› 6hy3

X-ray diffraction
1.3Å resolution

Three-dimensional structure of AgaC from Zobellia galactanivorans

Released:
DOI: 10.2210/pdb6hy3/pdb
PDB entry 6hy3 coloured by chain, front view.
PDB entry 6hy3 coloured by chain, side view.
PDB entry 6hy3 coloured by chain, top view.
Source organism: Zobellia galactanivorans
Primary publication:
The agar-specific hydrolase ZgAgaC from the marine bacterium Zobellia galactanivorans defines a new GH16 protein subfamily.
Naretto A, Fanuel M, Ropartz D, Rogniaux H, Larocque R, Czjzek M, Tellier C, Michel G
J Biol Chem 294 6923-6939 (2019)
PMID: 30846563

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-112855 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Beta-agarase C Chain: A
Molecule details ›
Chain: A
Length: 272 amino acids
Theoretical weight: 31.39 KDa
Source organism: Zobellia galactanivorans
Expression system: Escherichia coli
UniProt:
  • Canonical: D7GXG5 (Residues: 69-328; Coverage: 84%)
Gene names: agaC, zobellia_4267

Ligands and Environments

3 bound ligands:
Ligand MG 1 x MG
Ligand GOL 2 x GOL
Ligand EDO 2 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P21212
Unit cell:
a: 60.604Å b: 101.498Å c: 46.693Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.15 0.149 0.169
Expression system: Escherichia coli

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Citations

2 review citations

Role and Evolution of the Extracellular Matrix in the Acquisition of Complex Multicellularity in Eukaryotes: A Macroalgal Perspective.
Kloareg et al. (2021)
1 more

3 mentions without citation

The agar-specific hydrolase ZgAgaC from the marine bacterium Zobellia galactanivorans defines a new GH16 protein subfamily.
Naretto et al. (2019)
2 more