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

Acta Crystallogr F Struct Biol Commun. 2017 Feb 1;73(Pt 2):79-85. doi: 10.1107/S2053230X17001029. Epub 2017 Jan 27.

Abstract

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. 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.

Keywords: Methylobacterium extorquens; biofuels; malyl-CoA lyase; metabolic engineering; methanol.

MeSH terms

  • Acyl Coenzyme A / chemistry*
  • Acyl Coenzyme A / metabolism
  • Amino Acid Sequence
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Catalytic Domain
  • Cations, Divalent
  • Cloning, Molecular
  • Coenzyme A / chemistry
  • Coenzyme A / metabolism
  • Crystallography, X-Ray
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Gene Expression
  • Magnesium / chemistry*
  • Magnesium / metabolism
  • Methylobacterium extorquens / chemistry*
  • Methylobacterium extorquens / enzymology
  • Models, Molecular
  • Oxalic Acid / chemistry
  • Oxalic Acid / metabolism
  • Oxo-Acid-Lyases / chemistry*
  • Oxo-Acid-Lyases / genetics
  • Oxo-Acid-Lyases / metabolism
  • Plasmids / chemistry
  • Plasmids / metabolism
  • Protein Binding
  • Protein Conformation, alpha-Helical
  • Protein Conformation, beta-Strand
  • Protein Interaction Domains and Motifs
  • Protein Structure, Quaternary
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism
  • Rhodobacter sphaeroides / chemistry
  • Rhodobacter sphaeroides / enzymology
  • Substrate Specificity

Substances

  • Acyl Coenzyme A
  • Bacterial Proteins
  • Cations, Divalent
  • Recombinant Proteins
  • malyl-coenzyme A
  • Oxalic Acid
  • Oxo-Acid-Lyases
  • malyl-CoA lyase
  • Magnesium
  • Coenzyme A