DB code: D00236

RLCP classification 1.13.11100.261 : Hydrolysis
CATH domain 2.150.10.10 : Alkaline Protease, subunit P, domain 1
3.40.390.10 : Collagenase (Catalytic Domain) Catalytic domain
E.C. 3.4.24.40
CSA
M-CSA
MACiE

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

Uniprot Enzyme Name
UniprotKB Protein name Synonyms MEROPS Pfam
P07268 Serralysin
EC 3.4.24.40
Extracellular metalloproteinase
Serratiopeptidase
Serrapeptase
Serrapeptidase
Zinc proteinase
M10.051 (Metallo)
PF00353 (HemolysinCabind)
PF00413 (Peptidase_M10)
PF08548 (Peptidase_M10_C)
[Graphical View]
P23694 Serralysin
EC 3.4.24.40
Extracellular metalloproteinase
Zinc proteinase
M10.051 (Metallo)
PF00353 (HemolysinCabind)
PF00413 (Peptidase_M10)
PF08548 (Peptidase_M10_C)
[Graphical View]
O69771
Serralysin
EC 3.4.24.40
M10.062 (Metallo)
PF00353 (HemolysinCabind)
PF08548 (Peptidase_M10_C)
[Graphical View]

KEGG enzyme name
serralysin
Pseudomonas aeruginosa alkaline proteinase
Escherichia freundii proteinase
Serratia marcescens extracellular proteinase
Serratia marcescens metalloproteinase
Pseudomonas aeruginosa alk. protease
Serratia marcescens metalloprotease

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P07268 PRZN_SERME Preferential cleavage of bonds with hydrophobic residues in P1''. Secreted. Binds 7 calcium ions per subunit. Binds 1 zinc ion per subunit.
P23694 PRZN_SERMA Preferential cleavage of bonds with hydrophobic residues in P1''. Secreted. Binds 7 calcium ions per subunit. Binds 1 zinc ion per subunit.
O69771 O69771_9PSED

KEGG Pathways
Map code Pathways E.C.

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00038 C00076 C00001 C00012 C00017 C00012 C00017
E.C.
Compound Zinc Calcium H2O Peptide Protein Peptide Protein
Type heavy metal divalent metal (Ca2+, Mg2+) H2O peptide/protein peptide/protein peptide/protein peptide/protein
ChEBI 29105
29108
15377
PubChem 32051
271
22247451
962
1af0A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:7x_CA Unbound Unbound Unbound Unbound
1satA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:7x_CA Unbound Unbound Unbound Unbound
1smpA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:7x_CA Unbound Unbound Unbound Unbound
1srpA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:7x_CA Unbound Unbound Unbound Unbound
1g9kA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:7x_CA Unbound Unbound Unbound Unbound
1h71P01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:8x_CA Unbound Unbound Unbound Unbound
1o0qA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:6x_CA Unbound Unbound Unbound Unbound
1o0tA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:7x_CA Unbound Unbound Unbound Unbound
1om6A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:6x_CA Unbound Unbound Unbound Unbound
1om7A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:5x_CA Unbound Unbound Unbound Unbound
1om8A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:6x_CA Unbound Unbound Unbound Unbound
1omjA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:8x_CA Unbound Unbound Unbound Unbound
1af0A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Analogue:LEU-HMA (chain B) Unbound
1satA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Unbound Unbound
1smpA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Unbound Bound:SER_1(chain I)
1srpA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Unbound Unbound
1g9kA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Unbound Unbound
1h71P02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Unbound Unbound
1o0qA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1o0tA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1om6A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1om7A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1om8A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1omjA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
PDB;1af0, 1srp & Swiss-prot;P07268, P23694

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1af0A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1satA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1smpA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1srpA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1g9kA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1h71P01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1o0qA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1o0tA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1om6A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1om7A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1om8A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1omjA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1af0A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 177;TYR 216 HIS 176;HIS 180;HIS 186;TYR 216(Zinc binding)
1satA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 177;TYR 216 HIS 176;HIS 180;HIS 186;TYR 216(Zinc binding)
1smpA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 177;TYR 216 HIS 176;HIS 180;HIS 186;TYR 216(Zinc binding)
1srpA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 177;TYR 216 HIS 176;HIS 180;HIS 186;TYR 216(Zinc binding)
1g9kA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 170;TYR 209 HIS 169;HIS 173;HIS 179;TYR 209(Zinc binding)
1h71P02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 170;TYR 209 HIS 169;HIS 173;HIS 179;TYR 209(Zinc binding)
1o0qA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 170;TYR 209 HIS 169;HIS 173;HIS 179;TYR 209(Zinc binding)
1o0tA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 170;TYR 209 HIS 169;HIS 173;HIS 179;TYR 209(Zinc binding)
1om6A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 170;TYR 209 HIS 169;HIS 173;HIS 179;TYR 209(Zinc binding)
1om7A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 170;TYR 209 HIS 169;HIS 173;HIS 179;TYR 209(Zinc binding)
1om8A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 170;TYR 209 HIS 169;HIS 173;HIS 179;TYR 209(Zinc binding)
1omjA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 170;TYR 209 HIS 169;HIS 173;HIS 179;TYR 209(Zinc binding)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[4]
p.247
[8]
p.848
[10]
Scheme 3, p.4955-4958
[16]
Fig.9, p.608-609 4
[18]
p.639-642

References
[1]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 3908448
Journal J Biochem (Tokyo)
Year 1985
Volume 98
Pages 1139-42
Authors Katsuya Y, Hamada K, Hata Y, Tanaka N, Sato M, Katsube Y, Kakiuchi K, Miyata K
Title Preliminary X-ray studies on Serratia protease.
Related PDB 1srp
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 8253063
Journal EMBO J
Year 1993
Volume 12
Pages 3357-64
Authors Baumann U, Wu S, Flaherty KM, McKay DB
Title Three-dimensional structure of the alkaline protease of Pseudomonas aeruginosa: a two-domain protein with a calcium binding parallel beta roll motif.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 8508794
Journal Eur J Biochem
Year 1993
Volume 214
Pages 215-31
Authors Stocker W, Gomis-Ruth FX, Bode W, Zwilling R
Title Implications of the three-dimensional structure of astacin for the structure and function of the astacin family of zinc-endopeptidases.
Related PDB
Related UniProtKB
[4]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS).
Medline ID 94376295
PubMed ID 8089845
Journal J Mol Biol
Year 1994
Volume 242
Pages 244-51
Authors Baumann U
Title Crystal structure of the 50 kDa metallo protease from Serratia marcescens.
Related PDB 1af0 1sat
Related UniProtKB P23694
[5]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF COMPLEX WITH INHIBITOR.
Medline ID 95271655
PubMed ID 7752231
Journal J Mol Biol
Year 1995
Volume 248
Pages 653-61
Authors Baumann U, Bauer M, Letoffe S, Delepelaire P, Wandersman C
Title Crystal structure of a complex between Serratia marcescens metallo-protease and an inhibitor from Erwinia chrysanthemi.
Related PDB 1smp
Related UniProtKB P23694
[6]
Resource
Comments
Medline ID
PubMed ID 7663339
Journal Protein Sci
Year 1995
Volume 4
Pages 823-40
Authors Stocker W, Grams F, Baumann U, Reinemer P, Gomis-Ruth FX, McKay DB, Bode W
Title The metzincins--topological and sequential relations between the astacins, adamalysins, serralysins, and matrixins (collagenases) define a superfamily of zinc-peptidases.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 8874040
Journal Drug Des Discov
Year 1996
Volume 13
Pages 3-14
Authors Dhanaraj V, Ye QZ, Johnson LL, Hupe DJ, Ortwine DF, Dunbar JB Jr, Rubin JR, Pavlovsky A, Humblet C, Blundell TL
Title Designing inhibitors of the metalloproteinase superfamily: comparative analysis of representative structures.
Related PDB
Related UniProtKB
[8]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
Medline ID 96389988
PubMed ID 8797082
Journal J Biochem (Tokyo)
Year 1996
Volume 119
Pages 844-51
Authors Hamada K, Hata Y, Katsuya Y, Hiramatsu H, Fujiwara T, Katsube Y
Title Crystal 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 PDB
Related UniProtKB P07268
[9]
Resource
Comments
Medline ID
PubMed ID 8740360
Journal Structure
Year 1996
Volume 4
Pages 375-86
Authors Dhanaraj V, Ye QZ, Johnson LL, Hupe DJ, Ortwine DF, Dunbar JB Jr, Rubin JR, Pavlovsky A, Humblet C, Blundell TL
Title X-ray structure of a hydroxamate inhibitor complex of stromelysin catalytic domain and its comparison with members of the zinc metalloproteinase superfamily.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 9125517
Journal Biochemistry
Year 1997
Volume 36
Pages 4949-58
Authors Mock WL, Yao J
Title Kinetic characterization of the serralysins: a divergent catalytic mechanism pertaining to astacin-type metalloproteases.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 9385650
Journal Protein Sci
Year 1997
Volume 6
Pages 2462-4
Authors Villeret V, Chessa JP, Gerday C, Van Beeumen J
Title Preliminary crystal structure determination of the alkaline protease from the Antarctic psychrophile Pseudomonas aeruginosa.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 10517348
Journal J Chromatogr B Biomed Sci Appl
Year 1999
Volume 732
Pages 271-6
Authors Louis D, Bernillon J, Paisse JO, Wallach JM
Title Use of liquid chromatography-mass spectrometry coupling for monitoring the serralysin-catalyzed hydrolysis of a peptide library.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 10770939
Journal J Biol Chem
Year 2000
Volume 275
Pages 21002-9
Authors Feltzer RE, Gray RD, Dean WL, Pierce WM Jr
Title Alkaline proteinase inhibitor of Pseudomonas aeruginosa. Interaction of native and N-terminally truncated inhibitor proteins with Pseudomonas metalloproteinases.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 11445573
Journal J Biol Chem
Year 2001
Volume 276
Pages 35087-92
Authors Hege T, Feltzer RE, Gray RD, Baumann U
Title Crystal structure of a complex between Pseudomonas aeruginosa alkaline protease and its cognate inhibitor: inhibition by a zinc-NH2 coordinative bond.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 11976300
Journal J Bacteriol
Year 2002
Volume 184
Pages 2709-18
Authors Umelo-Njaka E, Bingle WH, Borchani F, Le KD, Awram P, Blake T, Nomellini JF, Smit J
Title Caulobacter crescentus synthesizes an S-layer-editing metalloprotease possessing a domain sharing sequence similarity with its paracrystalline S-layer protein.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 12072965
Journal J Biol Inorg Chem
Year 2002
Volume 7
Pages 600-10
Authors Park HI, Ming LJ
Title Mechanistic studies of the astacin-like Serratia metalloendopeptidase serralysin: highly active (>2000%) Co(II) and Cu(II) derivatives for further corroboration of a "metallotriad" mechanism.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 11779238
Journal J Mol Biol
Year 2002
Volume 315
Pages 183-91
Authors Watson JD, Milner-White EJ
Title The conformations of polypeptide chains where the main-chain parts of successive residues are enantiomeric. Their occurrence in cation and anion-binding regions of proteins.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 12577270
Journal Proteins
Year 2003
Volume 50
Pages 636-47
Authors Aghajari N, Van Petegem F, Villeret V, Chessa JP, Gerday C, Haser R, Van Beeumen J
Title Crystal structures of a psychrophilic metalloprotease reveal new insights into catalysis by cold-adapted proteases.
Related PDB 1g9k 1h71
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 12837794
Journal J Bacteriol
Year 2003
Volume 185
Pages 4195-203
Authors Ravaud S, Gouet P, Haser R, Aghajari N
Title Probing 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 PDB 1o0q 1o0t 1om6 1om7 1om8 1omj
Related UniProtKB

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.

Created Updated
2004-08-26 2009-02-26