A T ~ L E G D P ~ ~ ~ ~ ~ ~ ~ - - - - - - - - ~ ~ ~ ~ ~ T G Q K Y T

    ~~HI~.SSLPLWYTV-S ~ ~ ~ ~ ~ ~ ~ . ~ ~ ~ ~ ~ ~ ~ . . -~ ~ ~ . ~ ~ ~ ~ ~ A ~ ~ ~ ~ ~ ~ ~ ~ A L ~ I ~ ~ A K ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ Q ~ ~ ~ ~ ~ ~ ~ ~ ~ A L ~ L ~ ~ K

    I

    Fig. 2.

    Continued

    (see

    facing page for

    caption).

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    Subtilases

    sequence difference are not shown in Figure

    2

    but are listed in

    Table 2. Amino acid numbering used throughout this review cor-

    responds to that of mature subtilisin BPN (acronym basbpn), our

    reference sequence. Residues in inserts relative to this reference

    sequence are numbered in square brackets; for instance, residues

    inserted between positions 12and 13are numbered 12[+ 1],12[+2],

    etc.,

    or

    13[ -21, 13[- 11 if more appropriate.

    The conserved catalytic residues Asp 32, His 64, and Ser221 are

    highlighted in Figure 2, as is the oxyanion-hole residue Asn 155.

    Conserved core elements (black bars) and secondary structure are

    indicated (Siezen et al., 1991,Heringa et al., 1995).This structural

    framework can be used for homology modeling of subtilases of

    known p rimary structures but unkno wn three-dimensional structures.

    In some of the most highly diverged sequences there are regions

    with very weak sequence homology, even in the core, which re-

    sults in alignments that are not unambiguous. In those cases, al-

    ternative alignments to those in Figure 2 may need to be considered.

    These regions are found on the surface of the molecule and contain

    numerous olvent-exposed residues, allowing orgreater ide-

    chain variation. Examples are (a) the exposed regions 43-58 and

    182-21 8, which contain structurally conserved P-strands and turns;

    and (b) the exposed amphipathic helices 104-1 16, 133-144. and

    243-252. In the latter case, the sequence alignm ent of amphipathic

    helices is also based on the requirement that at certain positions

    non-polar side chains are conserved that point into the interior of

    the molecule, while polar residues face outward. When necessary,

    correct three-dimensional positioning of Cys residues to form

    putative disulfide bonds was used as an aid in proper sequence

    alignment.

    Sequence homology and family division

    In Figure 3, the pairwise sequence identity within the catalytic

    dom ains s plotted graphically for all members of the subtilase

    superfamily aligned in Figure 2. It is clear that clustering occurs

    into groups or families, in which members show higher sequence

    identity to each other.

    Figure 4 shows the parts of a family tree or cladogram, a mea-

    sure of the sequence homology between superfamily members,

    constructed from the sequence alignment of the catalytic domains

    in Figure 2. In our earlier paper, a less extensive tree identified two

    main classes and some subclasses (Siezen et al., 1991).This ex-

    panded sequence information now allows a new subdivision into

    six families, which are summarized below. The dendrograms in

    Figure 4B illustrate the sequence homology within these families

    and further subdivision into subgroups (or subfamilies). Many of

    these subgro ups are also apparent from the color patterns of se-

    quence identity in Figure 3.

    507

    Subtilisin family

    Only found in micro-organisms as yet. Includes mainly enzymes

    from Bacillus, with subgroups of true subtilisins (>64 identity),

    high-alkaline proteases

    (>55%

    identity), and intracellular prote-

    ases (>37 identity). Numerous minor variants of true subtilisins

    and high-alkaline proteases have been identified (Table 2). Long

    C-terminal exten sions are rare. Several 3D structures are known

    (see Tables 1 and 2).

    Thermitase family

    Enzym es found only in micro-organisms, including some thermo-

    philes (>55% identity) and halop hiles. The c haracteristic N-terminal

    sequencewas also ound in severalother Bacillus proteases

    (Table 3). Only one 3D structure is known (thermitase).

    Proteinase K fam ily

    Large family of secreted endopeptidases found only in fungi,

    yeasts, and gram-negative bacteria as yet; the bacterial subgroup

    has >55 sequence identity. This family is characterized by a

    high degree of sequence similarity (>37 identity), only minor

    insertions and deletions and the absence of the Ca2+ -bindi ng oop

    residues 76-81. Only a few of these enzymes have a significant

    C-terminal extension beyond the catalytic domain. One 3D struc-

    ture is known (proteinase K).

    Lantibioric peptidase family

    A small number of highly specialized enzymes for cleavage of

    leader peptides from precursors of lantibiotics, a unique group of

    post-translationally modified, antimicrobial peptides (Sahl et al.,

    1995). Theseendopeptidases have only been found in gram-

    positive bacteria, and several are intracellular. Only llnisp has a

    C-terminal extension, which acts as a membrane anchor. Charac-

    terized by low sequence similarity with each other and other sub-

    tilases (Fig. 3), and by numerous insertions/deletions. The most

    recently reported protein bspara from Bacillus subtilis is described

    as a putative protease required for plasmid stability; we speculate

    that it may also play a role in lantibiotic processing.

    A few 3D structures have been predicted by homology modeling

    (Siezen et a]., 1995a;Booth et al., 1996).

    Kexin family

    A large group of proprotein convertases (PCs) have been iden-

    tified, all involved in activation of peptide hormones, growth fac-

    tors, viral proteins, etc. (Barr,

    1991;

    van de Ven et al.,

    1993).

    High

    specificity is seen for cleavage after dibasic (Lys-Arg or Arg-Arg)

    or multiple basic residues. Nearly all are eukaryotic and have high

    sequence homology (>40 identity), while two more distant mem-

    bers from Aeromonas and Anabaena provide links to other subti-

    Fig. 2. ( f ucing page ) Alignment of amino acid sequences of catalytic domains of subtilases. Multiple sequence alignment was initially

    performed using the PILEUP program (Devereux et a l., 1984). Nex t, improvements were made manually by taking into accoun t the

    structure-based alignm ent (Siezen et al., 1991;Heringa et al., 1995).Inserts were udged to occur m ost likely in turns in external loops.

    Fam ilies A to F are indicated on the left. E nzym e acronyms are given in Table 1 . (*) New entries, and (c) corrected entries since S iezen

    et al.

    (1991).

    Residu e numbering at the top corresponds to that o f mature subtilisinBPN (basbpn). Catalytic residues A sp 32, His 64,

    and Ser

    221

    are in bold (hig hlighte d red), as is the o xyanio n-hole residue Asn 155. Green

    =

    highly conserved residues from Table 4;

    yellow = Cys residues. Structurally conserved regions of the coreABC and extended coreAB are shown as solid bars; common

    secondary structure elemen ts are show n as: h = helix,

    e

    = extended p-sh eet, b = bend and t =

    p-turn

    (see also Fig. I ) . The number

    of additional residue s in arge nserts n

    the

    catalytic domain, and n N- andC-terminal extension s, are show n in brackets.Each

    seque nce begins at the mature N-term inus; an N-terminus based on the predicted pro-peptide cleavage site is indicated as().

    Resid ues 146-156 of bspara are from a different reading frame than

    proposed by the authors.

  • 8/10/2019 Siezen, 1997, Subtilase

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  • 8/10/2019 Siezen, 1997, Subtilase

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  • 8/10/2019 Siezen, 1997, Subtilase

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    514 R.J. Siezen and J A M . Leunissen

    A

    A B

    C D

    E

    F

    Fig.

    .

    Pair-wise sequence dentity matrix. Sequences are plotted vertically and horizontally n the same order as in Figure 2; the

    incomplete sequenceof hvccvp is not included. Subdivision into families to F is indicated.A color codebar for percentage sequence

    identity is shown.

    lase families.Asubgroup of yeastenzymes is evident,asare

    subgroups ofPC1

    ( 2 3 %

    identity), PC2 (>73% identity), and

    furin ( X 5 5 dentity). In catfish herpes virus 1 a related but in-

    complete amino acid sequence has been found that is presumedo

    have been captured from a host (Rawlings and Barrett, 1994).

    Several 3D structures have been predicted bymodeling (see

    below).

    Pyrolysin family

    Heterogeneous group of enzymes of varied origin and low se-

    quence conservation (most 37% identity) are distinguished; the former are

    of

    higher

    eukaryotic origin, but onlyhe human and mouse enzymes have ac-

    tually been identified biochemically as tripeptidyl peptidases.

    Several 3D structures have been predicted by modeling (see

    below).

    Several other subtilases have been identified or which only the

    N-terminal or other partial sequence of the purified enzyme s

    available; based on sequence alignment with Figure 2, these sub-

    tilases presumably belong to families A,

    B,

    and C (Table 3).

    Conserved residues

    Highly conserved residuesare listed in Table 4 and highlighted in

    Figure 2. Only the essential catalytic triad residues D32, H64, and

    S221 and a single glycine residue (G219)

    are

    totally conserved n

    all sequences.

    Four

    other glycine residues34,65,83, and 154) are

    varied only once or twice; G34 and G154 have main-chain torsion

    angles that do not allow for

    amino

    acid residues with side chains.

    At several other positions the variation s limited to two

    or

    three

    residues,whichareusuallystructurallysimilar. In general, the

    residues of the two internal helices hCnd hFare the most highly

    conserved in

    all

    subtilases. Three

    amino

    acid sequences (lslasp,

    sepepp, and asaspa) are particularly poorly conserved; although t

    seems questionable whether these enzymes are functional, a mu-

    tation analysis of the

    pepP

    gene suggests that

    it

    indeed encodes a

    functional protease (Meyer et al., 1995).

    Many more residuesare totally conserved within each of the six

    families

    A to F,

    and hese can

    be

    used to identify new family

    members. In particular, families and C are most conserved, with

    a total of 32 and 41 invariant residues, respectively, while family

    E

    has 63 invariant residues if the

    two

    more divergent sequences

    (asaspa and avprca) are excluded.

    Residue N155 (in a conserved segment 152-155), which helps

    to stabilize the oxyanion generated

    in

    the tetrahedral ransition

    state (Carter and Wells, 1990), is not fully conserved. The only

    accepted substitution here is N155D, as is found in the PC2 sub-

    group of the kexin family. The effect of

    this

    substitution on the

  • 8/10/2019 Siezen, 1997, Subtilase

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    Subtilases

    Families

    E T d

    1

    Lantibiotic

    A

    peptidases

    B

    Fig. 4.

    Family tree

    or

    dendrogram analysis of the sub-

    tilase superfamily, based on sequence alignment of the

    catalytic domains only (Fig.

    2).

    A: General layout of

    the relationship between families A to F.

    B:

    Detailed

    dendrograms of the individual families, in which branch

    lengths are in inverse proportion to the degree of se-

    quence similarity. Not includedare members with >90%

    sequence identity to one of the listed enzymes

    (see

    Table

    2).

    Trees were constructed using the neighbor-

    joining method of Saitou and Nei (1987), as imple-

    mented in the programs NEIGHBOR (Felsenstein,

    1993)

    and GROWTREE (Devereuxet al.,

    1984).

    The dis-

    tance matrices that were used

    as

    input for the programs

    were calculated using DISTANCES (Devereux et al.,

    1984),

    PROTDIST (Felsenstein,

    1993),

    and

    HOMOL-

    OGIES (Leunissen. unpubl. obs.). Positions containing

    gaps were ignored,

    as

    were the large insertions indi-

    cated between brackets in Figure 2. Whenever appro-

    priate, the distances were correctedormultiple

    substitutions (Jukes and Cantor. 1969; Kimura, 1983).

    All

    methods used delivered in principle identical to-

    pologies, except for the branch lengths; these may vary,

    depending upon the method used to calculate the dis-

    tances between the proteins, and correcting for multi-

    ple substitutions.

    subtilisin

    true

    igh-alkaline

    7 1

    ntracellular

    515

    FAMILY

    Subtilisin

    c

    catalytic efficiency of these proteases has been investigated by

    protein engineering (Benjannet et al., 1995; Zhou et al., 1995).

    Homology modeling

    The procedure for homology modeling and protein engineering of

    the catalytic domain of subtilases of unknown 3D structure based

    on known crystal structures was described in our previous review

    (Siezen et al., 1991), and can be applied to any of the enzymes

    listed in Tables 1 and 2 .

    Modeling should be based on the known crystal structure of the

    most related enzyme, and this will be straightforward for members

    of the families A-C, because 3D structures are known in each

    family. For the families D-F, with

    no

    known 3D structures, mod-

    eling will be less straightforward and can be based on any

    known

    structure from families A-C or a combination of these. Problems

    will arise where large insertions occur, because these are still im-

    possible to model reliably. It would be extremely helpful for mod-

    Proteinase K

    1

    antibiotic

    peptidase

    Kexin

    7

    7

    gram-negative

    bacteria

    gram-positive

    bacteria

    3

    lant

    7

    ripeptidasr

    2 hermophile

    -

    Pyrolysin

    eling purposes to determine the crystal structure of at least one

    member of each of the D-F families, preferably those with large

    inserts.

    This homology method has since been refined and applied for

    modeling and engineering of (a) the cell-envelope proteinase llprtp

    of

    Lactococcus lactis

    (Siezen et al., 1993; Bruinenberg et

    al.,

    1994a,

    1994b); (b) the lantibiotic leader peptidases llnisp of

    Lactococcus

    lactis

    (Van der Meer et

    al.,

    1994; Siezen et al., 1995a), and efcyla

    of Enterococcus faeca lis (Booth et al., 1996); (c) the kexin family

    members furin (hsfur: Creemers et al., 1993; Siezen et al., 1994)

    and PC2/PC3 (Lipkind et al., 1995); and (d) the heat-stable pro-

    teases pfpyro and tsplst of the hyperthermophiles Pyrococcusfu-

    riosus and Thermococcus stetteri (W. Voorhorst, A. Warner, W. de

    Vos, R. Siezen, in prep.). These studies have provided predictions

    and evidence for inserted and disposable loops, disulfide bridges,

    &'+-ion binding sites, surface salt bridges and networks, aromatic

    surface clusters, and residues involved in enzyme-substrate inter-

    actions. Some examples are discussed below.

  • 8/10/2019 Siezen, 1997, Subtilase

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    516

    R.J. Siezen and J.A.M. Leunissen

    Table 3 . Incomplete amino acid sequences of subtifuses

    Organism Enzyme

    Acronym

    Residues determined

    N-term. Other Family References

    BACTERIA

    Gram-positive

    Bacillus

    subrilis

    A50

    Bacillus sp. (3x6644

    Bacillus

    sp. Y

    Bacillus thuringiensis israelensis

    Bacillus thuringiensis finitimus

    Bacillus thuringiensis kurstaki

    BaciNus cereus

    Bacillus intermedius

    3-19

    Nocardiopsis dassonvillei (prasina)

    Gram-negative

    Streptomyces rutgersensis

    Thermus

    Tok3A

    1

    Vibrio metschnikovii

    Cochliobolus carbonum

    EUKARYA

    Fungi

    Agaricus bisporus

    Malbranchea suljurea

    Ophiostoma piceae

    V e r r l c l l l iu ~ ~ h l a m y d o s p o r ~ u m

    Scedosporium apiospermum

    Intracell. serine protease

    Subtilisin GX

    Protease BYA

    Extracellular serine protease

    Extracellular serine protease

    Extracellular serine protease

    Extracellular

    serine

    protease

    Alkaline serine protease

    Alkaline serine protease

    Proteinase D

    Caldolysin

    Alkaline protease VapK

    Extracellular protease

    Extracellular serine protease

    Thermomycolin

    Extracellular protease

    Extracellular protease VCPl

    Extracellular protease

    bsia50

    bssugx

    bspbya

    btisra

    btfini

    btkurs

    bcespr

    biprot

    ndapII

    srespd

    tscald

    vmapk

    ccalp2

    abexpr

    msthmy

    opexpr

    vcexp

    1

    saalpr

    1-54

    1-16

    1-2 1

    1-14 223-243

    1-15

    6-20

    1-15 223-243

    1-15

    1-26

    1-23

    1-15

    1-36

    1-29

    1-19

    1-28 217-222

    1-18 170-193

    1-20

    1-13

    Strongin et al., 1978

    Durham, 1993

    Shimogaki et al., 1991

    Chestukhina et al., 1986

    Chestukhina et al., 1986

    Kunitate et al., 1989

    Chestukhina et al., 1986

    Balaban et al. , 1994

    Tsujibo et al., 1990

    C Lavrenova et al., 1984

    C Freeman et al., 1993

    A Kwon et al., 1994

    C Murphy

    &

    Walton, 1996

    C Burton et al., 1993

    C Gaucher

    &

    Stevenson, 1976

    C Abraham

    &

    Breuil, 1995

    C Segers et al., 1995

    C Larcher etl., 1996

    Table

    4. Highest conserved residues in subtilases v = variability)

    Residue

    u = I u =

    2

    u = 3

    Context/function Exception

    32

    34

    64

    65

    68

    69

    70

    83

    90

    125

    152

    154

    155

    189

    193

    20

    1

    219

    220

    22

    1

    223

    225

    229

    G

    S

    G

    N

    Catalytic triad residue

    Bend;

    4,

    @

    =

    99 , 179

    Catalytic triad residue

    Buried helix, close packing

    Buried helix,

    close

    packing, directly under catalytic triad

    Buried helix, close packing

    Buried helix, close packing

    Helix/turn, close packing

    Buried fi-strand, hydrophobic packing to helix C

    Bend, directly adjacent to catalytic triad

    Lines

    S 1

    pocket

    Lines

    S I

    pocket; 6,

    =

    114 , 163

    Oxyanion stabilization

    Turn

    at surface, side chain turned into pocket

    Begin turn

    Bend at end &strand, hydrophobic ring stacks with H226

    Bend between e9 and hF;

    4, @ =

    147 , 160

    OD1 H -bonded to backbone NH -154

    Catalytic triad residue

    Buried helix, close packing

    Buried helix, close packing

    Buried helix,

    close

    packing

    N (Islasp), A (smserp), P (smsspl, smssp2)

    del (asaspa)

    M (Islasp), I (sepepp, ddtagc)

    G

    (nahlys), T (bsb pf),

    I

    (sepepp)

    T

    (smstab), A (smsspl, paaf70)

    A (Islasp),

    T

    (efcyla)

    W (bsbpf), M (seepip)

    P (Islasp), C (hakx2), T (acfurl, bcpc2)

    M (sepepp), del (bssepr)

    D (Ispc2, bcpc2, cepc2, hspc2)

    del (sepepp), S

    (smserp),

    L (bspara)

    Y (=pe w), D (dmpga9). T (vmvapt)

    I (seepip, smstab)

    N (sepepp, Ilnisp)

    G (Islasp), S (sepepp, ddtagc)

    T

    (bssepr)

  • 8/10/2019 Siezen, 1997, Subtilase

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    Subtilases

    517

    Large insertions and deletions

    peptidases, and include large

    N-

    and C-terminal deletions. All but

    one of the internal deletions can be readily accommodated by

    The 190 residues that constitute the scrs, as defined from the connecting residues that are spatially adjacent in the 3D structures

    known crystal structures (Siezen et al., 1991) and shown in Fig- of subtilisin/thermitase. Particularly interesting in this respect is

    ure

    2

    are present in nearly all the subtilases. Som e unusual dele- the natural deletion of the Ca l-i on binding loop, residues 74-82,

    tions are found, however, as listed in Table

    5,

    and this implies that in the

    Enterococcus

    subtilase (efcyla), thereby presumably extend-

    not all of these core residues are essential for proper folding. Most ing helix

    C

    by another four residues (Booth et al., 1996); this is

    of these deletions occur in subtilase family

    D,

    the lantibiotic leader precisely the loop deletion that was engineered into subtilisin to

    Table 5. Large or unusual deletions and insertions

    Unusual deletion

    Missing residues Context Family Enzyme

    1-13

    65-66

    14-82

    96-102

    180-189

    257-215

    N-terminus, hA

    Part hC, adjacent catalytic His

    Ca-binding loop + hC extended

    Turn, substrate-binding region

    Turns

    C-terminus, hH

    sepepp

    asaspa

    efcyla

    smserp

    sePePP

    lslasp

    Large insertion

    Inserted residues

    Position Number Properties Family Enzyme

    vr5

    vr6

    v r l

    vr8

    V I 9

    v r l l

    vr13

    vr15

    vr16

    vr18

    vr19

    N-term. Up to 98

    59

    34

    vr

    1

    1 8

    vr4 30-33

    28-30

    26-3 1

    23

    147-213

    30

    42

    16

    51

    34

    18

    22

    16-18

    134-169

    13-15

    21

    20-22

    149

    2 1

    22

    20

    19

    38

    34

    25

    22-24

    21

    No homology

    Highly charged

    Highly charged

    Weak homology

    High homology

    Medium homology, conserved S-S bond

    ?

    High homology

    Weak homology, see alignment in Fig.

    5

    Highly charged (50%)

    Highly charged

    High homology

    Weak homology

    Weak homology in central section (Fig.

    5 )

    High homology

    Weak homology

    S - S

    bond ?

    High homology

    S-S bond ?

    High homology

    S-S bond?

    E

    F

    C

    C

    F

    B

    F

    F

    F

    F

    F

    C

    F

    F

    F

    F

    D

    F

    F

    F

    D

    A

    E

    F

    F

    B

    E

    E

    B

    F

    F

    Most family members

    spscpa

    scyct5

    scyct5

    spscpa, Ilprtp, ldprtb

    dnbpr, dnavp2, dnavp5, xcproa,

    alaprl

    llspO9, atserp, cmc ucu, agserp,

    lep69, paafl0

    smssp l, smssp2

    pfpyro, tsplst, dmpga9, hstpp2,

    CetPP

    PfPYro