Structures of Medicago truncatula L-Histidinol Dehydrogenase Show Rearrangements Required for NAD+ Binding and the Cofactor Positioned to Accept a Hydride

Ruszkowski, Milosz; Dauter, Zbigniew

doi:10.1038/s41598-017-10859-0

Structures of Medicago truncatula L-Histidinol Dehydrogenase Show Rearrangements Required for NAD+ Binding and the Cofactor Positioned to Accept a Hydride

Journal Article · Tue Sep 05 04:00:00 EDT 2017 · Scientific Reports

DOI:https://doi.org/10.1038/s41598-017-10859-0· OSTI ID:1393647

Ruszkowski, Milosz; Dauter, Zbigniew

Abstract not provided

Research Organization:: Advanced Photon Source (APS), Argonne National Laboratory (ANL), Argonne, IL (US)

Sponsoring Organization:: NCI

OSTI ID:: 1393647

Journal Information:: Scientific Reports, Journal Name: Scientific Reports Journal Issue: 1 Vol. 7; ISSN 2045-2322

Publisher:: Nature Publishing Group

Country of Publication:: United States

Language:: ENGLISH

References (56)

Salmonella typhimurium histidinol dehydrogenase: complete reaction stereochemistry and active site mapping Grubmeyer, Charles Timmis; Insinga, Salvatore; Bhatia, Mohit Biochemistry, Vol. 28, Issue 20 https://doi.org/10.1021/bi00446a032	journal	October 1989
Detection and properties of l-histidinol dehydrogenase in wheat germ Wong, Yum-Shing; Mazelis, Mendel Phytochemistry, Vol. 20, Issue 8 https://doi.org/10.1016/0031-9422(81)84014-9	journal	January 1981
Macromolecular TLS Refinement in REFMAC at Moderate Resolutions Winn, Martyn D.; Murshudov, Garib N.; Papiz, Miroslav Z. Methods in Enzymology https://doi.org/10.1016/S0076-6879(03)74014-2	book	January 2003
Basic local alignment search tool Altschul, Stephen F.; Gish, Warren; Miller, Webb Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410 https://doi.org/10.1016/S0022-2836(05)80360-2	journal	October 1990
Kinetic mechanism of histidinol dehydrogenase: histidinol binding and exchange reactions Grubmeyer, Charles Timmis; Chu, Kim Wai; Insinga, Salvatore Biochemistry, Vol. 26, Issue 12 https://doi.org/10.1021/bi00386a018	journal	June 1987
Comparison of super-secondary structures in proteins Rao, S. T.; Rossmann, Michael G. Journal of Molecular Biology, Vol. 76, Issue 2 https://doi.org/10.1016/0022-2836(73)90388-4	journal	May 1973
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
Enzymatic Transition States, Transition-State Analogs, Dynamics, Thermodynamics, and Lifetimes Schramm, Vern L. Annual Review of Biochemistry, Vol. 80, Issue 1 https://doi.org/10.1146/annurev-biochem-061809-100742	journal	July 2011
Crystal Structures Reveal that the Reaction Mechanism of Imidazoleglycerol-Phosphate Dehydratase Is Controlled by Switching Mn(II) Coordination Bisson, Claudine; Britton, K. Linda; Sedelnikova, Svetlana E. Structure, Vol. 23, Issue 7 https://doi.org/10.1016/j.str.2015.05.012	journal	July 2015
Targeting the Histidine Pathway in Mycobacterium tuberculosis Lunardi, Juleane; Nunes, José; Bizarro, Cristiano Current Topics in Medicinal Chemistry, Vol. 13, Issue 22 https://doi.org/10.2174/15680266113136660203	journal	November 2013
Isolation and Characterization of a Histidine Biosynthetic Gene in Arabidopsis Encoding a Polypeptide with Two Separate Domains for Phosphoribosyl-ATP Pyrophosphohydrolase and Phosphoribosyl-AMP Cyclohydrolase Fujimori, Ko; Ohta, Daisaku Plant Physiology, Vol. 118, Issue 1 https://doi.org/10.1104/pp.118.1.275	journal	September 1998
Use of TLS parameters to model anisotropic displacements in macromolecular refinement Winn, M. D.; Isupov, M. N.; Murshudov, G. N. Acta Crystallographica Section D Biological Crystallography, Vol. 57, Issue 1 https://doi.org/10.1107/S0907444900014736	journal	January 2001
Managing the manganese: molecular mechanisms of manganese transport and homeostasis: Research review Pittman, Jon K. New Phytologist, Vol. 167, Issue 3 https://doi.org/10.1111/j.1469-8137.2005.01453.x	journal	May 2005
Anti-virulence Strategy against Brucella suis: Synthesis, Biological Evaluation and Molecular Modeling of Selective Histidinol Dehydrogenase Inhibitors Abdo, Marie-Rose; Joseph, Pascale; Mortier, Jérémie Organic & Biomolecular Chemistry, Vol. 9, Issue 10 https://doi.org/10.1039/c1ob05149k	journal	January 2011
Molecular cloning and characterization of the gene encoding N'-[(5'-phosphoribosyl)-formimino]-5-aminoimidazole-4-carboxamide ribonucleotide (BBM II) isomerase from Arabidopsis thaliana Fujimori, K.; Tada, S.; Kanai, S. Molecular and General Genetics MGG, Vol. 259, Issue 2 https://doi.org/10.1007/s004380050807	journal	August 1998
The Immunosuppressive Metabolite of Leflunomide Is a Potent Inhibitor of Human Dihydroorotate Dehydrogenase Davis, June P.; Cain, Gary A.; Pitts, William J. Biochemistry, Vol. 35, Issue 4 https://doi.org/10.1021/bi952168g	journal	January 1996
UniProt: a hub for protein information Consortium, UniPot Nucleic Acids Research, Vol. 43, Issue D1, p. D204-D212 https://doi.org/10.1093/nar/gku989	journal	October 2014
Predicting Subcellular Localization of Proteins Based on their N-terminal Amino Acid Sequence Emanuelsson, Olof; Nielsen, Henrik; Brunak, Søren Journal of Molecular Biology, Vol. 300, Issue 4 https://doi.org/10.1006/jmbi.2000.3903	journal	July 2000
Gene-Enzyme Relations in Histidine Biosynthesis in Yeast Fink, G. R. Science, Vol. 146, Issue 3643 https://doi.org/10.1126/science.146.3643.525	journal	October 1964
The Missing Link in Plant Histidine Biosynthesis: Arabidopsis myoinositol monophosphatase - like2 Encodes a Functional Histidinol-Phosphate Phosphatase Petersen, Lindsay N.; Marineo, Sandra; Mandalà, Salvatore Plant Physiology, Vol. 152, Issue 3 https://doi.org/10.1104/pp.109.150805	journal	December 2009
Genomic-scale prioritization of drug targets: the TDR Targets database Agüero, Fernán; Al-Lazikani, Bissan; Aslett, Martin Nature Reviews Drug Discovery, Vol. 7, Issue 11 https://doi.org/10.1038/nrd2684	journal	October 2008
Structure and Mechanism of Imidazoleglycerol-Phosphate Dehydratase Glynn, Steven E.; Baker, Patrick J.; Sedelnikova, Svetlana E. Structure, Vol. 13, Issue 12 https://doi.org/10.1016/j.str.2005.08.012	journal	December 2005
MolProbity : all-atom structure validation for macromolecular crystallography Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1 https://doi.org/10.1107/S0907444909042073	journal	December 2009
High-throughput protein purification and quality assessment for crystallization Kim, Youngchang; Babnigg, Gyorgy; Jedrzejczak, Robert Methods, Vol. 55, Issue 1 https://doi.org/10.1016/j.ymeth.2011.07.010	journal	September 2011
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
Computational Modeling of a Binding Conformation of the Intermediate l -Histidinal to Histidinol Dehydrogenase Gohda, Keigo; Ohta, Daisaku; Iwasaki, Genji Journal of Chemical Information and Computer Sciences, Vol. 41, Issue 1 https://doi.org/10.1021/ci000332n	journal	December 2000
Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites Nielsen, H.; Engelbrecht, J.; Brunak, S. Protein Engineering Design and Selection, Vol. 10, Issue 1, p. 1-6 https://doi.org/10.1093/protein/10.1.1	journal	January 1997
Purification and characterization of histidinol dehydrogenase from cabbage Nagai, Atsuko; Scheidegger, Alfred Archives of Biochemistry and Biophysics, Vol. 284, Issue 1 https://doi.org/10.1016/0003-9861(91)90274-M	journal	January 1991
Clustal W and Clustal X version 2.0 Larkin, M. A.; Blackshields, G.; Brown, N. P. Bioinformatics, Vol. 23, Issue 21, p. 2947-2948 https://doi.org/10.1093/bioinformatics/btm404	journal	September 2007
Nonlinear partial differential equations and applications: The analysis of the intramacrophagic virulome of Brucella suis deciphers the environment encountered by the pathogen inside the macrophage host cell Kohler, S.; Foulongne, V.; Ouahrani-Bettache, S. Proceedings of the National Academy of Sciences, Vol. 99, Issue 24 https://doi.org/10.1073/pnas.232454299	journal	November 2002
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
BALBES : a molecular-replacement pipeline Long, Fei; Vagin, Alexei A.; Young, Paul Acta Crystallographica Section D Biological Crystallography, Vol. 64, Issue 1 https://doi.org/10.1107/S0907444907050172	journal	December 2007
ACHESYM : an algorithm and server for standardized placement of macromolecular models in the unit cell Kowiel, Marcin; Jaskolski, Mariusz; Dauter, Zbigniew Acta Crystallographica Section D Biological Crystallography, Vol. 70, Issue 12 https://doi.org/10.1107/S1399004714024572	journal	November 2014
Molecular cloning and expression of a cDNA sequence encoding histidinol phosphate aminotransferase from Nicotiana tabacum El Malki, Fatima; Frankard, Valérie; Jacobs, Michel Plant Molecular Biology, Vol. 37, Issue 6, p. 1013-1022 https://doi.org/10.1023/A:1006007125448	journal	August 1998
Molecular, kinetic, thermodynamic, and structural analyses of Mycobacterium tuberculosis hisD-encoded metal-dependent dimeric histidinol dehydrogenase (EC 1.1.1.23) Nunes, José E. S.; Ducati, Rodrigo G.; Breda, Ardala Archives of Biochemistry and Biophysics, Vol. 512, Issue 2 https://doi.org/10.1016/j.abb.2011.05.020	journal	August 2011
Starvation Survival Response of Mycobacterium tuberculosis Parish, Tanya Journal of Bacteriology, Vol. 185, Issue 22 https://doi.org/10.1128/JB.185.22.6702-6706.2003	journal	November 2003
l-Histidinol dehydrogenase, a Zn2+-metalloenzyme Grubmeyer, Charles; Skiadopoulos, Marios; Senior, Alan E. Archives of Biochemistry and Biophysics, Vol. 272, Issue 2 https://doi.org/10.1016/0003-9861(89)90224-5	journal	August 1989
The MORPHEUS protein crystallization screen Gorrec, Fabrice Journal of Applied Crystallography, Vol. 42, Issue 6 https://doi.org/10.1107/S0021889809042022	journal	November 2009
UCSF Chimera?A visualization system for exploratory research and analysis Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C. Journal of Computational Chemistry, Vol. 25, Issue 13 https://doi.org/10.1002/jcc.20084	journal	January 2004
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	journal	January 2010
Comparison of Hydride, Hydrogen Atom, and Proton-Coupled Electron Transfer Reactions Hammes-Schiffer, Sharon ChemPhysChem, Vol. 3, Issue 1 https://doi.org/10.1002/1439-7641(20020118)3:1<33::AID-CPHC33>3.0.CO;2-6	journal	January 2002
Structural and functional conservation of histidinol dehydrogenase between plants and microbes. Nagai, A.; Ward, E.; Beck, J. Proceedings of the National Academy of Sciences, Vol. 88, Issue 10 https://doi.org/10.1073/pnas.88.10.4133	journal	May 1991
Steady-State Kinetics of Cabbage Histidinol Dehydrogenase Kheirolomoom, A.; Mano, J.; Nagai, A. Archives of Biochemistry and Biophysics, Vol. 312, Issue 2 https://doi.org/10.1006/abbi.1994.1337	journal	August 1994
Structural Studies of Medicago truncatula Histidinol Phosphate Phosphatase from Inositol Monophosphatase Superfamily Reveal Details of Penultimate Step of Histidine Biosynthesis in Plants Ruszkowski, Milosz; Dauter, Zbigniew Journal of Biological Chemistry, Vol. 291, Issue 19 https://doi.org/10.1074/jbc.M115.708727	journal	March 2016
Histidine biosynthesis in plants Stepansky, A.; Leustek, T. Amino Acids, Vol. 30, Issue 2 https://doi.org/10.1007/s00726-005-0247-0	journal	March 2006
Improved R-factors for diffraction data analysis in macromolecular crystallography Diederichs, Kay; Karplus, P. Andrew Nature Structural Biology, Vol. 4, Issue 4 https://doi.org/10.1038/nsb0497-269	journal	April 1997
Steady-state investigations of the mechanism of histidinol dehydrogenase Görisch, H. Biochemical Journal, Vol. 181, Issue 1 https://doi.org/10.1042/bj1810153	journal	July 1979
An Arabidopsis cDNA encoding a bifunctional glutamine amidotransferase/cyclase suppresses the histidine auxotrophy of a Saccharomyces cerevisiae his7 mutant Fujimori, Ko; Ohta, Daisaku FEBS Letters, Vol. 428, Issue 3 https://doi.org/10.1016/S0014-5793(98)00535-3	journal	May 1998
Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard Terwilliger, Thomas C.; Grosse-Kunstleve, Ralf W.; Afonine, Pavel V. Acta Crystallographica Section D Biological Crystallography, Vol. 64, Issue 1 https://doi.org/10.1107/S090744490705024X	journal	December 2007
Inhibitors of amino acids biosynthesis as antifungal agents Jastrzębowska, Kamila; Gabriel, Iwona Amino Acids, Vol. 47, Issue 2 https://doi.org/10.1007/s00726-014-1873-1	journal	November 2014
Mutagenesis of Histidinol Dehydrogenase Reveals Roles for Conserved Histidine Residues ^† Teng, Henry; Grubmeyer, Charles Biochemistry, Vol. 38, Issue 22 https://doi.org/10.1021/bi982758p	journal	June 1999
Structural basis for the rational design of new anti-Brucella agents: The crystal structure of the C366S mutant of l-histidinol dehydrogenase from Brucella suis D'ambrosio, Katia; Lopez, Marie; Dathan, Nina A. Biochimie, Vol. 97 https://doi.org/10.1016/j.biochi.2013.09.028	journal	February 2014
L-Histidinol Dehydrogenase as a New Target for Old Diseases M. Monti, Simona; De Simone, Giuseppina; D'Ambrosio, Katia Current Topics in Medicinal Chemistry, Vol. 16, Issue 21 https://doi.org/10.2174/1568026616666160413140000	journal	June 2016
Histidine Biosynthesis Ingle, Robert A. The Arabidopsis Book, Vol. 9 https://doi.org/10.1199/tab.0141	journal	January 2011
Mechanism of action and NAD+-binding mode revealed by the crystal structure of L-histidinol dehydrogenase Barbosa, J. A. R. G.; Sivaraman, J.; Li, Y. Proceedings of the National Academy of Sciences, Vol. 99, Issue 4 https://doi.org/10.1073/pnas.022476199	journal	February 2002
Mechanism of Salmonella typhimurium Histidinol Dehydrogenase: Kinetic Isotope Effects and pH Profiles ^† Grubmeyer, Charles; Teng, Henry Biochemistry, Vol. 38, Issue 22 https://doi.org/10.1021/bi982757x	journal	June 1999

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