EzCatDB: S00513
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DB codeS00513
RLCP classification1.13.29990.17 : Hydrolysis
CATH domainDomain 13.40.710.10 : Beta-lactamaseCatalytic domain

CATH domainRelated DB codes (homologues)
3.40.710.10 : Beta-lactamaseS00512,S00529,S00414,T00222

Enzyme Name

Protein nameBeta-lactamase OXA-10beta-lactamase
penicillin beta-lactamase
penicillin amido-beta-lactamhydrolase
penicillinase I, II
beta-lactamase I-III
beta-lactamase A, B, C
beta-lactamase AME I
Beta-lactamase PSE-2
PfamPF00905 (Transpeptidase)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00311Penicillin and cephalosporin biosynthesis
MAP00312beta-Lactam resistance

UniProtKB:Accession NumberP14489
Entry nameBLO10_PSEAE
ActivityA beta-lactam + H(2)O = a substituted beta- amino acid.
Subcellular location

Compound table: links to PDB-related databases & PoSSuM

Compoundbeta-LactamPenicillinCephalosporinH2OSubstituted beta-amino acid
Typeamide groupamide group,carboxyl group,sulfide groupamide group,amine group,carboxyl group,sulfide groupH2Oamino acids




1e3uAUnboundUnboundUnbound Unbound
1e3uBUnboundUnboundUnbound Unbound
1e3uCUnboundUnboundUnbound Unbound
1e3uDUnboundUnboundUnbound Unbound
1e4dAUnboundUnboundUnbound Unbound
1e4dBUnboundUnboundUnbound Unbound
1e4dCUnboundUnboundUnbound Unbound
1e4dDUnboundUnboundUnbound Unbound
1ewzAUnboundUnboundUnbound Unbound
1ewzBUnboundUnboundUnbound Unbound
1ewzCUnboundUnboundUnbound Unbound
1ewzDUnboundUnboundUnbound Unbound
1fofAUnboundUnboundUnbound Unbound
1fofBUnboundUnboundUnbound Unbound

Active-site residues
literature [3]
pdbCatalytic residuesModified residuesMain-chain involved in catalysiscomment
1e3uASER 67;TRP 154
LYS 70
SER 67;PHE 208
1e3uBSER 67;TRP 154
LYS 70
SER 67;PHE 208
1e3uCSER 67;TRP 154
LYS 70
SER 67;PHE 208
1e3uDSER 67;TRP 154
LYS 70
SER 67;PHE 208
1e4dASER 67;TRP 154
KCX 70(Carbamylation)
SER 67;PHE 208
carbamated Lys70
1e4dBSER 67;TRP 154
KCX 70(Carbamylation)
SER 67;PHE 208
carbamated Lys70
1e4dCSER 67;TRP 154
KCX 70(Carbamylation)
SER 67;PHE 208
carbamated Lys70
1e4dDSER 67;TRP 154
KCX 70(Carbamylation)
SER 67;PHE 208
carbamated Lys70
1ewzASER 67;TRP 154
LYS 70
SER 67;PHE 208
1ewzBSER 67;TRP 154
LYS 70
SER 67;PHE 208
1ewzCSER 67;TRP 154
LYS 70
SER 67;PHE 208
1ewzDSER 67;TRP 154
LYS 70
SER 67;PHE 208
1fofASER 67;TRP 154
LYS 70
SER 67;PHE 208
1fofBSER 67;TRP 154
LYS 70
SER 67;PHE 208

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[4]p.2463, Scheme 12

JournalJ Am Chem Soc
AuthorsGolemi D, Maveyraud L, Vakulenko S, Tranier S, Ishiwata A, Kotra LP, Samama JP, Mobashery S
TitleThe first structural and mechanistic insights for class d beta-lactamases: evidence for a novel catalytic process for turnover of beta-lactam antibiotics.
Related PDB1ewz
CommentsX-ray crystallography (2.0 Angstroms)
PubMed ID11017203
JournalNat Struct Biol
AuthorsPaetzel M, Danel F, de Castro L, Mosimann SC, Page MG, Strynadka NC
TitleCrystal structure of the class D beta-lactamase OXA-10.
Related PDB1fof
CommentsX-ray crystallography (1.66 Angstroms)
Medline ID21029090
PubMed ID11188693
JournalStructure Fold Des
AuthorsMaveyraud L, Golemi D, Kotra LP, Tranier S, Vakulenko S, Mobashery S, Samama JP
TitleInsights into class D beta-lactamases are revealed by the crystal structure of the OXA10 enzyme from Pseudomonas aeruginosa.
Related PDB1e3u,1e4d
Related UniProtKBP14489
PubMed ID11890794
JournalJ Am Chem Soc
AuthorsMaveyraud L, Golemi-Kotra D, Ishiwata A, Meroueh O, Mobashery S, Samama JP
TitleHigh-resolution X-ray structure of an acyl-enzyme species for the class D OXA-10 beta-lactamase.

This enzyme belongs to the class-D beta-lactamase family.
This enzyme is also a serine hydrolase, in which Ser67 acts as a nucleophile to form acyl-enzyme intermediate ([1], [2], [3] & [4]).
In the early studies ([1] & [2]), although Lys70 was a possible candidate for the general base to activate a hydrolytic water in deacylation, the catalytic mechanism has remained to be elucidated. In more recent papers ([3] & [4]), it was reported that the lysine residue is carbamated, and that this carbamate acts as a general base, which can activate the nucleophilic Ser67 in the acylation step, and then, a water molecule in the deacylation step. According to the literature [4], the carbamate of Lys is modulated by Trp154, whereas mainchain amide groups of Ser67 and Phe208 (along with sidechain of Ser115) form an oxyanion hole as stabilizers.
Thus, the reaction proceeds as follows:
(1) Trp154 modulates the activity of carbamated Lys70.
(2) The carbamated Lys70 acts as a general base to deprotonate Ser67.
(3) Ser67 makes a nucleophilic attack on amide bond, forming acyl intermediate. (Here, the carbamated Lys70 must act as a general acid to protonate the leaving amine group. Otherwise, it can act as a general base in deacylation step.)
(4) The intermediate is stablized by an oxyanion hole, composed of mainchain amide of Ser67 and Phe208.
(5) The carbamated Lys70 acts as a general base again, to activate a water.
(6) The activated water makes a nucleophilic attack on the acyl intermediate.
(7) The carbamated Lys70 may act as a general acid again, to protonate Ser67.


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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