DB code: S00513

RLCP classification 1.13.29990.17 : Hydrolysis
CATH domain 3.40.710.10 : Beta-lactamase Catalytic domain
E.C. 3.5.2.6
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
3.40.710.10 : Beta-lactamase S00512 S00529 S00414 T00222

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam
P14489 Beta-lactamase OXA-10
EC 3.5.2.6
Beta-lactamase PSE-2
PF00905 (Transpeptidase)
[Graphical View]

KEGG enzyme name
beta-lactamase
penicillinase
cephalosporinase
neutrapen
penicillin beta-lactamase
exopenicillinase
ampicillinase
penicillin amido-beta-lactamhydrolase
penicillinase I, II
beta-lactamase I-III
beta-lactamase A, B, C
beta-lactamase AME I
cephalosporin-beta-lactamase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P14489 BLO10_PSEAE A beta-lactam + H(2)O = a substituted beta- amino acid.

KEGG Pathways
Map code Pathways E.C.
MAP00311 Penicillin and cephalosporin biosynthesis
MAP00312 beta-Lactam resistance

Compound table
Substrates Products Intermediates
KEGG-id C01866 C00395 C00875 C00001 C03806
E.C.
Compound beta-Lactam Penicillin Cephalosporin H2O Substituted beta-amino acid
Type amide group amide group,carboxyl group,sulfide group amide group,amine group,carboxyl group,sulfide group H2O amino acids
ChEBI 15377
PubChem 22247451
962
1e3uA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1e3uB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1e3uC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1e3uD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1e4dA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1e4dB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1e4dC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1e4dD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1ewzA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1ewzB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1ewzC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1ewzD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1fofA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1fofB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [3]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1e3uA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 67;TRP 154 LYS 70 SER 67;PHE 208
1e3uB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 67;TRP 154 LYS 70 SER 67;PHE 208
1e3uC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 67;TRP 154 LYS 70 SER 67;PHE 208
1e3uD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 67;TRP 154 LYS 70 SER 67;PHE 208
1e4dA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 67;TRP 154 KCX 70(Carbamylation) SER 67;PHE 208 carbamated Lys70
1e4dB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 67;TRP 154 KCX 70(Carbamylation) SER 67;PHE 208 carbamated Lys70
1e4dC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 67;TRP 154 KCX 70(Carbamylation) SER 67;PHE 208 carbamated Lys70
1e4dD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 67;TRP 154 KCX 70(Carbamylation) SER 67;PHE 208 carbamated Lys70
1ewzA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 67;TRP 154 LYS 70 SER 67;PHE 208
1ewzB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 67;TRP 154 LYS 70 SER 67;PHE 208
1ewzC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 67;TRP 154 LYS 70 SER 67;PHE 208
1ewzD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 67;TRP 154 LYS 70 SER 67;PHE 208
1fofA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 67;TRP 154 LYS 70 SER 67;PHE 208
1fofB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 67;TRP 154 LYS 70 SER 67;PHE 208

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
p.6133
[2]
p.922-924
[3]
p.1292-1296
[4]
p.2463, Scheme 1 2

References
[1]
Resource
Comments
Medline ID
PubMed ID
Journal J Am Chem Soc
Year 2000
Volume 122
Pages 6132-3
Authors Golemi D, Maveyraud L, Vakulenko S, Tranier S, Ishiwata A, Kotra LP, Samama JP, Mobashery S
Title The first structural and mechanistic insights for class d beta-lactamases: evidence for a novel catalytic process for turnover of beta-lactam antibiotics.
Related PDB 1ewz
Related UniProtKB
[2]
Resource
Comments X-ray crystallography (2.0 Angstroms)
Medline ID
PubMed ID 11017203
Journal Nat Struct Biol
Year 2000
Volume 7
Pages 918-25
Authors Paetzel M, Danel F, de Castro L, Mosimann SC, Page MG, Strynadka NC
Title Crystal structure of the class D beta-lactamase OXA-10.
Related PDB 1fof
Related UniProtKB
[3]
Resource
Comments X-ray crystallography (1.66 Angstroms)
Medline ID 21029090
PubMed ID 11188693
Journal Structure Fold Des
Year 2000
Volume 8
Pages 1289-98
Authors Maveyraud L, Golemi D, Kotra LP, Tranier S, Vakulenko S, Mobashery S, Samama JP
Title Insights into class D beta-lactamases are revealed by the crystal structure of the OXA10 enzyme from Pseudomonas aeruginosa.
Related PDB 1e3u 1e4d
Related UniProtKB P14489
[4]
Resource
Comments
Medline ID
PubMed ID 11890794
Journal J Am Chem Soc
Year 2002
Volume 124
Pages 2461-5
Authors Maveyraud L, Golemi-Kotra D, Ishiwata A, Meroueh O, Mobashery S, Samama JP
Title High-resolution X-ray structure of an acyl-enzyme species for the class D OXA-10 beta-lactamase.
Related PDB
Related UniProtKB

Comments
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.

Created Updated
2002-09-27 2009-02-26