› 2wda

X-ray diffraction
2.3Å resolution

The X-ray structure of the Streptomyces coelicolor A3 Chondroitin AC Lyase in Complex with Chondroitin sulphate

Released:
DOI: 10.2210/pdb2wda/pdb
PDB entry 2wda coloured by chain, front view.
PDB entry 2wda coloured by chain, side view.
PDB entry 2wda coloured by chain, top view.
Source organism: Streptomyces violaceoruber
Primary publication:
Crystal structures of a family 8 polysaccharide lyase reveal open and highly occluded substrate-binding cleft conformations.
Elmabrouk ZH, Vincent F, Zhang M, Smith NL, Turkenburg JP, Charnock SJ, Black GW, Taylor EJ
Proteins 79 965-74 (2011)
PMID: 21287626

Function and Biology Details

Reaction catalysed: 
Cleaves hyaluronate chains at a beta-D-GlcNAc-(1->4)-beta-D-GlcA bond, ultimately breaking the polysaccharide down to 3-(4-deoxy-beta-D-gluc-4-enuronosyl)-N-acetyl-D-glucosamine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-131475 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Secreted lyase Chain: A
Molecule details ›
Chain: A
Length: 765 amino acids
Theoretical weight: 83.02 KDa
Source organism: Streptomyces violaceoruber
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O86516 (Residues: 33-776; Coverage: 100%)
Gene names: SC1C2.15, SCO5534
Sequence domains:
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: ASG, GCD
Carbohydrate polymer
4 bound ligands:
Ligand FMT 5 x FMT
Ligand GOL 3 x GOL
Ligand PEG 9 x PEG
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-3
Spacegroup: P43212
Unit cell:
a: 140.508Å b: 140.508Å c: 100.764Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.151 0.149 0.193
Expression system: Escherichia coli BL21(DE3)

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Citations

13 citation in other articles

Induced-fit motion of a lid loop involved in catalysis in alginate lyase A1-III.
Mikami et al. (2012)
12 more

2 mentions without citation

Mating in the Closest Living Relatives of Animals Is Induced by a Bacterial Chondroitinase.
Woznica et al. (2017)
1 more