› 3wz1

X-ray diffraction
1.6Å resolution

Catalytic domain of beta-agarase from Microbulbifer thermotolerans JAMB-A94

Released:
DOI: 10.2210/pdb3wz1/pdb
PDB entry 3wz1 coloured by chain, front view.
PDB entry 3wz1 coloured by chain, side view.
PDB entry 3wz1 coloured by chain, top view.
Source organism: Microbulbifer thermotolerans
Primary publication:
Crystal structure of the catalytic domain of a GH16 β-agarase from a deep-sea bacterium, Microbulbifer thermotolerans JAMB-A94.
Takagi E, Hatada Y, Akita M, Ohta Y, Yokoi G, Miyazaki T, Nishikawa A, Tonozuka T
Biosci Biotechnol Biochem 79 625-32 (2015)
PMID: 25483365

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:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-179588 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Beta-agarase Chain: A
Molecule details ›
Chain: A
Length: 282 amino acids
Theoretical weight: 32.03 KDa
Source organism: Microbulbifer thermotolerans
Expression system: Bacillus subtilis
UniProt:
  • Canonical: Q6F4N4 (Residues: 19-300; Coverage: 68%)
Gene name: agaA
Structure domains: Jelly Rolls

Ligands and Environments

2 bound ligands:
Ligand NA 2 x NA
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P212121
Unit cell:
a: 49.624Å b: 69.394Å c: 90.367Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.153 0.152 0.165
Expression system: Bacillus subtilis

Quick links

Citations

1 review citation

Recombinant β-agarases: insights into molecular, biochemical, and physiochemical characteristics.
Veerakumar et al. (2018)
7 other articles

4 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)
3 more