› 2y41

X-ray diffraction
2.2Å resolution

Structure of Isopropylmalate dehydrogenase from Thermus thermophilus - complex with IPM and MN

Released:
DOI: 10.2210/pdb2y41/pdb
PDB entry 2y41 coloured by chain, front view.
PDB entry 2y41 coloured by chain, side view.
PDB entry 2y41 coloured by chain, top view.
Source organism: Thermus thermophilus
Primary publication:
Atomic level description of the domain closure in a dimeric enzyme: thermus thermophilus 3-isopropylmalate dehydrogenase.
Gráczer É, Merli A, Singh RK, Karuppasamy M, Závodszky P, Weiss MS, Vas M
Mol Biosyst 7 1646-59 (2011)
PMID: 21387033

Function and Biology Details

Reaction catalysed: 
(1a) (2R,3S)-3-isopropylmalate + NAD(+) = (2S)-2-isopropyl-3-oxosuccinate + NADH
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-177982 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
3-isopropylmalate dehydrogenase Chains: A, B
Molecule details ›
Chains: A, B
Length: 359 amino acids
Theoretical weight: 38.4 KDa
Source organism: Thermus thermophilus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q5SIY4 (Residues: 1-345; Coverage: 100%)
Gene names: TTHA1230, leuB
Sequence domains: Isocitrate/isopropylmalate dehydrogenase
Structure domains: Isopropylmalate Dehydrogenase

Ligands and Environments

2 bound ligands:
Ligand IPM 2 x IPM
Ligand MN 4 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X12
Spacegroup: C2221
Unit cell:
a: 50.24Å b: 146.33Å c: 175.21Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.187 0.186 0.224
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

From protein structure to function via single crystal optical spectroscopy.
Ronda et al. (2015)
1 more

1 mention without citation

Structure-energy-based predictions and network modelling of RASopathy and cancer missense mutations.
Kiel et al. (2014)