title: Crystal structure of a novel shikimate dehydrogenase from Haemophilus influenzae.
abstract: To date two classes of shikimate dehydrogenases have been identified and characterized, YdiB and AroE. YdiB is a bifunctional enzyme that catalyzes the reversible reductions of dehydroquinate to quinate and dehydroshikimate to shikimate in the presence of either NADH or NADPH. In contrast, AroE catalyzes the reversible reduction of dehydroshikimate to shikimate in the presence of NADPH. Here we report the crystal structure and biochemical characterization of HI0607, a novel class of shikimate dehydrogenase annotated as shikimate dehydrogenase-like. The kinetic properties of HI0607 are remarkably different from those of AroE and YdiB. In comparison with YdiB, HI0607 catalyzes the oxidation of shikimate but not quinate. The turnover rate for the oxidation of shikimate is approximately 1000-fold lower compared with that of AroE. Phylogenetic analysis reveals three independent clusters representing three classes of shikimate dehydrogenases, namely AroE, YdiB, and this newly characterized shikimate dehydrogenase-like protein. In addition, mutagenesis studies of two invariant residues, Asp-103 and Lys-67, indicate that they are important catalytic groups that may function as a catalytic pair in the shikimate dehydrogenase reaction. This is the first study that describes the crystal structure as well as mutagenesis and mechanistic analysis of this new class of shikimate dehydrogenase.
authors.affiliation: Department of Botany, University of Toronto, Toronto, Ontario M5S 3B2, Canada.
authors.forename: Sasha
authors.initials: S
authors.lastname: Singh
authors.forename: Sergey
authors.initials: S
authors.lastname: Korolev
authors.forename: Olga
authors.initials: O
authors.lastname: Koroleva
authors.forename: Thomas
authors.initials: T
authors.lastname: Zarembinski
authors.forename: Frank
authors.initials: F
authors.lastname: Collart
authors.forename: Andrzej
authors.initials: A
authors.lastname: Joachimiak
authors.forename: Dinesh
authors.initials: D
authors.lastname: Christendat
mesh_terms: D000429:Alcohol Oxidoreductases / Q000737:chemistry* / Q000235:genetics*; D001216:Asparagine / Q000737:chemistry; D001499:Bayes Theorem; D002384:Catalysis; D002942:Circular Dichroism; D003001:Cloning, Molecular; D018360:Crystallography, X-Ray; D006193:Haemophilus influenzae / Q000201:enzymology*; D006540:Herbicides / Q000737:chemistry; D006863:Hydrogen-Ion Concentration; D007477:Ions; D007700:Kinetics; D008239:Lysine / Q000737:chemistry; D008958:Models, Molecular; D016296:Mutagenesis; D016297:Mutagenesis, Site-Directed; D009243:NAD / Q000737:chemistry; D009249:NADP / Q000737:chemistry; D010100:Oxygen / Q000737:chemistry; D010802:Phylogeny; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013379:Substrate Specificity; D013696:Temperature
chemical_list: D006540:Herbicides; D007477:Ions; D009243:NAD; D009249:NADP; D001216:Asparagine; D000429:Alcohol Oxidoreductases; C022641:Shikimate dehydrogenase; D008239:Lysine; D010100:Oxygen
references.citation: Biochemistry. 1971 May 11;10(10):1947-52
references.pmid: 4397925
references.citation: J Infect Dis. 2002 Feb 15;185 Suppl 1:S25-36
references.pmid: 11865437
references.citation: Plant Cell. 1995 Jul;7(7):907-919
references.pmid: 12242393
references.citation: Exp Parasitol. 2000 Jan;94(1):23-32
references.pmid: 10631077
references.citation: Structure. 2000 May 15;8(5):R105-10
references.pmid: 10801499
references.citation: Acta Crystallogr D Biol Crystallogr. 2002 Nov;58(Pt 11):1937-40
references.pmid: 12393925
references.citation: Int J Parasitol. 2004 Jan;34(1):5-13
references.pmid: 14711585
references.citation: J Biomol NMR. 1996 Dec;8(4):477-86
references.pmid: 9008363
references.citation: Acta Crystallogr D Biol Crystallogr. 1999 Apr;55(Pt 4):849-61
references.pmid: 10089316
references.citation: Microbiol Rev. 1985 Sep;49(3):338-58
references.pmid: 2931582
references.citation: Nat Struct Biol. 1999 May;6(5):458-63
references.pmid: 10331874
references.citation: Acta Crystallogr A. 1991 Mar 1;47 ( Pt 2):110-9
references.pmid: 2025413
references.citation: Structure. 2003 Aug;11(8):902-3
references.pmid: 12906820
references.citation: J Biol Chem. 2000 Aug 11;275(32):24608-12
references.pmid: 10827167
references.citation: Annu Rev Plant Physiol Plant Mol Biol. 1999 Jun;50:473-503
references.pmid: 15012217
references.citation: Protein Expr Purif. 2002 Jun;25(1):8-15
references.pmid: 12071693
references.citation: Biochem J. 1996 Apr 1;315 ( Pt 1):195-205
references.pmid: 8670107
references.citation: J Biol Chem. 2005 Mar 18;280(11):10340-9
references.pmid: 15623532
references.citation: J Biol Chem. 2003 May 23;278(21):19463-72
references.pmid: 12637497
references.citation: Biochem J. 2000 Aug 1;349 Pt 3:853-61
references.pmid: 10903148
references.citation: Biochemistry. 1998 Nov 10;37(45):15703-12
references.pmid: 9843375
references.citation: Curr Opin Struct Biol. 1995 Dec;5(6):775-83
references.pmid: 8749365