PDBsum entry 4p75

Ligase/ligase inhibitor

PDB id: 4p75

Contents

Protein chains

791 a.a.

235 a.a.

Ligands

2NM ×2

Waters ×49

PDB id:

4p75

Name:

Ligase/ligase inhibitor

Title:

Phers in complex with compound 4a

Structure:

Phenylalanine--tRNA ligase beta subunit. Chain: a, b. Synonym: phenylalanyl-tRNA synthetase beta subunit,phers. Engineered: yes. Phenylalanine--tRNA ligase alpha subunit. Chain: c, d. Synonym: phenylalanyl-tRNA synthetase alpha subunit,phers. Engineered: yes

Source:

Pseudomonas aeruginosa. Organism_taxid: 208964. Strain: atcc 15692 / pao1 / 1c / prs 101 / lmg 12228. Gene: phet, pa2739. Expressed in: escherichia. Expression_system_taxid: 562. Gene: phes, pa2740. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.96Å R-factor: 0.185 R-free: 0.213

Authors:

A.D.Ferguson

Key ref:

A.Abibi et al. (2014). The role of a novel auxiliary pocket in bacterial phenylalanyl-tRNA synthetase druggability. J Biol Chem, 289, 21651-21662. PubMed id: 24936059 DOI: 10.1074/jbc.M114.574061

Date:

25-Mar-14 Release date: 25-Jun-14

Protein chains

Q9I0A4  (SYFB_PSEAE) -  Phenylalanine--tRNA ligase beta subunit from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)

Seq: 792 a.a.

Struc: 791 a.a.

Protein chains

Q9I0A3  (SYFA_PSEAE) -  Phenylalanine--tRNA ligase alpha subunit from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)

Seq: 338 a.a.

Struc: 235 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, C, D: E.C.6.1.1.20 - phenylalanine--tRNA ligase.
• Reaction: tRNA(Phe) + L-phenylalanine + ATP = L-phenylalanyl-tRNA(Phe) + AMP + diphosphate + H⁺

tRNA(Phe) + L-phenylalanine (Bound ligand (Het Group name = 2NM) matches with 52.63% similarity) + ATP = L-phenylalanyl-tRNA(Phe) + AMP + diphosphate + H(+)

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

reference

DOI no: 10.1074/jbc.M114.574061

J Biol Chem 289:21651-21662 (2014)

PubMed id: 24936059

The role of a novel auxiliary pocket in bacterial phenylalanyl-tRNA synthetase druggability.

A.Abibi, A.D.Ferguson, P.R.Fleming, N.Gao, L.I.Hajec, J.Hu, V.A.Laganas, D.C.McKinney, S.M.McLeod, D.B.Prince, A.B.Shapiro, E.T.Buurman.

ABSTRACT

The antimicrobial activity of phenyl-thiazolylurea-sulfonamides against Staphylococcus aureus PheRS are dependent upon phenylalanine levels in the extracellular fluids. Inhibitor efficacy in animal models of infection is substantially diminished by dietary phenylalanine intake, thereby reducing the perceived clinical utility of this inhibitor class. The search for novel antibacterial compounds against Gram-negative pathogens led to a re-evaluation of this phenomenon, which is shown here to be unique to S. aureus. Inhibition of macromolecular syntheses and characterization of novel resistance mutations in Escherichia coli demonstrate that antimicrobial activity of phenyl-thiazolylurea-sulfonamides is mediated by PheRS inhibition, validating this enzyme as a viable drug discovery target for Gram-negative pathogens. A search for novel inhibitors of PheRS yielded three novel chemical starting points. NMR studies were used to confirm direct target engagement for phenylalanine-competitive hits. The crystallographic structure of Pseudomonas aeruginosa PheRS defined the binding modes of these hits and revealed an auxiliary hydrophobic pocket that is positioned adjacent to the phenylalanine binding site. Three viable inhibitor-resistant mutants were mapped to this pocket, suggesting that this region is a potential liability for drug discovery.