4azw

X-ray diffraction
2.47Å resolution

Crystal structure of monomeric WbdD.

Released:

Function and Biology Details

Reactions catalysed:
S-adenosyl-L-methionine + 3-O-phospho-alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-(alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-Man-(1->2)-alpha-D-Man-(1->2))(N)-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol = S-adenosyl-L-homocysteine + 3-O-methylphospho-alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-(alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-Man-(1->2)-alpha-D-Man-(1->2))(N)-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol
ATP + alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-(alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-Man-(1->2)-alpha-D-Man-(1->2))(n)-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol = ADP + 3-O-phospho-alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-(alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-Man-(1->2)-alpha-D-Man-(1->2))(n)-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol
Biochemical function:
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
monomeric (preferred)
PDBe Complex ID:
PDB-CPX-175254 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
O-antigen chain terminator bifunctional methyltransferase/kinase WbdD Chain: A
Molecule details ›
Chain: A
Length: 471 amino acids
Theoretical weight: 54.15 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: Q47592 (Residues: 2-458; Coverage: 65%)
Gene names: ORF708, wbdD
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand SAM 1 x SAM
2 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P212121
Unit cell:
a: 40.67Å b: 89.6Å c: 135.46Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.193 0.19 0.237
Expression system: Escherichia coli