› 3uha

X-ray diffraction
2.3Å resolution

Crystal Structure of Saccharopine Dehydrogenase from Saccharomyces cervisiae complexed with NAD.

Released:
DOI: 10.2210/pdb3uha/pdb
Model geometry
Fit model/data
PDB entry 3uha coloured by chain, front view.
PDB entry 3uha coloured by chain, side view.
PDB entry 3uha coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Evidence in support of lysine 77 and histidine 96 as acid-base catalytic residues in saccharopine dehydrogenase from Saccharomyces cerevisiae.
Kumar VP, Thomas LM, Bobyk KD, Andi B, Cook PF, West AH
Biochemistry 51 857-66 (2012)
PMID: 22243403

Function and Biology Details

Reaction catalysed: 
L-saccharopine + NAD(+) + H2O = L-lysine + 2-oxoglutarate + NADH + H(+).
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
homo dimer (preferred)
homo tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-153796 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Saccharopine dehydrogenase [NAD(+), L-lysine-forming] Chains: A, B
Molecule details ›
Chains: A, B
Length: 373 amino acids
Theoretical weight: 41.51 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P38998 (Residues: 1-373; Coverage: 100%)
Gene names: LYS1, YIR034C
Sequence domains: Alanine dehydrogenase/PNT, N-terminal domain
Structure domains: NAD(P)-binding Rossmann-like Domain

Ligands and Environments


Cofactor: Ligand NAD 2 x NAD
1 bound ligand:
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: RIGAKU FR-E+ SUPERBRIGHT
Spacegroup: P21
Unit cell:
a: 64.01Å b: 104.45Å c: 69.08Å
α: 90° β: 116.6° γ: 90°
R-values:
R R work R free
0.21 0.207 0.27
Expression system: Escherichia coli

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Citations

1 review citation

Combining solvent isotope effects with substrate isotope effects in mechanistic studies of alcohol and amine oxidation by enzymes.
Fitzpatrick PF. (2015)
7 other articles

1 mention without citation

Evidence in support of lysine 77 and histidine 96 as acid-base catalytic residues in saccharopine dehydrogenase from Saccharomyces cerevisiae.
Kumar et al. (2012)