› 2jch

X-ray diffraction
2.4Å resolution

Structural and mechanistic basis of penicillin binding protein inhibition by lactivicins

Released:
DOI: 10.2210/pdb2jch/pdb
PDB entry 2jch coloured by chain, front view.
PDB entry 2jch coloured by chain, side view.
PDB entry 2jch coloured by chain, top view.
Source organism: Streptococcus pneumoniae R6
Primary publication:
Structural and mechanistic basis of penicillin-binding protein inhibition by lactivicins.
Macheboeuf P, Fischer DS, Brown T, Zervosen A, Luxen A, Joris B, Dessen A, Schofield CJ
Nat Chem Biol 3 565-9 (2007)
PMID: 17676039

Function and Biology Details

Reaction 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
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-130673 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
peptidoglycan glycosyltransferase Chain: A
Molecule details ›
Chain: A
Length: 720 amino acids
Theoretical weight: 78.43 KDa
Source organism: Streptococcus pneumoniae R6
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: O70038 (Residues: 72-791; Coverage: 88%)
Gene name: pbp1b
Sequence domains:
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand SO4 1 x SO4
Ligand CL 1 x CL
Ligand EDO 1 x EDO
Ligand PL7 1 x PL7
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: C2221
Unit cell:
a: 105.84Å b: 143.58Å c: 97.44Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.206 0.203 0.262
Expression system: Escherichia coli BL21

Quick links

Citations

17 review citations

Electrophilic natural products and their biological targets.
Gersch et al. (2012)
16 more

2 mentions without citation

Anti-plasmin inhibitor. VI. Structure of phlorofucofuroeckol A, a novel phlorotannin with both dibenzo-1,4-dioxin and dibenzofuran elements, from Ecklonia kurome Okamura.
Fukuyama et al. (1990)
1 more