1XG3 image
Deposition Date 2004-09-16
Release Date 2005-03-01
Last Version Date 2024-04-03
Entry Detail
PDB ID:
1XG3
Keywords:
Title:
Crystal structure of the C123S 2-methylisocitrate lyase mutant from Escherichia coli in complex with the reaction product, Mg(II)-pyruvate and succinate
Biological Source:
Source Organism:
Escherichia coli (Taxon ID: 562)
Method Details:
Experimental Method:
Resolution:
1.90 Å
R-Value Free:
0.19
R-Value Work:
0.16
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Probable methylisocitrate lyase
Gene (Uniprot):prpB
Mutations:C123S
Chain IDs:A, B, C, D
Chain Length:295
Number of Molecules:4
Biological Source:Escherichia coli
Primary Citation
Crystal Structures of 2-Methylisocitrate Lyase in Complex with Product and with Isocitrate Inhibitor Provide Insight into Lyase Substrate Specificity, Catalysis and Evolution
Biochemistry 44 2949 2962 (2005)
PMID: 15723538 DOI: 10.1021/bi0479712

Abstact

Two crystal structures of the C123S mutant of 2-methylisocitrate lyase have been determined, one with the bound reaction products, Mg(2+)-pyruvate and succinate, and the second with a bound Mg(2+)-(2R,3S)-isocitrate inhibitor. Comparison with the structure of the wild-type enzyme in the unbound state reveals that the enzyme undergoes a conformational transition that sequesters the ligand from solvent, as previously observed for two other enzyme superfamily members, isocitrate lyase and phosphoenolpyruvate mutase. The binding modes reveal the determinants of substrate specificity and stereoselectivity, and the stringent specificity is verified in solution using various potential substrates. A model of bound 2-methylisocitrate has been developed based on the experimentally determined structures. We propose a catalytic mechanism involving an alpha-carboxy-carbanion intermediate/transition state, which is consistent with previous stereochemical experiments showing inversion of configuration at the C(3) of 2-methylisocitrate. Structure-based sequence analysis and phylogenic tree construction reveal determinants of substrate specificity, highlight nodes of divergence of families, and predict enzyme families with new functions.

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