› 2nzm

X-ray diffraction
1.8Å resolution

Hexasaccharide I bound to Bacillus subtilis pectate lyase

Released:
DOI: 10.2210/pdb2nzm/pdb
PDB entry 2nzm coloured by chain, front view.
PDB entry 2nzm coloured by chain, side view.
PDB entry 2nzm coloured by chain, top view.
Source organism: Bacillus subtilis
Primary publication:
Structural insights into substrate specificity and the anti beta-elimination mechanism of pectate lyase.
Seyedarabi A, To TT, Ali S, Hussain S, Fries M, Madsen R, Clausen MH, Teixteira S, Brocklehurst K, Pickersgill RW
Biochemistry 49 539-46 (2010)
PMID: 20000851

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-153836 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Pectate lyase Chain: A
Molecule details ›
Chain: A
Length: 399 amino acids
Theoretical weight: 43.36 KDa
Source organism: Bacillus subtilis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P39116 (Residues: 22-420; Coverage: 100%)
Gene names: BSU07560, pel
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 CA 3 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-3
Spacegroup: P21
Unit cell:
a: 50.736Å b: 68.919Å c: 59.408Å
α: 90° β: 113.09° γ: 90°
R-values:
R R work R free
0.156 0.155 0.185
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 review citations

The biochemistry and structural biology of plant cell wall deconstruction.
Gilbert HJ. (2010)
2 more

2 mentions without citation

Genome Comparison Identifies Different Bacillus Species in a Bast Fibre-Retting Bacterial Consortium and Provides Insights into Pectin Degrading Genes.
Datta et al. (2020)
1 more