4ax8

X-ray diffraction
3Å resolution

Medium resolution structure of the bifunctional kinase- methyltransferase WbdD

Released:
Source organism: Escherichia coli
Entry authors: Hagelueken G, Huang H, Naismith JH

Function and Biology Details

Reactions catalysed:
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
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
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
monomeric (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
O-antigen chain terminator bifunctional methyltransferase/kinase WbdD Chain: A
Molecule details ›
Chain: A
Length: 569 amino acids
Theoretical weight: 65.09 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: J7I4B7 (Residues: 2-556; Coverage: 78%)
Gene name: wbdD
Sequence domains:
Structure domains:

Ligands and Environments


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

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND
Spacegroup: I23
Unit cell:
a: 167.34Å b: 167.34Å c: 167.34Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.213 0.212 0.233
Expression system: Escherichia coli