› 2yim

X-ray diffraction
1.41Å resolution

The enolisation chemistry of a thioester-dependent racemase: the 1.4 A crystal structure of a complex with a planar reaction intermediate analogue

Released:
DOI: 10.2210/pdb2yim/pdb
PDB entry 2yim coloured by chain, front view.
PDB entry 2yim coloured by chain, side view.
PDB entry 2yim coloured by chain, top view.
Source organism: Mycobacterium tuberculosis H37Rv
Primary publication:
The enolization chemistry of a thioester-dependent racemase: the 1.4 Å crystal structure of a reaction intermediate complex characterized by detailed QM/MM calculations.
Sharma S, Bhaumik P, Schmitz W, Venkatesan R, Hiltunen JK, Conzelmann E, Juffer AH, Wierenga RK
J Phys Chem B 116 3619-29 (2012)
PMID: 22360758

Function and Biology Details

Reaction catalysed: 
(2S)-2-methylacyl-CoA = (2R)-2-methylacyl-CoA
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-126518 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Alpha-methylacyl-CoA racemase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 360 amino acids
Theoretical weight: 38.72 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O06543 (Residues: 1-360; Coverage: 100%)
Gene names: Rv1143, mcr
Sequence domains: CoA-transferase family III
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand GOL 5 x GOL
Ligand MC4 4 x MC4
Ligand PO4 2 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-2
Spacegroup: C2
Unit cell:
a: 181.59Å b: 80.17Å c: 118.88Å
α: 90° β: 91.41° γ: 90°
R-values:
R R work R free
0.187 0.186 0.205
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 review citations

Specificity in transition state binding: the Pauling model revisited.
Amyes et al. (2013)
2 more