› 5vxs

X-ray diffraction
2.95Å resolution

Crystal Structure Analysis of human CLYBL in apo form

Released:
DOI: 10.2210/pdb5vxs/pdb
PDB entry 5vxs coloured by chain, front view.
PDB entry 5vxs coloured by chain, side view.
PDB entry 5vxs coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The Human Knockout Gene CLYBL Connects Itaconate to Vitamin B12.
Shen H, Campanello GC, Flicker D, Grabarek Z, Hu J, Luo C, Banerjee R, Mootha VK
Cell 171 771-782.e11 (2017)
PMID: 29056341

Function and Biology Details

Reactions catalysed: 
Acetyl-CoA + H(2)O + glyoxylate = (S)-malate + CoA
(S)-malyl-CoA + H(2)O = (S)-malate + CoA
(3S)-citramalyl-CoA = acetyl-CoA + pyruvate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-185345 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Citramalyl-CoA lyase, mitochondrial Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 325 amino acids
Theoretical weight: 36.08 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8N0X4 (Residues: 30-340; Coverage: 92%)
Gene names: CLB, CLYBL
Sequence domains: HpcH/HpaI aldolase/citrate lyase family

Ligands and Environments

1 bound ligand:
Ligand CIT 2 x CIT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.2
Spacegroup: P3121
Unit cell:
a: 154.629Å b: 154.629Å c: 156.506Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.208 0.205 0.272
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

18 review citations

Mitochondrial TCA cycle metabolites control physiology and disease.
Martínez-Reyes et al. (2020)
17 more

2 mentions without citation

The Human Knockout Gene CLYBL Connects Itaconate to Vitamin B12.
Shen et al. (2017)
1 more