› 4yzx

X-ray diffraction
1.25Å resolution

C. bescii Family 3 pectate lyase double mutant K108A/D107N in complex with trigalacturonic acid

Released:
DOI: 10.2210/pdb4yzx/pdb
PDB entry 4yzx coloured by chain, front view.
PDB entry 4yzx coloured by chain, side view.
PDB entry 4yzx coloured by chain, top view.
Source organism: Caldicellulosiruptor bescii DSM 6725
Primary publication:
The catalytic mechanism and unique low pH optimum of Caldicellulosiruptor bescii family 3 pectate lyase.
Alahuhta M, Taylor LE, Brunecky R, Sammond DW, Michener W, Adams MW, Himmel ME, Bomble YJ, Lunin V
Acta Crystallogr D Biol Crystallogr 71 1946-54 (2015)
PMID: 26327384

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:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-110862 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
pectate lyase Chains: A, B
Molecule details ›
Chains: A, B
Length: 204 amino acids
Theoretical weight: 22.1 KDa
Source organism: Caldicellulosiruptor bescii DSM 6725
Expression system: Escherichia coli
UniProt:
  • Canonical: B9MKT4 (Residues: 268-460; Coverage: 42%)
Gene name: Athe_1854
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
7 bound ligands:
Ligand CA 8 x CA
Ligand IMD 2 x IMD
Ligand MPD 4 x MPD
Ligand MRD 2 x MRD
Ligand CL 2 x CL
Ligand GTR 1 x GTR
Ligand ADA 2 x ADA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL11-1
Spacegroup: C2
Unit cell:
a: 138.334Å b: 36.352Å c: 100.106Å
α: 90° β: 132.67° γ: 90°
R-values:
R R work R free
0.112 0.11 0.156
Expression system: Escherichia coli

Quick links

Citations

1 review citation

The biology and biotechnology of the genus Caldicellulosiruptor: recent developments in 'Caldi World'.
Lee et al. (2020)
5 other articles

1 mention without citation

The catalytic mechanism and unique low pH optimum of Caldicellulosiruptor bescii family 3 pectate lyase.
Alahuhta et al. (2015)