4GEC

Crystal Structure of E.coli MenH R124A Mutant

Summary for 4GEC

• Entry DOI: 10.2210/pdb4gec/pdb
• Related: 4GDM 4GEG
• Descriptor: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase, SULFATE ION, GLYCEROL, ... (6 entities in total)
• Functional Keywords: menaquinone biosynthesis, alpha beta hydrolase, 2-succinyl-6-hydroxy-2, 4-cyclohexadiene-1-carboxylate synthase, mutant r124a, menh mutant r124a, lyase
• Biological source: Escherichia coli
• Total number of polymer chains: 3
• Total formula weight: 88932.47

Authors

Johnston, J.M.,Baker, E.N.,Guo, Z.,Jiang, M. (deposition date: 2012-08-01, release date: 2013-05-08, Last modification date: 2024-02-28)

Primary citation

Johnston, J.M.,Jiang, M.,Guo, Z.,Baker, E.N.
Crystal Structures of E. coli Native MenH and Two Active Site Mutants.
Plos One, 8:e61325-e61325, 2013

PubMed Abstract: Recent revision of the biosynthetic pathway for menaquinone has led to the discovery of a previously unrecognized enzyme 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase, also known as MenH. This enzyme has an α/β hydrolase fold with a catalytic triad comprising Ser86, His232, and Asp210. Mutational studies identified a number of conserved residues of importance to activity, and modeling further implicated the side chains of Tyr85 and Trp147 in formation of a non-standard oxyanion hole. We have solved the structure of E. coli MenH (EcMenH) at 2.75 Å resolution, together with the structures of the active site mutant proteins Tyr85Phe and Arg124Ala, both at 2.5 Å resolution. EcMenH has the predicted α/β hydrolase fold with its core α/β domain capped by a helical lid. The active site, a long groove beneath the cap, contains a number of conserved basic residues and is found to bind exogeneous anions, modeled as sulfate and chloride, in all three crystal structures. Docking studies with the MenH substrate and a transition state model indicate that the bound anions mark the binding sites for anionic groups on the substrate. The docking studies, and careful consideration of the active site geometry, further suggest that the oxyanion hole is of a conventional nature, involving peptide NH groups, rather than the proposed site involving Tyr85 and Trp147. This is in accord with conclusions from the structure of S. aureus MenH. Comparisons with the latter do, however, indicate differences in the periphery of the active site that could be of relevance to selective inhibition of MenH enzymes.

PubMed: 23637813
DOI: 10.1371/journal.pone.0061325

Experimental method

X-RAY DIFFRACTION (2.5 Å)