› 2d8l

X-ray diffraction
1.7Å resolution

Crystal Structure of Unsaturated Rhamnogalacturonyl Hydrolase in complex with dGlcA-GalNAc

Released:
DOI: 10.2210/pdb2d8l/pdb
PDB entry 2d8l coloured by chain, front view.
PDB entry 2d8l coloured by chain, side view.
PDB entry 2d8l coloured by chain, top view.
Source organism: Bacillus subtilis
Primary publication:
A novel glycoside hydrolase family 105: the structure of family 105 unsaturated rhamnogalacturonyl hydrolase complexed with a disaccharide in comparison with family 88 enzyme complexed with the disaccharide.
Itoh T, Ochiai A, Mikami B, Hashimoto W, Murata K
J Mol Biol 360 573-85 (2006)
PMID: 16781735

Function and Biology Details

Reaction catalysed: 
2-O-(4-deoxy-beta-L-threo-hex-4-enopyranuronosyl)-alpha-L-rhamnopyranose + H(2)O = 5-dehydro-4-deoxy-D-glucuronate + L-rhamnopyranose
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-128560 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Unsaturated rhamnogalacturonyl hydrolase YteR Chain: A
Molecule details ›
Chain: A
Length: 373 amino acids
Theoretical weight: 43.02 KDa
Source organism: Bacillus subtilis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O34559 (Residues: 1-373; Coverage: 100%)
Gene names: BSU30120, yteR
Sequence domains: Glycosyl Hydrolase Family 88
Structure domains: Glycosyltransferase

Ligands and Environments

Carbohydrate polymer : NEW Components: NGA, GCD
Carbohydrate polymer
No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL38B1
Spacegroup: P6122
Unit cell:
a: 91.831Å b: 91.831Å c: 178.865Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.162 not available 0.219
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 review citations

Enzymatic deconstruction of backbone structures of the ramified regions in pectins.
Wong D. (2008)
2 more

3 mentions without citation

Modeling Protein-Glycosaminoglycan Complexes: Does the Size Matter?
Marcisz et al. (2021)
2 more