Molecular structure of an N-formyltransferase from Providencia alcalifaciens O30. 2015

Nicholas A Genthe, and James B Thoden, and Matthew M Benning, and Hazel M Holden
Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, 53706.

The existence of N-formylated sugars in the O-antigens of Gram-negative bacteria has been known since the middle 1980s, but only recently have the biosynthetic pathways for their production been reported. In these pathways, glucose-1-phosphate is first activated by attachment to a dTMP moiety. This step is followed by a dehydration reaction and an amination. The last step in these pathways is catalyzed by N-formyltransferases that utilize N(10) -formyltetrahydrofolate as the carbon source. Here we describe the three-dimensional structure of one of these N-formyltransferases, namely VioF from Providencia alcalifaciens O30. Specifically, this enzyme catalyzes the conversion of dTDP-4-amino-4,6-dideoxyglucose (dTDP-Qui4N) to dTDP-4,6-dideoxy-4-formamido-d-glucose (dTDP-Qui4NFo). For this analysis, the structure of VioF was solved to 1.9 Å resolution in both its apoform and in complex with tetrahydrofolate and dTDP-Qui4N. The crystals used in the investigation belonged to the space group R32 and demonstrated reticular merohedral twinning. The overall catalytic core of the VioF subunit is characterized by a six stranded mixed β-sheet flanked on one side by three α-helices and on the other side by mostly random coil. This N-terminal domain is followed by an α-helix and a β-hairpin that form the subunit:subunit interface. The active site of the enzyme is shallow and solvent-exposed. Notably, the pyranosyl moiety of dTDP-Qui4N is positioned into the active site by only one hydrogen bond provided by Lys 77. Comparison of the VioF model to that of a previously determined N-formyltransferase suggests that substrate specificity is determined by interactions between the protein and the pyrophosphoryl group of the dTDP-sugar substrate.

UI MeSH Term Description Entries
D008958 Models, Molecular Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures. Molecular Models,Model, Molecular,Molecular Model
D011487 Protein Conformation The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain). Conformation, Protein,Conformations, Protein,Protein Conformations
D011532 Providencia Gram-negative rods isolated from human urine and feces.
D005575 Formyltetrahydrofolates Tetrahydrofolates which are substituted by a formyl group at either the nitrogen atom in the 5 position or the nitrogen atom in the 10 position. N(5)-Formyltetrahydrofolate is leucovorin (citrovorum factor) while N(10)-formyltetrahydrofolate is an active coenzyme which functions as a carrier of the formyl group in a number of enzymatic reactions. Formyltetrahydrofolic Acids,N(10)-Formyltetrahydrofolate
D001426 Bacterial Proteins Proteins found in any species of bacterium. Bacterial Gene Products,Bacterial Gene Proteins,Gene Products, Bacterial,Bacterial Gene Product,Bacterial Gene Protein,Bacterial Protein,Gene Product, Bacterial,Gene Protein, Bacterial,Gene Proteins, Bacterial,Protein, Bacterial,Proteins, Bacterial
D018360 Crystallography, X-Ray The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed) X-Ray Crystallography,Crystallography, X Ray,Crystallography, Xray,X Ray Crystallography,Xray Crystallography,Crystallographies, X Ray,X Ray Crystallographies
D019877 Hydroxymethyl and Formyl Transferases Enzymes that catalyze the transfer of hydroxymethyl or formyl groups. EC 2.1.2. Formyl Transferase,Formyltransferase,Hydroxymethyl Transferase,Hydroxymethyl and Formyl Transferase,Hydroxymethyltransferase,Transhydroxymethylase,Formyl Transferases,Formyltransferases,Hydroxymethyl Transferases,Hydroxymethyltransferases,Transformylase,Transformylases,Transhydroxymethylases,Transferase, Formyl,Transferase, Hydroxymethyl,Transferases, Formyl,Transferases, Hydroxymethyl
D020134 Catalytic Domain The region of an enzyme that interacts with its substrate to cause the enzymatic reaction. Active Site,Catalytic Core,Catalytic Region,Catalytic Site,Catalytic Subunit,Reactive Site,Active Sites,Catalytic Cores,Catalytic Domains,Catalytic Regions,Catalytic Sites,Catalytic Subunits,Core, Catalytic,Cores, Catalytic,Domain, Catalytic,Domains, Catalytic,Reactive Sites,Region, Catalytic,Regions, Catalytic,Site, Active,Site, Catalytic,Site, Reactive,Sites, Active,Sites, Catalytic,Sites, Reactive,Subunit, Catalytic,Subunits, Catalytic

Related Publications

Nicholas A Genthe, and James B Thoden, and Matthew M Benning, and Hazel M Holden
May 2006, Carbohydrate research,
Nicholas A Genthe, and James B Thoden, and Matthew M Benning, and Hazel M Holden
January 2015, Biochemistry,
Nicholas A Genthe, and James B Thoden, and Matthew M Benning, and Hazel M Holden
June 2012, Biochemistry. Biokhimiia,
Nicholas A Genthe, and James B Thoden, and Matthew M Benning, and Hazel M Holden
January 2001, Journal of medical microbiology,
Nicholas A Genthe, and James B Thoden, and Matthew M Benning, and Hazel M Holden
January 2004, Carbohydrate research,
Nicholas A Genthe, and James B Thoden, and Matthew M Benning, and Hazel M Holden
December 1979, Journal of clinical microbiology,
Nicholas A Genthe, and James B Thoden, and Matthew M Benning, and Hazel M Holden
October 2002, Carbohydrate research,
Nicholas A Genthe, and James B Thoden, and Matthew M Benning, and Hazel M Holden
January 2012, Carbohydrate research,
Nicholas A Genthe, and James B Thoden, and Matthew M Benning, and Hazel M Holden
July 2006, Carbohydrate research,
Copied contents to your clipboard!