› 2y2k

X-ray diffraction
2.09Å resolution

PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (ZA5)

Released:
DOI: 10.2210/pdb2y2k/pdb
PDB 2y2k coloured by chain and viewed from the front.
PDB 2y2k coloured by chain and viewed from the side.
PDB 2y2k coloured by chain and viewed from the top.
Source organism: Streptococcus pneumoniae R6
Primary publication:
Structure-guided design of cell wall biosynthesis inhibitors that overcome β-lactam resistance in Staphylococcus aureus (MRSA).
Contreras-Martel C, Amoroso A, Woon EC, Zervosen A, Inglis S, Martins A, Verlaine O, Rydzik AM, Job V, Luxen A, Joris B, Schofield CJ, Dessen A
ACS Chem. Biol. 6 943-51 (2011)
PMID: 21732689

Function and Biology Details

Reactions catalysed: 
Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine.
(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
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DD-transpeptidase Chain: A
Molecule details ›
Chain: A
Length: 494 amino acids
Theoretical weight: 54.1 KDa
Source organism: Streptococcus pneumoniae R6
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q7CRA4 (Residues: 321-791; Coverage: 57%)
Gene names: pbp1b, spr1909
Sequence domains: Penicillin binding protein transpeptidase domain
Structure domains:

Ligands and Environments

5 bound ligands:
Ligand ZA5 1 x ZA5
Ligand SO4 1 x SO4
Ligand CL 17 x CL
Ligand NA 1 x NA
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: C2221
Unit cell:
a: 98.309Å b: 149.908Å c: 97.578Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.208 0.202 0.263
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

11 review citations

Will morphing boron-based inhibitors beat the β-lactamases?
Krajnc et al. (2019)
10 more