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Catalytic Site Atlas

CSA LITERATURE entry for 2bmi

E.C. namebeta-lactamase
SpeciesBacteroides fragilis (Bacteria)
E.C. Number (IntEnz)
CSA Homologues of 2bmiThere are 72 Homologs
CSA Entries With UniProtID P25910
CSA Entries With EC Number
PDBe Entry 2bmi
PDBSum Entry 2bmi
MACiE Entry M0015

Literature Report

IntroductionBeta-lactamase is a key antibiotic resistance enzyme as it cleaves the essential beta-lactam ring structure in penicillin and cephalosporinase type antibiotics. Substrate specificity varies considerably within the beta-lactamases, with some enzymes preferring penicillins and some cephalosporins. There are four classes of beta-lactamases (A-D). Classes A, C, and D use a serine nucleophilic mechanism, whilst class B uses a bimetallic zinc mechanism. Considerable variety in substrate specificity exists within classes also, though class C enzymes tend to have a high cephalosporinase activity. Pdb files exist for all except class D. This entry covers the class B beta-lactamase structures in the pdb.
Mechansim(1bmi numbering) A mechanism has been proposed by Fabiane et al [REF: 2]. The beta-lactam carbonyl interacts with zinc1 polarising the bond and enhancing its susceptibility to nucleophilic attack. A zinc1 associated water/hydroxide is the nucleophile which attacks the beta-lactam carbonyl carbon. The substrate carboxylate moiety interacts with zinc2 and lysine 167. Asparagine 176 and zinc1 stabilise the oxyanion. Aspartate 86 acts the general acid/base abstracting a proton from the zinc1 water and donating it to the developing amino nitrogen.

Catalytic Sites for 2bmi

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription

Literature References

Fitzgerald PM
Unanticipated inhibition of the metallo-beta-lactamase from Bacteroides fragilis by 4-morpholineethanesulfonic acid (MES): a crystallographic study at 1.85-A resolution.
Biochemistry 1998 37 6791-6800
PubMed: 9578564
Fabiane SM
Crystal structure of the zinc-dependent beta-lactamase from Bacillus cereus at 1.9 A resolution: binuclear active site with features of a mononuclear enzyme.
Biochemistry 1998 37 12404-12411
PubMed: 9730812