PDBsum entry 4jpm

Hydrolase/hydrolase inhibitor

PDB id: 4jpm

Contents

Protein chain

265 a.a.

Ligands

MA4 ×2

1OG-EPE

Waters ×338

PDB id:

4jpm

Name:

Hydrolase/hydrolase inhibitor

Title:

Structure of shv-1 beta-lactamase in complex with the 7- alkylidenecephalosporin dcm-1-10 at 1.14 ang resolution

Structure:

Beta-lactamase shv-1. Chain: a. Fragment: svh-1 beta-lactamase. Synonym: pit-2. Engineered: yes

Source:

Klebsiella pneumoniae. Organism_taxid: 573. Gene: bla, shv1. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.14Å R-factor: 0.132 R-free: 0.164

Authors:

E.A.Rodkey,F.Van Den Akker

Key ref:

E.A.Rodkey et al. (2013). β-Lactamase inhibition by 7-alkylidenecephalosporin sulfones: allylic transposition and formation of an unprecedented stabilized acyl-enzyme. J Am Chem Soc, 135, 18358-18369. PubMed id: 24219313 DOI: 10.1021/ja403598g

Date:

19-Mar-13 Release date: 04-Dec-13

Protein chain

P0AD64  (BLA1_KLEPN) -  Beta-lactamase SHV-1 from Klebsiella pneumoniae

Seq: 286 a.a.

Struc: 265 a.a.

Enzyme reactions

• Enzyme class: E.C.3.5.2.6 - beta-lactamase.
• Pathway: Penicillin Biosynthesis and Metabolism
• Reaction: a beta-lactam + H2O = a substituted beta-amino acid
• Cofactor: Zn(2+)

DOI no: 10.1021/ja403598g

J Am Chem Soc 135:18358-18369 (2013)

PubMed id: 24219313

β-Lactamase inhibition by 7-alkylidenecephalosporin sulfones: allylic transposition and formation of an unprecedented stabilized acyl-enzyme.

E.A.Rodkey, D.C.McLeod, C.R.Bethel, K.M.Smith, Y.Xu, W.Chai, T.Che, P.R.Carey, R.A.Bonomo, F.van den Akker, J.D.Buynak.

ABSTRACT

The inhibition of the class A SHV-1 β-lactamase by 7-(tert-butoxycarbonyl)methylidenecephalosporin sulfone was examined kinetically, spectroscopically, and crystallographically. An 1.14 Å X-ray crystal structure shows that the stable acyl-enzyme, which incorporates an eight-membered ring, is a covalent derivative of Ser70 linked to the 7-carboxy group of 2-H-5,8-dihydro-1,1-dioxo-1,5-thiazocine-4,7-dicarboxylic acid. A cephalosporin-derived enzyme complex of this type is unprecedented, and the rearrangement leading to its formation may offer new possibilities for inhibitor design. The observed acyl-enzyme derives its stability from the resonance stabilization conveyed by the β-aminoacrylate (i.e., vinylogous urethane) functionality as there is relatively little interaction of the eight-membered ring with active site residues. Two mechanistic schemes are proposed, differing in whether, subsequent to acylation of the active site serine and opening of the β-lactam, the resultant dihydrothiazine fragments on its own or is assisted by an adjacent nucleophilic atom, in the form of the carbonyl oxygen of the C7 tert-butyloxycarbonyl group. This compound was also found to be a submicromolar inhibitor of the class C ADC-7 and PDC-3 β-lactamases.