› 4be3

X-ray diffraction
1.75Å resolution

crystal structure of the exolytic PL7 alginate lyase AlyA5 from Zobellia galactanivorans

Released:
DOI: 10.2210/pdb4be3/pdb
PDB entry 4be3 coloured by chain, front view.
PDB entry 4be3 coloured by chain, side view.
PDB entry 4be3 coloured by chain, top view.
Source organism: Zobellia galactanivorans
Primary publication:
Comparative characterization of two marine alginate lyases from Zobellia galactanivorans reveals distinct modes of action and exquisite adaptation to their natural substrate.
Thomas F, Lundqvist LC, Jam M, Jeudy A, Barbeyron T, Sandström C, Michel G, Czjzek M
J Biol Chem 288 23021-37 (2013)
PMID: 23782694

Function and Biology Details

Reaction catalysed: 
Eliminative cleavage of alginate to give oligosaccharides with 4-deoxy-alpha-L-erythro-hex-4-enuronosyl groups at their non-reducing ends and beta-D-mannuronate at their reducing end.
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-123844 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Alginate lyase 2 domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 314 amino acids
Theoretical weight: 35.28 KDa
Source organism: Zobellia galactanivorans
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: G0L2Y1 (Residues: 39-352; Coverage: 89%)
Gene names: alyA5, zobellia_4131
Sequence domains: Alginate lyase
Structure domains: Jelly Rolls

Ligands and Environments

4 bound ligands:
Ligand SRT 1 x SRT
Ligand NA 1 x NA
Ligand TAR 1 x TAR
Ligand TLA 1 x TLA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: P212121
Unit cell:
a: 93.42Å b: 93.91Å c: 130.15Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.157 0.156 0.178
Expression system: Escherichia coli BL21

Quick links

Citations

8 review citations

Alginate lyase: Review of major sources and classification, properties, structure-function analysis and applications.
Zhu et al. (2015)
7 more

13 mentions without citation

Diversity of Three-Dimensional Structures and Catalytic Mechanisms of Alginate Lyases.
Xu et al. (2018)
12 more