PDBsum entry 1g2a

Hydrolase

PDB id: 1g2a

Contents

Protein chains

164 a.a. *

Ligands

BB2 ×3

Metals

_NI ×3

Waters ×725

* Residue conservation analysis

PDB id:

1g2a

Name:

Hydrolase

Title:

The crystal structure of e.Coli peptide deformylase complexed with actinonin

Structure:

Polypeptide deformylase. Chain: a, b, c. Synonym: n-formylmethionylaminoacyl-tRNA deformylase, pdf, fms. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: def. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.75Å R-factor: 0.191 R-free: 0.250

Authors:

J.M.Clements,P.Beckett,A.Brown,C.Catlin,M.Lobell,S.Palan,W.Thomas, M.Whittaker,P.J.Baker,H.F.Rodgers,V.Barynin,D.W.Rice,M.G.Hunter

Key ref:

J.M.Clements et al. (2001). Antibiotic activity and characterization of BB-3497, a novel peptide deformylase inhibitor. Antimicrob Agents Chemother, 45, 563-570. PubMed id: 11158755

Date:

18-Oct-00 Release date: 17-Oct-01

Protein chains

P0A6K3  (DEF_ECOLI) -  Peptide deformylase from Escherichia coli (strain K12)

Seq: 169 a.a.

Struc: 164 a.a.

Enzyme reactions

• Enzyme class: E.C.3.5.1.88 - peptide deformylase.
• Reaction: N-terminal N-formyl-L-methionyl-[peptide] + H2O = N-terminal L-methionyl- [peptide] + formate
• Cofactor: Fe(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key reference

Antimicrob Agents Chemother 45:563-570 (2001)

PubMed id: 11158755

Antibiotic activity and characterization of BB-3497, a novel peptide deformylase inhibitor.

J.M.Clements, R.P.Beckett, A.Brown, G.Catlin, M.Lobell, S.Palan, W.Thomas, M.Whittaker, S.Wood, S.Salama, P.J.Baker, H.F.Rodgers, V.Barynin, D.W.Rice, M.G.Hunter.

ABSTRACT

Peptide deformylase (PDF) is an essential bacterial metalloenzyme which deformylates the N-formylmethionine of newly synthesized polypeptides and as such represents a novel target for antibacterial chemotherapy. To identify novel PDF inhibitors, we screened a metalloenzyme inhibitor library and identified an N-formyl-hydroxylamine derivative, BB-3497, and a related natural hydroxamic acid antibiotic, actinonin, as potent and selective inhibitors of PDF. To elucidate the interactions that contribute to the binding affinity of these inhibitors, we determined the crystal structures of BB-3497 and actinonin bound to Escherichia coli PDF at resolutions of 2.1 and 1.75 A, respectively. In both complexes, the active-site metal atom was pentacoordinated by the side chains of Cys 90, His 132, and His 136 and the two oxygen atoms of N-formyl-hydroxylamine or hydroxamate. BB-3497 had activity against gram-positive bacteria, including methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecalis, and activity against some gram-negative bacteria. Time-kill analysis showed that the mode of action of BB-3497 was primarily bacteriostatic. The mechanism of resistance was via mutations within the formyltransferase gene, as previously described for actinonin. While actinonin and its derivatives have not been used clinically because of their poor pharmacokinetic properties, BB-3497 was shown to be orally bioavailable. A single oral dose of BB-3497 given 1 h after intraperitoneal injection of S. aureus Smith or methicillin-resistant S. aureus protected mice from infection with median effective doses of 8 and 14 mg/kg of body weight, respectively. These data validate PDF as a novel target for the design of a new generation of antibacterial agents.