› 2v8i

X-ray diffraction
1.5Å resolution

Structure of a Family 2 Pectate Lyase in a Native Form

Released:
DOI: 10.2210/pdb2v8i/pdb
PDB entry 2v8i coloured by chain, front view.
PDB entry 2v8i coloured by chain, side view.
PDB entry 2v8i coloured by chain, top view.
Source organism: Yersinia enterocolitica
Primary publication:
A family 2 pectate lyase displays a rare fold and transition metal-assisted beta-elimination.
Abbott DW, Boraston AB
J Biol Chem 282 35328-36 (2007)
PMID: 17881361

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 domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-106634 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Periplasmic pectate lyase Chain: A
Molecule details ›
Chain: A
Length: 543 amino acids
Theoretical weight: 61.26 KDa
Source organism: Yersinia enterocolitica
Expression system: Escherichia coli
UniProt:
  • Canonical: A1JSS8 (Residues: 27-569; Coverage: 99%)
Gene names: YE4069, pelY
Sequence domains: Periplasmic pectate lyase
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand IOD 51 x IOD
No modified residues

Experiments and Validation Details

Entry percentile scores
Spacegroup: P212121
Unit cell:
a: 58.486Å b: 95.642Å c: 126.608Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.223 0.222 0.243
Expression system: Escherichia coli

Quick links

Citations

6 review citations

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

1 mention without citation

Structural biology of pectin degradation by Enterobacteriaceae.
Abbott et al. (2008)