› 3krg

X-ray diffraction
1.9Å resolution

Structural insights into substrate specificity and the anti beta-elimination mechanism of pectate lyase

Released:
DOI: 10.2210/pdb3krg/pdb
PDB entry 3krg coloured by chain, front view.
PDB entry 3krg coloured by chain, side view.
PDB entry 3krg 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: 43.3 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
2 bound ligands:
Ligand CO 1 x CO
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SRS BEAMLINE PX10.1
Spacegroup: P21
Unit cell:
a: 50.626Å b: 69.066Å c: 59.656Å
α: 90° β: 113.85° γ: 90°
R-values:
R R work R free
0.135 0.132 0.196
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

13 mentions without citation

An imputation platform to enhance integration of rice genetic resources.
Wang et al. (2018)
12 more