PDBsum entry 1xg4

Lyase

PDB id: 1xg4

Contents

Protein chains

287 a.a. *

Ligands

ICT ×3

Metals

_MG ×3

Waters ×982

* Residue conservation analysis

PDB id:

1xg4

Name:

Lyase

Title:

Crystal structure of the c123s 2-methylisocitrate lyase mutant from escherichia coli in complex with the inhibitor isocitrate

Structure:

Probable methylisocitrate lyase. Chain: a, b, c, d. Synonym: 2-methylisocitrate lyase. Engineered: yes. Mutation: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: prpb. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Tetramer (from PQS)

Resolution:

1.60Å R-factor: 0.181 R-free: 0.201

Authors:

S.Liu,Z.Lu,Y.Han,E.Melamud,D.Dunaway-Mariano,O.Herzberg

Key ref:

S.Liu et al. (2005). 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. PubMed id: 15723538 DOI: 10.1021/bi0479712

Date:

16-Sep-04 Release date: 01-Mar-05

Protein chains

P77541  (PRPB_ECOLI) -  2-methylisocitrate lyase from Escherichia coli (strain K12)

Seq: 296 a.a.

Struc: 287 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.4.1.3.30 - methylisocitrate lyase.
• Reaction: (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = pyruvate + succinate

(2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate (Bound ligand (Het Group name = ICT) matches with 92.86% similarity) = pyruvate + succinate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1021/bi0479712

Biochemistry 44:2949-2962 (2005)

PubMed id: 15723538

Crystal structures of 2-methylisocitrate lyase in complex with product and with isocitrate inhibitor provide insight into lyase substrate specificity, catalysis and evolution.

S.Liu, Z.Lu, Y.Han, E.Melamud, D.Dunaway-Mariano, O.Herzberg.

ABSTRACT

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.