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 · 27 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), Los Alamos, NM (United States)

Sponsoring Organization:: USDOE Laboratory Directed Research and Development (LDRD) Program

Grant/Contract Number:: AC52-06NA25396

OSTI ID:: 1342868

Report Number(s):: LA-UR-16-29566; ACSFEN; TRN: US1700925

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

Publisher:: International Union of CrystallographyCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 1 work

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References (25)

Overview of the CCP 4 suite and current developments Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444910045749	journal	March 2011
The Pfam protein families database: towards a more sustainable future Finn, Robert D.; Coggill, Penelope; Eberhardt, Ruth Y. Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1344	journal	December 2015
[58] Malyl-CoA lyase from methylobacterium extorquens AM 1 Hacking, A. J.; Quayle, J. . R. Hydrocarbons and Methylotrophy https://doi.org/10.1016/0076-6879(90)88060-N	book	January 1990
The Apparent Malate Synthase Activity of Rhodobacter sphaeroides Is Due to Two Paralogous Enzymes, (3S)-Malyl-Coenzyme A (CoA)/ -Methylmalyl-CoA Lyase and (3S)- Malyl-CoA Thioesterase Erb, T. J.; Frerichs-Revermann, L.; Fuchs, G. Journal of Bacteriology, Vol. 192, Issue 5 https://doi.org/10.1128/JB.01267-09	journal	January 2010
Deciphering key features in protein structures with the new ENDscript server Robert, Xavier; Gouet, Patrice Nucleic Acids Research, Vol. 42, Issue W1 https://doi.org/10.1093/nar/gku316	journal	April 2014
Genetics of serine pathway enzymes in Methylobacterium extorquens AM1: phosphoenolpyruvate carboxylase and malyl coenzyme A lyase. Arps, P. J.; Fulton, G. F.; Minnich, E. C. Journal of Bacteriology, Vol. 175, Issue 12 https://doi.org/10.1128/jb.175.12.3776-3783.1993	journal	June 1993
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
New paradigm for macromolecular crystallography experiments at SSRL: automated crystal screening and remote data collection Soltis, S. Michael; Cohen, Aina E.; Deacon, Ashley Acta Crystallographica Section D Biological Crystallography, Vol. 64, Issue 12 https://doi.org/10.1107/S0907444908030564	journal	November 2008
REFMAC 5 for the refinement of macromolecular crystal structures Murshudov, Garib N.; Skubák, Pavol; Lebedev, Andrey A. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444911001314	journal	March 2011
The crystal structures of the tri-functional Chloroflexus aurantiacus and bi-functional Rhodobacter sphaeroides malyl-CoA lyases and comparison with CitE-like superfamily enzymes and malate synthases Zarzycki, Jan; Kerfeld, Cheryl A. BMC Structural Biology, Vol. 13, Issue 1 https://doi.org/10.1186/1472-6807-13-28	journal	January 2013
SFCHECK : a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model Vaguine, Alexei A.; Richelle, Jean; Wodak, S. J. Acta Crystallographica Section D Biological Crystallography, Vol. 55, Issue 1 https://doi.org/10.1107/S0907444998006684	journal	January 1999
Cloning, mutagenesis, and physiological effect of a hydroxypyruvate reductase gene from Methylobacterium extorquens AM1. Chistoserdova, L. V.; Lidstrom, M. E. Journal of Bacteriology, Vol. 174, Issue 1 https://doi.org/10.1128/jb.174.1.71-77.1992	journal	January 1992
On the treatment of negative intensity observations French, S.; Wilson, K. Acta Crystallographica Section A, Vol. 34, Issue 4 https://doi.org/10.1107/S0567739478001114	journal	July 1978
How good are my data and what is the resolution? Evans, Philip R.; Murshudov, Garib N. Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 7 https://doi.org/10.1107/S0907444913000061	journal	June 2013
An automated system to mount cryo-cooled protein crystals on a synchrotron beamline, using compact sample cassettes and a small-scale robot Cohen, Aina E.; Ellis, Paul J.; Miller, Mitchell D. Journal of Applied Crystallography, Vol. 35, Issue 6 https://doi.org/10.1107/S0021889802016709	journal	November 2002
Identifying the missing steps of the autotrophic 3-hydroxypropionate CO₂ fixation cycle in Chloroflexus aurantiacus Zarzycki, Jan; Brecht, Volker; Müller, Michael Proceedings of the National Academy of Sciences, Vol. 106, Issue 50, p. 21317-21322 https://doi.org/10.1073/pnas.0908356106	journal	December 2009
L-Malyl-Coenzyme A Lyase/β-Methylmalyl-Coenzyme A Lyase from Chloroflexus aurantiacus, a Bifunctional Enzyme Involved in Autotrophic CO₂ Fixation Herter, S.; Busch, A.; Fuchs, G. Journal of Bacteriology, Vol. 184, Issue 21, p. 5999-6006 https://doi.org/10.1128/JB.184.21.5999-6006.2002	journal	November 2002
Purification and properties of malyl-coenzyme A lyase from Pseudomonas AM1 Hacking, A. J.; Quayle, J. R. Biochemical Journal, Vol. 139, Issue 2 https://doi.org/10.1042/bj1390399	journal	May 1974
Systematic analysis of domain motions in proteins from conformational change: New results on citrate synthase and T4 lysozyme Hayward, Steven; Berendsen, Herman J. C. Proteins: Structure, Function, and Genetics, Vol. 30, Issue 2 https://doi.org/10.1002/(SICI)1097-0134(19980201)30:2<144::AID-PROT4>3.0.CO;2-N	journal	February 1998
Calculation of protein extinction coefficients from amino acid sequence data Gill, Stanley C.; von Hippel, Peter H. Analytical Biochemistry, Vol. 182, Issue 2 https://doi.org/10.1016/0003-2697(89)90602-7	journal	November 1989
Scaling and assessment of data quality Evans, Philip Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 1, p. 72-82 https://doi.org/10.1107/S0907444905036693	journal	December 2005
Integration, scaling, space-group assignment and post-refinement Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 133-144 https://doi.org/10.1107/S0907444909047374	journal	January 2010
Inference of Macromolecular Assemblies from Crystalline State Krissinel, Evgeny; Henrick, Kim Journal of Molecular Biology, Vol. 372, Issue 3 https://doi.org/10.1016/j.jmb.2007.05.022	journal	September 2007
Autoindexing diffraction images with iMosflm Powell, Harold R.; Johnson, Owen; Leslie, Andrew G. W. Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 7 https://doi.org/10.1107/S0907444912048524	journal	June 2013
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007