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› 6kfn

X-ray diffraction
0.89Å resolution

Crystal structure of alginate lyase from Paenibacillus sp. str. FPU-7

Released:
DOI: 10.2210/pdb6kfn/pdb
Model geometry
Fit model/data
PDB entry 6kfn coloured by chain, front view.
PDB entry 6kfn coloured by chain, side view.
PDB entry 6kfn coloured by chain, top view.
Source organism: Paenibacillus sp. FPU-7
Primary publication:
Structural and biochemical characterisation of a novel alginate lyase from Paenibacillus sp. str. FPU-7.
Itoh T, Nakagawa E, Yoda M, Nakaichi A, Hibi T, Kimoto H
OpenAccess logo Sci Rep 9 14870 (2019)
PMID: 31619701

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 andbeta-D-mannuronate at their reducing end.]
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-288675 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Right handed beta helix domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 307 amino acids
Theoretical weight: 32.33 KDa
Source organism: Paenibacillus sp. FPU-7
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A5S8WF57 (Residues: 1-307; Coverage: 100%)
Sequence domains: Right handed beta helix region

Ligands and Environments

2 bound ligands:
Ligand NA 2 x NA
Ligand IMD 1 x IMD
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SPRING-8 BEAMLINE BL38B1
Spacegroup: C2
Unit cell:
a: 125.635Å b: 57.764Å c: 39.714Å
α: 90° β: 91.1° γ: 90°
R-values:
R R work R free
0.106 0.105 0.122
Expression system: Escherichia coli

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Citations

2 review citations

Bacterial alginate metabolism: an important pathway for bioconversion of brown algae.
Zhang et al. (2021)
1 more

6 mentions without citation

Evolving strategies for marine enzyme engineering: recent advances on the molecular modification of alginate lyase.
Cao et al. (2022)
5 more