› 1ofl

X-ray diffraction
1.7Å resolution

CRYSTAL STRUCTURE OF CHONDROITINASE B COMPLEXED TO DERMATAN SULFATE HEXASACCHARIDE

Released:
DOI: 10.2210/pdb1ofl/pdb
PDB entry 1ofl coloured by chain, front view.
PDB entry 1ofl coloured by chain, side view.
PDB entry 1ofl coloured by chain, top view.
Source organism: Pedobacter heparinus
Primary publication:
The structure of chondroitin B lyase complexed with glycosaminoglycan oligosaccharides unravels a calcium-dependent catalytic machinery.
Michel G, Pojasek K, Li Y, Sulea T, Linhardt RJ, Raman R, Prabhakar V, Sasisekharan R, Cygler M
J Biol Chem 279 32882-96 (2004)
PMID: 15155751

Function and Biology Details

Reaction catalysed: 
Eliminative cleavage of dermatan sulfate containing (1->4)-beta-D-hexosaminyl and (1->3)-beta-D-glucurosonyl or (1->3)-alpha-L-iduronosyl linkages to disaccharides containing 4-deoxy-beta-D-gluc-4-enuronosyl groups to yield a 4,5-unsaturated dermatan-sulfate disaccharide (Delta-UA-GalNAc-4S).
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-175093 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (4 distinct):
Chondroitinase-B Chain: A
Molecule details ›
Chain: A
Length: 481 amino acids
Theoretical weight: 53.69 KDa
Source organism: Pedobacter heparinus
Expression system: Pedobacter heparinus
UniProt:
  • Canonical: Q46079 (Residues: 26-506; Coverage: 100%)
Gene names: Phep_0789, cslB
Sequence domains: Chondroitinase B
Structure domains: Single-stranded right-handed beta-helix, Pectin lyase-like

Ligands and Environments

Carbohydrate polymer : NEW Components: MAN, GCU, XYP, MXZ, GLA, BGC, RAM
Carbohydrate polymer
Carbohydrate polymer : NEW Components: ASG, GCD
Carbohydrate polymer
Carbohydrate polymer : NEW Components: GCD, NGK
Carbohydrate polymer
1 bound ligand:
Ligand CA 1 x CA
1 modified residue:
Ligand PCA 1 x PCA

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X8C
Spacegroup: P21
Unit cell:
a: 50.574Å b: 73.989Å c: 59.063Å
α: 90° β: 93.93° γ: 90°
R-values:
R R work R free
0.135 0.133 0.176
Expression system: Pedobacter heparinus

Quick links

Citations

11 review citations

Structural insights into biological roles of protein-glycosaminoglycan interactions.
Raman et al. (2005)
10 more

10 mentions without citation

The Sea as a Rich Source of Structurally Unique Glycosaminoglycans and Mimetics.
Vasconcelos et al. (2017)
9 more