› 3zhr

X-ray diffraction
2.1Å resolution

Crystal structure of the H747A mutant of the SucA domain of Mycobacterium smegmatis KGD showing the active site lid closed

Released:
DOI: 10.2210/pdb3zhr/pdb
PDB entry 3zhr coloured by chain, front view.
PDB entry 3zhr coloured by chain, side view.
PDB entry 3zhr coloured by chain, top view.
Source organism: Mycolicibacterium smegmatis
Primary publication:
A dual conformation of the post-decarboxylation intermediate is associated with distinct enzyme states in mycobacterial KGD (α-ketoglutarate decarboxylase).
Wagner T, Barilone N, Alzari PM, Bellinzoni M
Biochem J 457 425-34 (2014)
PMID: 24171907

Function and Biology Details

Reactions catalysed: 
2-oxoglutarate + [dihydrolipoyllysine-residue succinyltransferase] lipoyllysine = [dihydrolipoyllysine-residue succinyltransferase] S-succinyldihydrolipoyllysine + CO(2)
2-oxoglutarate + glyoxylate = 2-hydroxy-3-oxoadipate + CO(2)
Succinyl-CoA + enzyme N(6)-(dihydrolipoyl)lysine = CoA + enzyme N(6)-(S-succinyldihydrolipoyl)lysine
2-oxoglutarate = succinate semialdehyde + CO(2)
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-106428 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Multifunctional 2-oxoglutarate metabolism enzyme Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 868 amino acids
Theoretical weight: 97.1 KDa
Source organism: Mycolicibacterium smegmatis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0R2B1 (Residues: 361-1227; Coverage: 71%)
Gene names: MSMEG_5049, MSMEI_4922, kgd, sucA
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand TPP 4 x TPP
3 bound ligands:
Ligand MG 4 x MG
Ligand CA 4 x CA
Ligand MPD 4 x MPD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: P1
Unit cell:
a: 79.97Å b: 83.45Å c: 159.67Å
α: 99.64° β: 98.82° γ: 100.98°
R-values:
R R work R free
0.181 0.18 0.202
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Emerging Approaches to Tuberculosis Drug Development: At Home in the Metabolome.
Jansen et al. (2017)
1 more