› 3ss9

X-ray diffraction
1.97Å resolution

Crystal structure of holo D-serine dehydratase from Escherichia coli at 1.97 A resolution

Released:
DOI: 10.2210/pdb3ss9/pdb
PDB entry 3ss9 coloured by chain, front view.
PDB entry 3ss9 coloured by chain, side view.
PDB entry 3ss9 coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Crystal structure of D-serine dehydratase from Escherichia coli.
Urusova DV, Isupov MN, Antonyuk S, Kachalova GS, Obmolova G, Vagin AA, Lebedev AA, Burenkov GP, Dauter Z, Bartunik HD, Lamzin VS, Melik-Adamyan WR, Mueller TD, Schnackerz KD
Biochim Biophys Acta 1824 422-32 (2012)
PMID: 22197591

Function and Biology Details

Reaction catalysed: 
(1a) D-serine = 2-aminoprop-2-enoate + H(2)O
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133691 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
D-serine dehydratase Chain: X
Molecule details ›
Chain: X
Length: 442 amino acids
Theoretical weight: 47.95 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P00926 (Residues: 1-442; Coverage: 100%)
Gene names: JW2363, b2366, dsdA
Sequence domains: Pyridoxal-phosphate dependent enzyme
Structure domains: Rossmann fold

Ligands and Environments


Cofactor: Ligand PLP 1 x PLP
1 bound ligand:
Ligand K 1 x K
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: MPG/DESY, HAMBURG BEAMLINE BW6
Spacegroup: P21212
Unit cell:
a: 143.16Å b: 47.738Å c: 72.3Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.173 0.172 0.216
Expression system: Escherichia coli

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Citations

1 review citation

A Survey of Pyridoxal 5'-Phosphate-Dependent Proteins in the Gram-Positive Model Bacterium Bacillus subtilis.
Richts et al. (2019)
9 other articles

1 mention without citation

Crystal structure of D-serine dehydratase from Escherichia coli.
Urusova et al. (2012)