Structure of Methylobacterium extorquens malyl-CoA lyase: CoA-substrate binding correlates with domain shift.
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.
Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
Javier M
JM
González
Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
Ricardo
R
Marti-Arbona
Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
Julian C H
JC
Chen
Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
Clifford J
CJ
Unkefer
D000214:Acyl Coenzyme A / Q000737:chemistry* / Q000378:metabolism; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D020134:Catalytic Domain; D002413:Cations, Divalent; D003001:Cloning, Molecular; D003065:Coenzyme A / Q000737:chemistry / Q000378:metabolism; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression; D008274:Magnesium / Q000737:chemistry* / Q000378:metabolism; D020601:Methylobacterium extorquens / Q000737:chemistry* / Q000201:enzymology; D008958:Models, Molecular; D019815:Oxalic Acid / Q000737:chemistry / Q000378:metabolism; D007652:Oxo-Acid-Lyases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D010957:Plasmids / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D000072756:Protein Conformation, alpha-Helical; D000072757:Protein Conformation, beta-Strand; D054730:Protein Interaction Domains and Motifs; D020836:Protein Structure, Quaternary; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012242:Rhodobacter sphaeroides / Q000737:chemistry / Q000201:enzymology; D013379:Substrate Specificity
D000214:Acyl Coenzyme A; D001426:Bacterial Proteins; D002413:Cations, Divalent; D011994:Recombinant Proteins; C042519:malyl-coenzyme A; D019815:Oxalic Acid; D007652:Oxo-Acid-Lyases; C021536:malyl-CoA lyase; D008274:Magnesium; D003065:Coenzyme A
Methylobacterium extorquens; biofuels; malyl-CoA lyase; metabolic engineering; methanol