› 4bq2

X-ray diffraction
1.9Å resolution

Structural analysis of an exo-beta-agarase

Released:
DOI: 10.2210/pdb4bq2/pdb
PDB entry 4bq2 coloured by chain, front view.
PDB entry 4bq2 coloured by chain, side view.
PDB entry 4bq2 coloured by chain, top view.
Source organism: Saccharophagus degradans 2-40
Primary publication:
Substrate recognition and hydrolysis by a family 50 exo-β-agarase, Aga50D, from the marine bacterium Saccharophagus degradans.
Pluvinage B, Hehemann JH, Boraston AB
J Biol Chem 288 28078-88 (2013)
PMID: 23921382

Function and Biology Details

Reaction catalysed: 
Hydrolysis of (1->4)-beta-D-galactosidic linkages in agarose, giving the tetramer as the predominant product
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-557533 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
B-agarase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 750 amino acids
Theoretical weight: 84.3 KDa
Source organism: Saccharophagus degradans 2-40
Expression system: Escherichia coli
UniProt:
  • Canonical: Q21HC5 (Residues: 47-793; Coverage: 94%)
Gene names: Sde_2644, aga50B
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand GOL 22 x GOL
Ligand CA 4 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-2
Spacegroup: P41
Unit cell:
a: 166.666Å b: 166.666Å c: 114.559Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.172 0.17 0.215
Expression system: Escherichia coli

Quick links

Citations

7 review citations

Microorganisms living on macroalgae: diversity, interactions, and biotechnological applications.
Martin et al. (2014)
6 more

3 mentions without citation

A Novel Enzyme Portfolio for Red Algal Polysaccharide Degradation in the Marine Bacterium Paraglaciecola hydrolytica S66T Encoded in a Sizeable Polysaccharide Utilization Locus.
Schultz-Johansen et al. (2018)
2 more