6WFH

Streptomyces coelicolor methylmalonyl-CoA epimerase substrate complex

Summary for 6WFH

• Entry DOI: 10.2210/pdb6wfh/pdb
• Descriptor: Methylmalonyl-CoA epimerase, COBALT (II) ION, (3S,5R,9R,19E)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9,19-tetrahydroxy-8,8,20-trimethyl-10,14-dioxo-2,4,6-trioxa-18-thia-11,15-diaza-3,5-diphosphahenicos-19-en-21-oic acid 3,5-dioxide (non-preferred name), ... (7 entities in total)
• Functional Keywords: epimerase, acid-base, enol, enolate, isomerase
• Biological source: Streptomyces coelicolor
• Total number of polymer chains: 1
• Total formula weight: 17330.06

Authors

Stunkard, L.M.,Benjamin, A.B.,Bower, J.B.,Huth, T.J.,Lohman, J.R. (deposition date: 2020-04-03, release date: 2020-07-08, Last modification date: 2023-10-18)

Primary citation

Stunkard, L.M.,Benjamin, A.B.,Bower, J.B.,Huth, T.J.,Lohman, J.R.
Substrate Enolate Intermediate and Mimic Captured in the Active Site of Streptomyces coelicolor Methylmalonyl-CoA Epimerase.
Chembiochem, 23:e202100487-e202100487, 2022

PubMed Abstract: Methylmalonyl-CoA epimerase (MMCE) is proposed to use general acid-base catalysis, but the proposed catalytic glutamic acids are highly asymmetrical in the active site unlike many other racemases. To gain insight into the puzzling relationships between catalytic mechanism, structure, and substrate preference, we solved Streptomyces coelicolor MMCE structures with substrate or 2-nitropropionyl-CoA, an intermediate/transition state analogue. Both ligand bound structures have a planar methylmalonate/2-nitropropionyl moiety indicating a deprotonated C2 with ≥4 Å distances to either catalytic acid. Both glutamates interact with the carboxylate/nitro group, either directly or through other residues. This suggests the proposed catalytic acids sequentially catalyze proton shifts between C2 and carboxylate of the substrate with an enolate intermediate. In addition, our structures provide a platform to design mutations for expanding substrate scope to support combinatorial biosynthesis.

PubMed: 34856049
DOI: 10.1002/cbic.202100487

Experimental method

X-RAY DIFFRACTION (1.84 Å)