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› 6vb9

X-ray diffraction
1.88Å resolution

Covalent adduct of cis-2,3-epoxysuccinic acid with Isocitrate Lyase-1 from Mycobacterium tuberculosis

Released:
DOI: 10.2210/pdb6vb9/pdb
Model geometry
Fit model/data
PDB entry 6vb9 coloured by chain, front view.
PDB entry 6vb9 coloured by chain, side view.
PDB entry 6vb9 coloured by chain, top view.
Source organism: Mycobacterium tuberculosis
Primary publication:
Covalent Inactivation of Mycobacterium tuberculosis Isocitrate Lyase by cis-2,3-Epoxy-Succinic Acid.
Pham TV, Mellott DM, Moghadamchargari Z, Chen K, Krieger I, Laganowsky A, Sacchettini JC, Meek TD
ACS Chem Biol 16 463-470 (2021)
PMID: 33688722

Function and Biology Details

Reaction catalysed: 
D-threo-isocitrate = glyoxylate + succinate.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-161751 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Isocitrate lyase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 431 amino acids
Theoretical weight: 47.55 KDa
Source organism: Mycobacterium tuberculosis
Expression system: Escherichia coli
UniProt:
  • Canonical: P9WKK7 (Residues: 1-428; Coverage: 100%)
Gene names: MTV038.11, Rv0467, icl
Sequence domains: Isocitrate lyase family

Ligands and Environments

4 bound ligands:
Ligand MG 7 x MG
Ligand OXD 4 x OXD
Ligand ACY 9 x ACY
Ligand PEG 2 x PEG
1 modified residue:
Ligand QVA 4 x QVA

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P212121
Unit cell:
a: 75.065Å b: 129.065Å c: 167.825Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.181 0.179 0.228
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Targeting Non-Replicating Mycobacterium tuberculosis and Latent Infection: Alternatives and Perspectives (Mini-Review).
Egorova et al. (2021)
1 more