› 4d9b

X-ray diffraction
1.67Å resolution

Pyridoxamine 5' phosphate (PMP) bound form of Salmonella typhimurium D-Cysteine desulfhydrase obtained after co-crystallization with D-cycloserine

Released:
DOI: 10.2210/pdb4d9b/pdb
PDB entry 4d9b coloured by chain, front view.
PDB entry 4d9b coloured by chain, side view.
PDB entry 4d9b coloured by chain, top view.
Source organism: Salmonella enterica subsp. enterica serovar Typhimurium
Primary publication:
Structural and mutational studies on substrate specificity and catalysis of Salmonella typhimurium D-cysteine desulfhydrase.
Bharath SR, Bisht S, Harijan RK, Savithri HS, Murthy MR
PLoS One 7 e36267 (2012)
PMID: 22574144

Function and Biology Details

Reaction catalysed: 
D-cysteine + H(2)O = H(2)S + NH(3) + pyruvate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-187318 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
D-cysteine desulfhydrase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 342 amino acids
Theoretical weight: 36.55 KDa
Source organism: Salmonella enterica subsp. enterica serovar Typhimurium
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8ZNT7 (Residues: 1-328; Coverage: 100%)
Gene names: STM1953, dcyD
Sequence domains: Pyridoxal-phosphate dependent enzyme
Structure domains: Rossmann fold

Ligands and Environments


Cofactor: Ligand PMP 4 x PMP
2 bound ligands:
Ligand BEN 3 x BEN
Ligand EDO 6 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM14
Spacegroup: P21
Unit cell:
a: 66.318Å b: 164.926Å c: 68.314Å
α: 90° β: 118.97° γ: 90°
R-values:
R R work R free
0.172 0.171 0.206
Expression system: Escherichia coli

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Citations

1 review citation

Ethylene, ACC, and the Plant Growth-Promoting Enzyme ACC Deaminase.
Gamalero et al. (2023)
9 other articles

1 mention without citation

Structural and mutational studies on substrate specificity and catalysis of Salmonella typhimurium D-cysteine desulfhydrase.
Bharath et al. (2012)