Crystal structure of mevalonate 3,5-bisphosphate decarboxylase reveals insight into the evolution of decarboxylases in the mevalonate metabolic pathways

Aoki, Mizuki; Vinokur, Jeffrey; Motoyama, Kento; Ishikawa, Rino; Collazo, Michael; Cascio, Duilio; Sawaya, Michael R.; Ito, Tomokazu; Bowie, James U.; Hemmi, Hisashi

doi:10.1016/j.jbc.2022.102111

Title: Crystal structure of mevalonate 3,5-bisphosphate decarboxylase reveals insight into the evolution of decarboxylases in the mevalonate metabolic pathways

Journal Article · Fri Jul 01 00:00:00 EDT 2022 · Journal of Biological Chemistry

DOI:https://doi.org/10.1016/j.jbc.2022.102111· OSTI ID:1872487

Aoki, Mizuki;

; Motoyama, Kento; Ishikawa, Rino; Collazo, Michael; Cascio, Duilio;

;

View Journal Article

Cite

Export

Save

Research Organization:: Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: USDOE Office of Science (SC); National Institutes of Health (NIH); Japan Society for the Promotion of Science (JSPS KAKENHI)

Grant/Contract Number:: AC02-06CH11357; AR0000556; FC02-02ER63421; P41 GM103403; S10 RR029205; 16K14882; 17H05437; 20H02899

OSTI ID:: 1872487

Alternate ID(s):: OSTI ID: 1875165; OSTI ID: 1900959

Journal Information:: Journal of Biological Chemistry, Journal Name: Journal of Biological Chemistry Vol. 298 Journal Issue: 7; ISSN 0021-9258

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

References (38)

Evidence of a Novel Mevalonate Pathway in Archaea Vinokur, Jeffrey M.; Korman, Tyler P.; Cao, Zheng Biochemistry, Vol. 53, Issue 25 https://doi.org/10.1021/bi500566q	journal	June 2014
The Buccaneer software for automated model building. 1. Tracing protein chains Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 9 https://doi.org/10.1107/S0907444906022116	journal	August 2006
Verification of protein structures: Patterns of nonbonded atomic interactions Colovos, Chris; Yeates, Todd O. Protein Science, Vol. 2, Issue 9 https://doi.org/10.1002/pro.5560020916	journal	September 1993
Identification in Haloferax volcanii of Phosphomevalonate Decarboxylase and Isopentenyl Phosphate Kinase as Catalysts of the Terminal Enzyme Reactions in an Archaeal Alternate Mevalonate Pathway VanNice, J. C.; Skaff, D. A.; Keightley, A. Journal of Bacteriology, Vol. 196, Issue 5 https://doi.org/10.1128/JB.01230-13	journal	December 2013
Biochemical evidence supporting the presence of the classical mevalonate pathway in the thermoacidophilic archaeon Sulfolobus solfataricus Nishimura, Hiroto; Azami, Yasuhiro; Miyagawa, Masahito The Journal of Biochemistry, Vol. 153, Issue 5 https://doi.org/10.1093/jb/mvt006	journal	February 2013
Biochemical and Structural Basis for Feedback Inhibition of Mevalonate Kinase and Isoprenoid Metabolism ^† ^, ^‡ Fu, Zhuji; Voynova, Natalia E.; Herdendorf, Timothy J. Biochemistry, Vol. 47, Issue 12 https://doi.org/10.1021/bi7024386	journal	March 2008
Characterization of Thermophilic Archaeal Isopentenyl Phosphate Kinases Chen, Mo; Poulter, C. Dale Biochemistry, Vol. 49, Issue 1 https://doi.org/10.1021/bi9017957	journal	January 2010
Crystal Structures of Trypanosoma brucei and Staphylococcus aureus Mevalonate Diphosphate Decarboxylase Inform on the Determinants of Specificity and Reactivity Byres, Emma; Alphey, Magnus S.; Smith, Terry K. Journal of Molecular Biology, Vol. 371, Issue 2 https://doi.org/10.1016/j.jmb.2007.05.094	journal	August 2007
Coot model-building tools for molecular graphics Emsley, Paul; Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132 https://doi.org/10.1107/S0907444904019158	journal	November 2004
Substrate Specificity and Engineering of Mevalonate 5-Phosphate Decarboxylase Thomas, Suzanne T.; Louie, Gordon V.; Lubin, Johnathan W. ACS Chemical Biology, Vol. 14, Issue 8 https://doi.org/10.1021/acschembio.9b00322	journal	June 2019
An Adaptation To Life In Acid Through A Novel Mevalonate Pathway Vinokur, Jeffrey M.; Cummins, Matthew C.; Korman, Tyler P. Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep39737	journal	December 2016
Structural analysis of mevalonate-3-kinase provides insight into the mechanisms of isoprenoid pathway decarboxylases: Structural Analysis of Mevalonate-3-Kinase Vinokur, Jeffrey M.; Korman, Tyler P.; Sawaya, Michael R. Protein Science, Vol. 24, Issue 2 https://doi.org/10.1002/pro.2607	journal	December 2014
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
Characterization of a Feedback-Resistant Mevalonate Kinase from the Archaeon Methanosarcina mazei Primak, Yuliya A.; Du, Mai; Miller, Michael C. Applied and Environmental Microbiology, Vol. 77, Issue 21 https://doi.org/10.1128/AEM.05761-11	journal	September 2011
Structural Basis for Nucleotide Binding and Reaction Catalysis in Mevalonate Diphosphate Decarboxylase Barta, Michael L.; McWhorter, William J.; Miziorko, Henry M. Biochemistry, Vol. 51, Issue 28 https://doi.org/10.1021/bi300591x	journal	July 2012
Post-translational regulation of mevalonate kinase by intermediates of the cholesterol and nonsterol isoprene biosynthetic pathways Hinson, D. D.; Chambliss, K. L.; Toth, M. J. Journal of Lipid Research, Vol. 38, Issue 11 https://doi.org/10.1016/S0022-2275(20)34935-X	journal	November 1997
Crystal Structures of Staphylococcus epidermidis Mevalonate Diphosphate Decarboxylase Bound to Inhibitory Analogs Reveal New Insight into Substrate Binding and Catalysis Barta, Michael L.; Skaff, D. Andrew; McWhorter, William J. Journal of Biological Chemistry, Vol. 286, Issue 27 https://doi.org/10.1074/jbc.M111.242016	journal	May 2011
Staphylococcus aureus Mevalonate Kinase: Isolation and Characterization of an Enzyme of the Isoprenoid Biosynthetic Pathway Voynova, Natalya E.; Rios, Sandra E.; Miziorko, Henry M. Journal of Bacteriology, Vol. 186, Issue 1 https://doi.org/10.1128/JB.186.1.61-67.2004	journal	January 2004
Cloning, Expression, and Characterization of cis -Polyprenyl Diphosphate Synthase from the Thermoacidophilic Archaeon Sulfolobus acidocaldarius Hemmi, Hisashi; Yamashita, Satoshi; Shimoyama, Takefumi Journal of Bacteriology, Vol. 183, Issue 1 https://doi.org/10.1128/JB.183.1.401-404.2001	journal	January 2001
PROCHECK: a program to check the stereochemical quality of protein structures Laskowski, R. A.; MacArthur, M. W.; Moss, D. S. Journal of Applied Crystallography, Vol. 26, Issue 2 https://doi.org/10.1107/S0021889892009944	journal	April 1993
MrBUMP : an automated pipeline for molecular replacement Keegan, Ronan M.; Winn, Martyn D. Acta Crystallographica Section D Biological Crystallography, Vol. 64, Issue 1 https://doi.org/10.1107/S0907444907037195	journal	December 2007
Mevalonate 5-diphosphate mediates ATP binding to the mevalonate diphosphate decarboxylase from the bacterial pathogen Enterococcus faecalis Chen, Chun-Liang; Mermoud, James C.; Paul, Lake N. Journal of Biological Chemistry, Vol. 292, Issue 52 https://doi.org/10.1074/jbc.M117.802223	journal	October 2017
Modified mevalonate pathway of the archaeon Aeropyrum pernix proceeds via trans -anhydromevalonate 5-phosphate Hayakawa, Hajime; Motoyama, Kento; Sobue, Fumiaki Proceedings of the National Academy of Sciences, Vol. 115, Issue 40 https://doi.org/10.1073/pnas.1809154115	journal	September 2018
( R )-Mevalonate 3-Phosphate Is an Intermediate of the Mevalonate Pathway in Thermoplasma acidophilum Azami, Yasuhiro; Hattori, Ai; Nishimura, Hiroto Journal of Biological Chemistry, Vol. 289, Issue 23 https://doi.org/10.1074/jbc.M114.562686	journal	April 2014
A Single Amino Acid Mutation Converts ( R )-5-Diphosphomevalonate Decarboxylase into a Kinase Motoyama, Kento; Unno, Hideaki; Hattori, Ai Journal of Biological Chemistry, Vol. 292, Issue 6 https://doi.org/10.1074/jbc.M116.752535	journal	December 2016
Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7 Langer, Gerrit; Cohen, Serge X.; Lamzin, Victor S. Nature Protocols, Vol. 3, Issue 7 https://doi.org/10.1038/nprot.2008.91	journal	June 2008
Methanocaldococcus jannaschii Uses a Modified Mevalonate Pathway for Biosynthesis of Isopentenyl Diphosphate Grochowski, Laura L.; Xu, Huimin; White, Robert H. Journal of Bacteriology, Vol. 188, Issue 9 https://doi.org/10.1128/JB.188.9.3192-3198.2006	journal	May 2006
Discovery of a metabolic alternative to the classical mevalonate pathway Dellas, Nikki; Thomas, Suzanne T.; Manning, Gerard eLife, Vol. 2 https://doi.org/10.7554/eLife.00672	journal	December 2013
In Vivo Formation of the Protein Disulfide Bond That Enhances the Thermostability of Diphosphomevalonate Decarboxylase, an Intracellular Enzyme from the Hyperthermophilic Archaeon Sulfolobus solfataricus Hattori, Ai; Unno, Hideaki; Goda, Shuichiro Journal of Bacteriology, Vol. 197, Issue 21 https://doi.org/10.1128/JB.00352-15	journal	November 2015
Mutation and inhibition studies of mevalonate 5-diphosphate decarboxylase Qiu, Yongge; Gao, Jinbo; Guo, Fei Bioorganic & Medicinal Chemistry Letters, Vol. 17, Issue 22 https://doi.org/10.1016/j.bmcl.2007.09.033	journal	November 2007
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	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
Human mevalonate diphosphate decarboxylase: Characterization, investigation of the mevalonate diphosphate binding site, and crystal structure Voynova, Natalia E.; Fu, Zhuji; Battaile, Kevin P. Archives of Biochemistry and Biophysics, Vol. 480, Issue 1 https://doi.org/10.1016/j.abb.2008.08.024	journal	December 2008
Characterization of feedback-resistant mevalonate kinases from the methanogenic archaeons Methanosaeta concilii and Methanocella paludicola Kazieva, Ekaterina; Yamamoto, Yoko; Tajima, Yoshinori Microbiology, Vol. 163, Issue 9 https://doi.org/10.1099/mic.0.000510	journal	September 2017
The Putative Mevalonate Diphosphate Decarboxylase from Picrophilus torridus Is in Reality a Mevalonate-3-Kinase with High Potential for Bioproduction of Isobutene Rossoni, Luca; Hall, Stephen J.; Eastham, Graham Applied and Environmental Microbiology, Vol. 81, Issue 7 https://doi.org/10.1128/AEM.04033-14	journal	January 2015
Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis Bonanno, J. B.; Edo, C.; Eswar, N. Proceedings of the National Academy of Sciences, Vol. 98, Issue 23, p. 12896-12901 https://doi.org/10.1073/pnas.181466998	journal	November 2001
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
Visualizing the enzyme mechanism of mevalonate diphosphate decarboxylase Chen, Chun-Liang; Paul, Lake N.; Mermoud, James C. Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-17733-0	journal	August 2020

Similar Records

Crystal structure of the Streptomyces coelicolor sortase E1 transpeptidase provides insight into the binding mode of the novel class E sorting signal

Journal Article · Fri Dec 09 00:00:00 EST 2016 · PLoS ONE · OSTI ID:1872487

Kattke, Michele D.; Chan, Albert H.; Duong, Andrew; +6 more

Structural analysis of mevalonate‐3‐kinase provides insight into the mechanisms of isoprenoid pathway decarboxylases

Journal Article · Fri Dec 26 00:00:00 EST 2014 · Protein Science · OSTI ID:1872487

Vinokur, Jeffrey M.; Korman, Tyler P.; Sawaya, Michael R.; +3 more

Structural basis for divergent and convergent evolution of catalytic machineries in plant aromatic amino acid decarboxylase proteins

Journal Article · Tue May 05 00:00:00 EDT 2020 · Proceedings of the National Academy of Sciences of the United States of America · OSTI ID:1872487

Torrens-Spence, Michael P.; Chiang, Ying-Chih; Smith, Tyler; +3 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
mevalonate pathway
archaea
isoprenoid
crystal structure
mutagenesis
molecular evolution

Title: Crystal structure of mevalonate 3,5-bisphosphate decarboxylase reveals insight into the evolution of decarboxylases in the mevalonate metabolic pathways

Citation Formats

References (38)

Similar Records

Related Subjects