› 3ss7

X-ray diffraction
1.55Å resolution

Crystal structure of holo D-serine dehydratase from Escherichia coli at 1.55 A resolution

Released:
DOI: 10.2210/pdb3ss7/pdb
PDB entry 3ss7 coloured by chain, front view.
PDB entry 3ss7 coloured by chain, side view.
PDB entry 3ss7 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
2 bound ligands:
Ligand GOL 1 x GOL
Ligand K 1 x K
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SRS BEAMLINE PX10.1
Spacegroup: P21
Unit cell:
a: 73.774Å b: 47.806Å c: 75.193Å
α: 90° β: 104.96° γ: 90°
R-values:
R R work R free
0.161 0.159 0.194
Expression system: Escherichia coli

Quick links

Citations

9 citation in other articles

Catalytic mechanism of serine racemase from Dictyostelium discoideum.
Ito et al. (2013)
8 more

4 mentions without citation

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