PDBsum entry 5c5h

Ligase

PDB id: 5c5h

Contents

Protein chains

443 a.a.

Ligands

4YB ×2

Metals

_MG ×3

Waters ×223

PDB id:

5c5h

Name:

Ligase

Title:

R195k e. Coli mene with bound osb-ams

Structure:

2-succinylbenzoate--coa ligase. Chain: a, b. Synonym: o-succinylbenzoyl-coa synthetase,osb-coa synthetase. Engineered: yes. Mutation: yes

Source:

Escherichia coli (strain k12). Organism_taxid: 83333. Strain: k12. Gene: mene, b2260, jw2255. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.40Å R-factor: 0.203 R-free: 0.247

Authors:

J.S.Matarlo,R.Shek,K.R.Rajashankar,P.J.Tonge,J.B.French

Key ref:

J.S.Matarlo et al. (2015). Mechanism of MenE inhibition by acyl-adenylate analogues and discovery of novel antibacterial agents. Biochemistry, 54, 6514-6524. PubMed id: 26394156 DOI: 10.1021/acs.biochem.5b00966

Date:

19-Jun-15 Release date: 07-Oct-15

Protein chains

P37353  (MENE_ECOLI) -  2-succinylbenzoate--CoA ligase from Escherichia coli (strain K12)

Seq: 451 a.a.

Struc: 443 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.6.2.1.26 - o-succinylbenzoate--CoA ligase.
• Pathway: Vitamin K Biosynthesis
• Reaction: 2-succinylbenzoate + ATP + CoA = 2-succinylbenzoyl-CoA + AMP + diphosphate

2-succinylbenzoate + ATP + CoA = 2-succinylbenzoyl-CoA + AMP (Bound ligand (Het Group name = 4YB) matches with 45.24% similarity) + diphosphate

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

reference

DOI no: 10.1021/acs.biochem.5b00966

Biochemistry 54:6514-6524 (2015)

PubMed id: 26394156

Mechanism of MenE inhibition by acyl-adenylate analogues and discovery of novel antibacterial agents.

J.S.Matarlo, C.E.Evans, I.Sharma, L.J.Lavaud, S.C.Ngo, R.Shek, K.R.Rajashankar, J.B.French, D.S.Tan, P.J.Tonge.

ABSTRACT

MenE is an o-succinylbenzoyl-CoA (OSB-CoA) synthetase in the bacterial menaquinone biosynthesis pathway and is a promising target for the development of novel antibacterial agents. The enzyme catalyzes CoA ligation via an acyl-adenylate intermediate, and we have previously reported tight-binding inhibitors of MenE based on stable acyl-sulfonyladenosine analogues of this intermediate, including OSB-AMS (1), which has an IC50 value of ≤25 nM for Escherichia coli MenE. Herein, we show that OSB-AMS reduces menaquinone levels in Staphylococcus aureus, consistent with its proposed mechanism of action, despite the observation that the antibacterial activity of OSB-AMS is ∼1000-fold lower than the IC50 for enzyme inhibition. To inform the synthesis of MenE inhibitors with improved antibacterial activity, we have undertaken a structure-activity relationship (SAR) study stimulated by the knowledge that OSB-AMS can adopt two isomeric forms in which the OSB side chain exists either as an open-chain keto acid or a cyclic lactol. These studies revealed that negatively charged analogues of the keto acid form bind, while neutral analogues do not, consistent with the hypothesis that the negatively charged keto acid form of OSB-AMS is the active isomer. X-ray crystallography and site-directed mutagenesis confirm the importance of a conserved arginine for binding the OSB carboxylate. Although most lactol isomers tested were inactive, a novel difluoroindanediol inhibitor (11) with improved antibacterial activity was discovered, providing a pathway toward the development of optimized MenE inhibitors in the future.