› 3zht

X-ray diffraction
2.15Å resolution

Crystal structure of the SucA domain of Mycobacterium smegmatis KGD, first post-decarboxylation intermediate from 2-oxoadipate

Released:
DOI: 10.2210/pdb3zht/pdb
PDB entry 3zht coloured by chain, front view.
PDB entry 3zht coloured by chain, side view.
PDB entry 3zht 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:
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: 97.17 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 TD9 4 x TD9
2 bound ligands:
Ligand MG 4 x MG
Ligand CA 4 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: P1
Unit cell:
a: 80.366Å b: 83.8Å c: 159.513Å
α: 99.76° β: 99.06° γ: 100.61°
R-values:
R R work R free
0.224 0.223 0.246
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Emerging Approaches to Tuberculosis Drug Development: At Home in the Metabolome.
Jansen et al. (2017)
8 other articles

2 mentions without citation

Toward an Understanding of the Structural and Mechanistic Aspects of Protein-Protein Interactions in 2-Oxoacid Dehydrogenase Complexes.
Nemeria et al. (2021)
1 more