› 3eka

X-ray diffraction
3.1Å resolution

Crystal structure of the complex of hyaluranidase trimer with ascorbic acid at 3.1 A resolution reveals the locations of three binding sites

Released:
DOI: 10.2210/pdb3eka/pdb
PDB entry 3eka coloured by chain, front view.
PDB entry 3eka coloured by chain, side view.
PDB entry 3eka coloured by chain, top view.
Source organism: Streptococcus pyogenes
Primary publication:
Polysaccharide binding sites in hyaluronate lyase--crystal structures of native phage-encoded hyaluronate lyase and its complexes with ascorbic acid and lactose.
Mishra P, Prem Kumar R, Ethayathulla AS, Singh N, Sharma S, Perbandt M, Betzel C, Kaur P, Srinivasan A, Bhakuni V, Singh TP
FEBS J 276 3392-402 (2009)
PMID: 19438710

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:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-189445 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Major tropism determinant N-terminal domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 332 amino acids
Theoretical weight: 35.8 KDa
Source organism: Streptococcus pyogenes
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9A0M7 (Residues: 7-337; Coverage: 98%)
Gene names: SPy_0701, hylP1
Sequence domains:

Ligands and Environments

1 bound ligand:
Ligand ASC 3 x ASC
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X31
Spacegroup: R32
Unit cell:
a: 58.502Å b: 58.502Å c: 583.54Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.212 0.197 0.234
Expression system: Escherichia coli

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Citations

5 review citations

Structural and mechanistic classification of uronic acid-containing polysaccharide lyases.
Garron et al. (2010)
4 more