Structure of Methylobacterium extorquens malyl-CoA lyase: CoA-substrate binding correlates with domain shift

Gonzalez, Javier M.; Marti-Arbona, Ricardo; Chen, Julian C. -H.; Unkefer, Clifford Jay

doi:10.1107/S2053230X17001029

Title: Structure of Methylobacterium extorquens malyl-CoA lyase: CoA-substrate binding correlates with domain shift

Journal Article · 26 January 2017 · Acta Crystallographica. Section F, Structural Biology Communications

DOI: https://doi.org/10.1107/S2053230X17001029 · OSTI ID:1342868

Gonzalez, Javier M. ^[1];

^[2];

^[2]; Unkefer, Clifford Jay ^[2]

Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Univ. Nacional de Santiago del Estero, Santiago del Estero (Argentina)
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

Malyl-CoA lyase (MCL) is an Mg²⁺-dependent enzyme that catalyzes the reversible cleavage of (2S)-4-malyl-CoA to yield acetyl-CoA and glyoxylate. MCL enzymes, which are found in a variety of bacteria, are members of the citrate lyase-like family and are involved in the assimilation of one- and two-carbon compounds. Here, the 1.56 Å resolution X-ray crystal structure of MCL from Methylobacterium extorquens AM1 with bound Mg²⁺is presented. Structural alignment with the closely related Rhodobacter sphaeroides malyl-CoA lyase complexed with Mg²⁺, oxalate and CoA allows a detailed analysis of the domain motion of the enzyme caused by substrate binding. Alignment of the structures shows that a simple hinge motion centered on the conserved residues Phe268 and Thr269 moves the C-terminal domain by about 30° relative to the rest of the molecule. Furthermore, this domain motion positions a conserved aspartate residue located in the C-terminal domain in the active site of the adjacent monomer, which may serve as a general acid/base in the catalytic mechanism.

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Research Organization:: Los Alamos National Laboratory (LANL)

Sponsoring Organization:: LDRD; USDOE

Grant/Contract Number:: AC52-06NA25396

OSTI ID:: 1342868

Report Number(s):: LA-UR-16-29566

Journal Information:: Acta Crystallographica. Section F, Structural Biology Communications, Journal Name: Acta Crystallographica. Section F, Structural Biology Communications Journal Issue: 2 Vol. 73; ISSN ACSFEN; ISSN 2053-230X

Publisher:: International Union of CrystallographyCopyright Statement

Country of Publication:: United States

Language:: English

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