› 3vmw

X-ray diffraction
1.9Å resolution

Crystal structure of pectate lyase Bsp165PelA from Bacillus sp. N165 in complex with trigalacturonate

Released:
DOI: 10.2210/pdb3vmw/pdb
PDB entry 3vmw coloured by chain, front view.
PDB entry 3vmw coloured by chain, side view.
PDB entry 3vmw coloured by chain, top view.
Source organism: Bacillus sp. N16-5
Primary publication:
Crystal structure and substrate-binding mode of a novel pectate lyase from alkaliphilic Bacillus sp. N16-5.
Zheng Y, Huang CH, Liu W, Ko TP, Xue Y, Zhou C, Guo RT, Ma Y
Biochem Biophys Res Commun 420 269-74 (2012)
PMID: 22414692

Function and Biology Details

Reaction catalysed: 
Eliminative cleavage of (1->4)-alpha-D-galacturonan to give oligosaccharides with 4-deoxy-alpha-D-galact-4-enuronosyl groups at their non-reducing ends
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-504788 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Pectate lyase domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 326 amino acids
Theoretical weight: 35.98 KDa
Source organism: Bacillus sp. N16-5
Expression system: Escherichia coli
UniProt:
  • Canonical: D0VP31 (Residues: 37-362; Coverage: 98%)
Gene name: pelA
Sequence domains: Pectate lyase
Structure domains: Single-stranded right-handed beta-helix, Pectin lyase-like

Ligands and Environments

Carbohydrate polymer : NEW Components: ADA
Carbohydrate polymer
1 bound ligand:
Ligand SO4 5 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE BL13C1
Spacegroup: P21212
Unit cell:
a: 137.902Å b: 48.174Å c: 52.47Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.157 0.154 0.204
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Homogalacturonan-modifying enzymes: structure, expression, and roles in plants.
Sénéchal et al. (2014)
16 other articles

2 mentions without citation

Directed Evolution and Structural Analysis of Alkaline Pectate Lyase from the Alkaliphilic Bacterium Bacillus sp. Strain N16-5 To Improve Its Thermostability for Efficient Ramie Degumming.
Zhou et al. (2015)
1 more