› 2xd5

X-ray diffraction
2.5Å resolution

Structural insights into the catalytic mechanism and the role of Streptococcus pneumoniae PBP1b

Released:
DOI: 10.2210/pdb2xd5/pdb
Model geometry
Fit model/data
PDB entry 2xd5 coloured by chain, front view.
PDB entry 2xd5 coloured by chain, side view.
PDB entry 2xd5 coloured by chain, top view.
Source organism: Streptococcus pneumoniae R6
Entry authors: Macheboeuf P, Lemaire D, Jamin M, Dideberg O, Dessen A

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:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-181431 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Penicillin-binding protein 1b Chains: A, B
Molecule details ›
Chains: A, B
Length: 494 amino acids
Theoretical weight: 54.14 KDa
Source organism: Streptococcus pneumoniae R6
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q7CRA4 (Residues: 323-791; Coverage: 57%)
Gene names: pbp1b, spr1909
Sequence domains: Penicillin binding protein transpeptidase domain
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand SO4 2 x SO4
Ligand S2D 2 x S2D
Ligand CL 2 x CL
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: ESRF BEAMLINE BM30A
Spacegroup: P212121
Unit cell:
a: 96.8Å b: 101.1Å c: 145Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.184 0.181 0.233
Expression system: Escherichia coli BL21

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