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Mechanism of action and NAD+-binding mode revealed by the crystal structure of L-histidinol dehydrogenase.

Barbosa JA, Sivaraman J, Li Y, Larocque R, Matte A, Schrag JD, Cygler M
Proc Natl Acad Sci U S A 99 1859-64 (2002)
Related entries: 1k75, 1kah, 1kar

Cited: 28 times
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Abstract

The histidine biosynthetic pathway is an ancient one found in bacteria, archaebacteria, fungi, and plants that converts 5-phosphoribosyl 1-pyrophosphate to l-histidine in 10 enzymatic reactions. This pathway provided a paradigm for the operon, transcriptional regulation of gene expression, and feedback inhibition of a pathway. l-histidinol dehydrogenase (HisD, EC ) catalyzes the last two steps in the biosynthesis of l-histidine: sequential NAD-dependent oxidations of l-histidinol to l-histidinaldehyde and then to l-histidine. HisD functions as a homodimer and requires the presence of one Zn(2+) cation per monomer. We have determined the three-dimensional structure of Escherichia coli HisD in the apo state as well as complexes with substrate, Zn(2+), and NAD(+) (best resolution is 1.7 A). Each monomer is made of four domains, whereas the intertwined dimer possibly results from domain swapping. Two domains display a very similar incomplete Rossmann fold that suggests an ancient event of gene duplication. Residues from both monomers form the active site. Zn(2+) plays a crucial role in substrate binding but is not directly involved in catalysis. The active site residue His-327 participates in acid-base catalysis, whereas Glu-326 activates a water molecule. NAD(+) binds weakly to one of the Rossmann fold domains in a manner different from that previously observed for other proteins having a Rossmann fold.

Reviews - 1kae mentioned but not cited (1)

  1. Contribution of structural genomics to understanding the biology of Escherichia coli. Matte A, Sivaraman J, Ekiel I, Gehring K, Jia Z, Cygler M. J Bacteriol 185 3994-4002 (2003)

Articles - 1kae mentioned but not cited (7)

  1. Self-association of a highly charged arginine-rich cell-penetrating peptide. Tesei G, Vazdar M, Jensen MR, Cragnell C, Mason PE, Heyda J, Skepö M, Jungwirth P, Lund M. Proc Natl Acad Sci U S A 114 11428-11433 (2017)
  2. Mechanism of action and NAD+-binding mode revealed by the crystal structure of L-histidinol dehydrogenase. Barbosa JA, Sivaraman J, Li Y, Larocque R, Matte A, Schrag JD, Cygler M. Proc Natl Acad Sci U S A 99 1859-1864 (2002)
  3. Improving detection of protein-ligand binding sites with 3D segmentation. Stepniewska-Dziubinska MM, Zielenkiewicz P, Siedlecki P. Sci Rep 10 5035 (2020)
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  5. Helical shape of Helicobacter pylori requires an atypical glutamine as a zinc ligand in the carboxypeptidase Csd4. Chan AC, Blair KM, Liu Y, Frirdich E, Gaynor EC, Tanner ME, Salama NR, Murphy ME. J Biol Chem 290 3622-3638 (2015)
  6. The Role of Gene Elongation in the Evolution of Histidine Biosynthetic Genes. Del Duca S, Chioccioli S, Vassallo A, Castronovo LM, Fani R. Microorganisms 8 E732 (2020)
  7. Structures of Medicago truncatula L-Histidinol Dehydrogenase Show Rearrangements Required for NAD+ Binding and the Cofactor Positioned to Accept a Hydride. Ruszkowski M, Dauter Z. Sci Rep 7 10476 (2017)


Reviews citing this publication (1)

  1. Histidine biosynthesis, its regulation and biotechnological application in Corynebacterium glutamicum. Kulis-Horn RK, Persicke M, Kalinowski J. Microb Biotechnol 7 5-25 (2014)

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  2. QM/MM X-ray refinement of zinc metalloenzymes. Li X, Hayik SA, Merz KM. J Inorg Biochem 104 512-522 (2010)
  3. Biosynthesis of Histidine. Winkler ME, Ramos-Montañez S. EcoSal Plus 3 (2009)
  4. Brucella suis histidinol dehydrogenase: synthesis and inhibition studies of a series of substituted benzylic ketones derived from histidine. Abdo MR, Joseph P, Boigegrain RA, Liautard JP, Montero JL, Köhler S, Winum JY. Bioorg Med Chem 15 4427-4433 (2007)
  5. Mutagenesis of uracil-DNA glycosylase deficient mutants of the extremely thermophilic eubacterium Thermus thermophilus. Sakai T, Tokishita S, Mochizuki K, Motomiya A, Yamagata H, Ohta T. DNA Repair (Amst) 7 663-669 (2008)
  6. Anti-virulence strategy against Brucella suis: synthesis, biological evaluation and molecular modeling of selective histidinol dehydrogenase inhibitors. Abdo MR, Joseph P, Mortier J, Turtaut F, Montero JL, Masereel B, Köhler S, Winum JY. Org Biomol Chem 9 3681-3690 (2011)
  7. Detection and alignment of 3D domain swapping proteins using angle-distance image-based secondary structural matching techniques. Chu CH, Lo WC, Wang HW, Hsu YC, Hwang JK, Lyu PC, Pai TW, Tang CY. PLoS One 5 e13361 (2010)
  8. 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 K, Lopez M, Dathan NA, Ouahrani-Bettache S, Köhler S, Ascione G, Monti SM, Winum JY, De Simone G. Biochimie 97 114-120 (2014)
  9. Diversity of the trifunctional histidine biosynthesis gene (his) in cereal Phaeosphaeria species. Wang CL, Malkus A, Zuzga SM, Chang PF, Cunfer BM, Arseniuk E, Ueng PP. Genome 50 595-609 (2007)
  10. Brucella suis histidinol dehydrogenase: synthesis and inhibition studies of substituted N-L-histidinylphenylsulfonyl hydrazide. Abdo MR, Joseph P, Boigegrain RA, Montero JL, Köhler S, Winum JY. J Enzyme Inhib Med Chem 23 357-361 (2008)
  11. Determinants of histamine recognition: implications for the design of antihistamines. Konkimalla VB, Chandra N. Biochem Biophys Res Commun 309 425-431 (2003)
  12. In-silico pharmacodynamics: correlation of adverse effects of H2-antihistamines with histamine N-methyl transferase binding potential. Vinod PK, Konkimalla B, Chandra N. Appl Bioinformatics 5 141-150 (2006)
  13. Rational Engineering of a Flavoprotein Oxidase for Improved Direct Oxidation of Alcohols to Carboxylic Acids. Pickl M, Winkler CK, Glueck SM, Fraaije MW, Faber K. Molecules 22 E2205 (2017)
  14. HisB from Mycobacterium tuberculosis: cloning, overexpression in Mycobacterium smegmatis, purification, crystallization and preliminary X-ray crystallographic analysis. Ahangar MS, Khandokar Y, Nasir N, Vyas R, Biswal BK. Acta Crystallogr Sect F Struct Biol Cryst Commun 67 1451-1456 (2011)
  15. Histidine is essential for growth of Komagataella phaffii cultured in YPA medium. Gupta A, Rangarajan PN. FEBS Open Bio 12 1241-1252 (2022)
  16. Mimicking the active site of aldehyde dehydrogenases: stabilization of carbonyl hydrates through hydrogen bonds. Roth AJ, Tretbar M, Stark CB. Chem Commun (Camb) 51 14175-14178 (2015)
  17. Competitive inhibition of a non-natural cofactor dependent formaldehyde dehydrogenase by imidazole. Wang J, Wan L, Guo X, Wang X, Zhao ZK. Biotechnol Lett 45 679-687 (2023)
  18. New Role of Water in Transketolase Catalysis. Solovjeva ON. Int J Mol Sci 24 2068 (2023)
  19. The GDP-Mannose Dehydrogenase of Pseudomonas aeruginosa: An Old and New Target to Fight against Antibiotics Resistance of Mucoid Strains. Hulen C. Antibiotics (Basel) 12 1649 (2023)


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