› 5cxw

X-ray diffraction
1.75Å resolution

Structure of the PonA1 protein from Mycobacterium Tuberculosis in complex with penicillin V

Released:
DOI: 10.2210/pdb5cxw/pdb
PDB entry 5cxw coloured by chain, front view.
PDB entry 5cxw coloured by chain, side view.
PDB entry 5cxw coloured by chain, top view.
Source organism: Mycobacterium tuberculosis H37Rv
Primary publication:
Crystal structures of the transpeptidase domain of the Mycobacterium tuberculosis penicillin-binding protein PonA1 reveal potential mechanisms of antibiotic resistance.
Filippova EV, Kieser KJ, Luan CH, Wawrzak Z, Kiryukhina O, Rubin EJ, Anderson WF
FEBS J 283 2206-18 (2016)
PMID: 27101811

Function and Biology Details

Reactions catalysed: 
(GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala))(n)-diphosphoundecaprenol + GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol = (GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala))(n+1)-diphosphoundecaprenol + undecaprenyl diphosphate
Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine.
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-159814 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Penicillin-binding protein 1A Chain: A
Molecule details ›
Chain: A
Length: 430 amino acids
Theoretical weight: 44.31 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P71707 (Residues: 391-820; Coverage: 52%)
Gene names: MTCY21D4.13, Rv0050, ponA1
Sequence domains: Penicillin binding protein transpeptidase domain
Structure domains: DD-peptidase/beta-lactamase superfamily

Ligands and Environments

3 bound ligands:
Ligand EPE 1 x EPE
Ligand 35P 1 x 35P
Ligand PEG 2 x PEG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: P212121
Unit cell:
a: 47.341Å b: 60.58Å c: 133.904Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.149 0.147 0.189
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 review citations

Cell wall peptidoglycan in Mycobacterium tuberculosis: An Achilles' heel for the TB-causing pathogen.
Maitra et al. (2019)
3 more

3 mentions without citation

Crystal structures of the transpeptidase domain of the Mycobacterium tuberculosis penicillin-binding protein PonA1 reveal potential mechanisms of antibiotic resistance.
Filippova et al. (2016)
2 more