› 8csf

X-ray diffraction
2.4Å resolution

WbbB D232C-Kdo adduct + alpha-Rha(1,3)GlcNAc ternary complex

Released:
DOI: 10.2210/pdb8csf/pdb
PDB entry 8csf coloured by chain, front view.
PDB entry 8csf coloured by chain, side view.
PDB entry 8csf coloured by chain, top view.
Source organism: Raoultella terrigena
Primary publication:
The retaining β-Kdo glycosyltransferase WbbB uses a double-displacement mechanism with an intermediate adduct rearrangement step.
Forrester TJB, Ovchinnikova OG, Li Z, Kitova EN, Nothof JT, Koizumi A, Klassen JS, Lowary TL, Whitfield C, Kimber MS
OpenAccess logo Nat Commun 13 6277 (2022)
PMID: 36271007

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-180404 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Glycosyltransferase 99 N-terminal domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 410 amino acids
Theoretical weight: 46.12 KDa
Source organism: Raoultella terrigena
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6U8B0 (Residues: 2-401; Coverage: 36%)
Gene name: wbbB
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, RAM
Carbohydrate polymer
3 bound ligands:
Ligand C5P 2 x C5P
Ligand NA 4 x NA
Ligand KDO 2 x KDO
1 modified residue:
Ligand CSO 4 x CSO

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08B1-1
Spacegroup: C2221
Unit cell:
a: 92.5Å b: 158.07Å c: 116.68Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.175 0.172 0.221
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Architecture, Function, Regulation, and Evolution of α-Glucans Metabolic Enzymes in Prokaryotes.
Cifuente et al. (2024)
4 other articles

1 mention without citation

Trapping and retaining intermediates in glycosyltransferases.
Guerin ME. (2023)