title: Neutron diffraction studies towards deciphering the protonation state of catalytic residues in the bacterial KDN9P phosphatase.
abstract: The enzyme 2-keto-3-deoxy-9-O-phosphonononic acid phosphatase (KDN9P phosphatase) functions in the pathway for the production of 2-keto-3-deoxy-D-glycero-D-galacto-nononic acid, a sialic acid that is important for the survival of commensal bacteria in the human intestine. The enzyme is a member of the haloalkanoate dehalogenase superfamily and represents a good model for the active-site protonation state of family members. Crystals of approximate dimensions 1.5 × 1.0 × 1.0 mm were obtained in space group P2(1)2(1)2, with unit-cell parameters a = 83.1, b = 108.9, c = 75.7 Å. A complete neutron data set was collected from a medium-sized H/D-exchanged crystal at BIODIFF at the Heinz Maier-Leibnitz Zentrum (MLZ), Garching, Germany in 18 d. Initial refinement to 2.3 Å resolution using only neutron data showed significant density for catalytically important residues.
authors.affiliation: Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131, USA.
authors.forename: Tyrel
authors.initials: T
authors.lastname: Bryan
authors.forename: Javier M
authors.initials: JM
authors.lastname: González
authors.forename: John P
authors.initials: JP
authors.lastname: Bacik
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: DeNunzio
authors.forename: Clifford J
authors.initials: CJ
authors.lastname: Unkefer
authors.forename: Tobias E
authors.initials: TE
authors.lastname: Schrader
authors.forename: Andreas
authors.initials: A
authors.lastname: Ostermann
authors.forename: Debra
authors.initials: D
authors.lastname: Dunaway-Mariano
authors.forename: Karen N
authors.initials: KN
authors.lastname: Allen
authors.forename: S Zoë
authors.initials: SZ
authors.lastname: Fisher
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics; D001665:Binding Sites; D020134:Catalytic Domain; D002413:Cations, Divalent; D003461:Crystallography; D041961:Deuterium Exchange Measurement; D004926:Escherichia coli / Q000235:genetics; D015870:Gene Expression; D008024:Ligands; D008274:Magnesium / Q000737:chemistry*; D008958:Models, Molecular; D033363:Neutron Diffraction; D010744:Phosphoric Monoester Hydrolases / Q000737:chemistry* / Q000235:genetics; D011485:Protein Binding; D011522:Protons; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics; D053838:Scattering, Small Angle; D012794:Sialic Acids / Q000737:chemistry*; D013379:Substrate Specificity
chemical_list: D001426:Bacterial Proteins; D002413:Cations, Divalent; D008024:Ligands; D011522:Protons; D011994:Recombinant Proteins; D012794:Sialic Acids; D010744:Phosphoric Monoester Hydrolases; D008274:Magnesium
keywords: KDN9P phosphatase; neutron diffraction; protonation states