EzCatDB: D00236
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DB codeD00236
RLCP classification1.13.11100.261 : Hydrolysis
CATH domainDomain 12.150.10.10 : Alkaline Protease, subunit P, domain 1
Domain 23.40.390.10 : Collagenase (Catalytic Domain)Catalytic domain
E.C.3.4.24.40

CATH domainRelated DB codes (homologues)
3.40.390.10 : Collagenase (Catalytic Domain)S00394,S00395,S00397,S00398,S00399,D00232,M00101

Enzyme Name
UniProtKBKEGG

P07268P23694O69771
Protein nameSerralysinSerralysin
serralysin
Pseudomonas aeruginosa alkaline proteinase
Escherichia freundii proteinase
Serratia marcescens extracellular proteinase
Serratia marcescens metalloproteinase
Pseudomonas aeruginosa alk. protease
Serratia marcescens metalloprotease
SynonymsEC 3.4.24.40
Extracellular metalloproteinase
Zinc proteinase
Serratiopeptidase
Serrapeptidase
Serrapeptase
EC 3.4.24.40
Extracellular metalloproteinase
Zinc proteinase
Serralysin
EC 3.4.24.40
MEROPSM10.051 (Metallo)
M10.051 (Metallo)
M10.062 (Metallo)
PfamPF00353 (HemolysinCabind)
PF00413 (Peptidase_M10)
PF08548 (Peptidase_M10_C)
[Graphical view]
PF00353 (HemolysinCabind)
PF00413 (Peptidase_M10)
PF08548 (Peptidase_M10_C)
[Graphical view]
PF00353 (HemolysinCabind)
PF08548 (Peptidase_M10_C)
[Graphical view]


UniProtKB:Accession NumberP07268P23694O69771
Entry namePRZN_SERMEPRZN_SERMAO69771_9PSED
ActivityPreferential cleavage of bonds with hydrophobic residues in P1''.Preferential cleavage of bonds with hydrophobic residues in P1''.
Subunit


Subcellular locationSecreted.Secreted.
CofactorBinds 7 calcium ions per subunit.,Binds 1 zinc ion per subunit.Binds 7 calcium ions per subunit.,Binds 1 zinc ion per subunit.

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00038C00076C00001C00012C00017C00012C00017
CompoundZincCalciumH2OPeptideProteinPeptideProtein
Typeheavy metaldivalent metal (Ca2+, Mg2+)H2Opeptide/proteinpeptide/proteinpeptide/proteinpeptide/protein
ChEBI29105
29108
15377




PubChem32051
271
962
22247451




               
1af0A01UnboundBound:7x_CA UnboundUnboundUnboundUnbound
1satA01UnboundBound:7x_CA UnboundUnboundUnboundUnbound
1smpA01UnboundBound:7x_CA UnboundUnboundUnboundUnbound
1srpA01UnboundBound:7x_CA UnboundUnboundUnboundUnbound
1g9kA01UnboundBound:7x_CA UnboundUnboundUnboundUnbound
1h71P01UnboundBound:8x_CA UnboundUnboundUnboundUnbound
1o0qA01UnboundBound:6x_CA UnboundUnboundUnboundUnbound
1o0tA01UnboundBound:7x_CA UnboundUnboundUnboundUnbound
1om6A01UnboundBound:6x_CA UnboundUnboundUnboundUnbound
1om7A01UnboundBound:5x_CA UnboundUnboundUnboundUnbound
1om8A01UnboundBound:6x_CA UnboundUnboundUnboundUnbound
1omjA01UnboundBound:8x_CA UnboundUnboundUnboundUnbound
1af0A02Bound:_ZNUnbound UnboundUnboundAnalogue:LEU-HMA(chain B)Unbound
1satA02Bound:_ZNUnbound UnboundUnboundUnboundUnbound
1smpA02Bound:_ZNUnbound UnboundUnboundUnboundBound:SER 1(chain I)
1srpA02Bound:_ZNUnbound UnboundUnboundUnboundUnbound
1g9kA02Bound:_ZNUnbound UnboundUnboundUnboundUnbound
1h71P02Bound:_ZNUnbound UnboundUnboundUnboundUnbound
1o0qA02UnboundUnbound UnboundUnboundUnboundUnbound
1o0tA02UnboundUnbound UnboundUnboundUnboundUnbound
1om6A02UnboundUnbound UnboundUnboundUnboundUnbound
1om7A02UnboundUnbound UnboundUnboundUnboundUnbound
1om8A02UnboundUnbound UnboundUnboundUnboundUnbound
1omjA02Bound:_ZNUnbound UnboundUnboundUnboundUnbound

Active-site residues
resource
PDB;1af0, 1srp & Swiss-prot;P07268, P23694
pdbCatalytic residuesCofactor-binding residues
          
1af0A01 
 
1satA01 
 
1smpA01 
 
1srpA01 
 
1g9kA01 
 
1h71P01 
 
1o0qA01 
 
1o0tA01 
 
1om6A01 
 
1om7A01 
 
1om8A01 
 
1omjA01 
 
1af0A02GLU 177;TYR 216
HIS 176;HIS 180;HIS 186;TYR 216(Zinc binding)
1satA02GLU 177;TYR 216
HIS 176;HIS 180;HIS 186;TYR 216(Zinc binding)
1smpA02GLU 177;TYR 216
HIS 176;HIS 180;HIS 186;TYR 216(Zinc binding)
1srpA02GLU 177;TYR 216
HIS 176;HIS 180;HIS 186;TYR 216(Zinc binding)
1g9kA02GLU 170;TYR 209
HIS 169;HIS 173;HIS 179;TYR 209(Zinc binding)
1h71P02GLU 170;TYR 209
HIS 169;HIS 173;HIS 179;TYR 209(Zinc binding)
1o0qA02GLU 170;TYR 209
HIS 169;HIS 173;HIS 179;TYR 209(Zinc binding)
1o0tA02GLU 170;TYR 209
HIS 169;HIS 173;HIS 179;TYR 209(Zinc binding)
1om6A02GLU 170;TYR 209
HIS 169;HIS 173;HIS 179;TYR 209(Zinc binding)
1om7A02GLU 170;TYR 209
HIS 169;HIS 173;HIS 179;TYR 209(Zinc binding)
1om8A02GLU 170;TYR 209
HIS 169;HIS 173;HIS 179;TYR 209(Zinc binding)
1omjA02GLU 170;TYR 209
HIS 169;HIS 173;HIS 179;TYR 209(Zinc binding)

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[4]p.247
[8]p.848
[10]Scheme 3, p.4955-4958
[16]Fig.9, p.608-6094
[18]p.639-642

references
[1]
CommentsX-ray crystallography
PubMed ID3908448
JournalJ Biochem (Tokyo)
Year1985
Volume98
Pages1139-42
AuthorsKatsuya Y, Hamada K, Hata Y, Tanaka N, Sato M, Katsube Y, Kakiuchi K, Miyata K
TitlePreliminary X-ray studies on Serratia protease.
Related PDB1srp
[2]
PubMed ID8253063
JournalEMBO J
Year1993
Volume12
Pages3357-64
AuthorsBaumann U, Wu S, Flaherty KM, McKay DB
TitleThree-dimensional structure of the alkaline protease of Pseudomonas aeruginosa: a two-domain protein with a calcium binding parallel beta roll motif.
[3]
PubMed ID8508794
JournalEur J Biochem
Year1993
Volume214
Pages215-31
AuthorsStocker W, Gomis-Ruth FX, Bode W, Zwilling R
TitleImplications of the three-dimensional structure of astacin for the structure and function of the astacin family of zinc-endopeptidases.
[4]
CommentsX-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS).
Medline ID94376295
PubMed ID8089845
JournalJ Mol Biol
Year1994
Volume242
Pages244-51
AuthorsBaumann U
TitleCrystal structure of the 50 kDa metallo protease from Serratia marcescens.
Related PDB1af0,1sat
Related UniProtKBP23694
[5]
CommentsX-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF COMPLEX WITH INHIBITOR.
Medline ID95271655
PubMed ID7752231
JournalJ Mol Biol
Year1995
Volume248
Pages653-61
AuthorsBaumann U, Bauer M, Letoffe S, Delepelaire P, Wandersman C
TitleCrystal structure of a complex between Serratia marcescens metallo-protease and an inhibitor from Erwinia chrysanthemi.
Related PDB1smp
Related UniProtKBP23694
[6]
PubMed ID7663339
JournalProtein Sci
Year1995
Volume4
Pages823-40
AuthorsStocker W, Grams F, Baumann U, Reinemer P, Gomis-Ruth FX, McKay DB, Bode W
TitleThe metzincins--topological and sequential relations between the astacins, adamalysins, serralysins, and matrixins (collagenases) define a superfamily of zinc-peptidases.
[7]
PubMed ID8874040
JournalDrug Des Discov
Year1996
Volume13
Pages3-14
AuthorsDhanaraj V, Ye QZ, Johnson LL, Hupe DJ, Ortwine DF, Dunbar JB Jr, Rubin JR, Pavlovsky A, Humblet C, Blundell TL
TitleDesigning inhibitors of the metalloproteinase superfamily: comparative analysis of representative structures.
[8]
CommentsX-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
Medline ID96389988
PubMed ID8797082
JournalJ Biochem (Tokyo)
Year1996
Volume119
Pages844-51
AuthorsHamada K, Hata Y, Katsuya Y, Hiramatsu H, Fujiwara T, Katsube Y
TitleCrystal structure of Serratia protease, a zinc-dependent proteinase from Serratia sp. E-15, containing a beta-sheet coil motif at 2.0 A resolution.
Related UniProtKBP07268
[9]
PubMed ID8740360
JournalStructure
Year1996
Volume4
Pages375-86
AuthorsDhanaraj V, Ye QZ, Johnson LL, Hupe DJ, Ortwine DF, Dunbar JB Jr, Rubin JR, Pavlovsky A, Humblet C, Blundell TL
TitleX-ray structure of a hydroxamate inhibitor complex of stromelysin catalytic domain and its comparison with members of the zinc metalloproteinase superfamily.
[10]
PubMed ID9125517
JournalBiochemistry
Year1997
Volume36
Pages4949-58
AuthorsMock WL, Yao J
TitleKinetic characterization of the serralysins: a divergent catalytic mechanism pertaining to astacin-type metalloproteases.
[11]
PubMed ID9385650
JournalProtein Sci
Year1997
Volume6
Pages2462-4
AuthorsVilleret V, Chessa JP, Gerday C, Van Beeumen J
TitlePreliminary crystal structure determination of the alkaline protease from the Antarctic psychrophile Pseudomonas aeruginosa.
[12]
PubMed ID10517348
JournalJ Chromatogr B Biomed Sci Appl
Year1999
Volume732
Pages271-6
AuthorsLouis D, Bernillon J, Paisse JO, Wallach JM
TitleUse of liquid chromatography-mass spectrometry coupling for monitoring the serralysin-catalyzed hydrolysis of a peptide library.
[13]
PubMed ID10770939
JournalJ Biol Chem
Year2000
Volume275
Pages21002-9
AuthorsFeltzer RE, Gray RD, Dean WL, Pierce WM Jr
TitleAlkaline proteinase inhibitor of Pseudomonas aeruginosa. Interaction of native and N-terminally truncated inhibitor proteins with Pseudomonas metalloproteinases.
[14]
PubMed ID11445573
JournalJ Biol Chem
Year2001
Volume276
Pages35087-92
AuthorsHege T, Feltzer RE, Gray RD, Baumann U
TitleCrystal structure of a complex between Pseudomonas aeruginosa alkaline protease and its cognate inhibitor: inhibition by a zinc-NH2 coordinative bond.
[15]
PubMed ID11976300
JournalJ Bacteriol
Year2002
Volume184
Pages2709-18
AuthorsUmelo-Njaka E, Bingle WH, Borchani F, Le KD, Awram P, Blake T, Nomellini JF, Smit J
TitleCaulobacter crescentus synthesizes an S-layer-editing metalloprotease possessing a domain sharing sequence similarity with its paracrystalline S-layer protein.
[16]
PubMed ID12072965
JournalJ Biol Inorg Chem
Year2002
Volume7
Pages600-10
AuthorsPark HI, Ming LJ
TitleMechanistic studies of the astacin-like Serratia metalloendopeptidase serralysin: highly active (>2000%) Co(II) and Cu(II) derivatives for further corroboration of a "metallotriad" mechanism.
[17]
PubMed ID11779238
JournalJ Mol Biol
Year2002
Volume315
Pages183-91
AuthorsWatson JD, Milner-White EJ
TitleThe conformations of polypeptide chains where the main-chain parts of successive residues are enantiomeric. Their occurrence in cation and anion-binding regions of proteins.
[18]
PubMed ID12577270
JournalProteins
Year2003
Volume50
Pages636-47
AuthorsAghajari N, Van Petegem F, Villeret V, Chessa JP, Gerday C, Haser R, Van Beeumen J
TitleCrystal structures of a psychrophilic metalloprotease reveal new insights into catalysis by cold-adapted proteases.
Related PDB1g9k,1h71
[19]
PubMed ID12837794
JournalJ Bacteriol
Year2003
Volume185
Pages4195-203
AuthorsRavaud S, Gouet P, Haser R, Aghajari N
TitleProbing the role of divalent metal ions in a bacterial psychrophilic metalloprotease: binding studies of an enzyme in the crystalline state by x-ray crystallography.
Related PDB1o0q,1o0t,1om6,1om7,1om8,1omj

comments
This enzyme belongs to the peptidase family-M10B.
Although an alternative machanism has been reported [10], in which Tyr216 (of 1af0), instead of Glu177 (of 1af0), functions as a general base to deprotonate a solvent water molecule, this mechanism is unlikely for many reasons (see [16]). More recent paper [16] confirmed that Glu177 and Tyr216 act as a general base and a stabilizer of the transition state, respectively. This mechanism is similar to that of astacin (S00394 in EzCatDB).
According to the paper [16], the catalytic reaction proceeds as follows:
(1) The zinc ion and the general base, Glu177, facilitate the deprotonation of the coordinated water moleucle.
(2) Upon substrate (peptide) binding, the cofactor zinc ion enhance the polarity of the carbonyl group of the scissile peptidyl bond, for the nucleophilic attack by the water. At this step, the breakage of the interaction between the Tyr216 and the zinc ion (a six-coordinate transition-state) assists the enhancement of the polarity at the carbonyl group.
(3) The detachment of Tyr216 from the zinc ion is accompanied by the nucleophilic attack on the carbonyl group of the peptide substrate by the activated water (hydroxide), forming the gem-diolate transition-state. (This detachment of Tyr216 leads to a slight decrease in pKa of the coordinated water.)
(4) The gem-diolate transition-state is stabilized by Tyr216 along with the cofactor zinc ion.
(5) Bond cleavage occurs and product is released.

createdupdated
2004-08-262009-02-26


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