Show legend Show as text

Structure type: monomer
Trivial name: UDP-hexos-4-ulose sugar, UDP-2-acetamido-2,6-dideoxy-β-L-arabino-hex-4-ulose, UDP-2-acetamido-2,6-dideoxy-β-L-arabino-hexos-4-ulose, UDP-2-acetamido-2,6-dideoxy-β-L-arabino-4-hexulose
Compound class: nucleoside diphosphate sugar

• Article ID: 3141
  McNally DJ, Schoenhofen IC, Mulrooney EF, Whitfield DM, Vinogradov E, Lam JS, Logan SM, Brisson JR "Identification of Labile UDP-Ketosugars in Helicobacter pylori, Campylobacter jejuni and Pseudomonas aeruginosa: Key Metabolites used to make Glycan Virulence Factors" - Chembiochem: a European Journal of Chemical Biology 7(12) (2006) 1865-1868
  

  biosynthesis, carbohydrates, Pseudomonas, Campylobacter jejuni, bacteria, Helicobacter pylori, metabolite, hexos-4-ulose

  NCBI PubMed ID: 17031886
  Publication DOI: 10.1002/cbic.200600298
  Journal NLM ID: 100937360
  Publisher: Weinheim, Germany: Wiley Interscience
  Correspondence: david.mcnally@nrc-cnrc.gc.ca
  Institutions: National Research Council of Canada-Institute for Biological Sciences, Ottawa ON, K1A 0R6, Canada, Fax: (+1) 613-952-9092
  Methods: NMR, genetic methods
  
   
  
  Helicobacter pylori, Campylobacter jejuni, Pseudomonas aeruginosa
  CSDB ID 21190 (all data & tools)
• Article ID: 3196
  Schoenhofen IC, Lunin VV, Julien JP, Li Y, Ajamian E, Matte A, Cygler M, Brisson JR, Aubry A, Logan SM, Bhatia S, Wakarchuk WW, Young NM "Structural and functional characterization of PseC, an aminotransferase involved in the biosynthesis of pseudaminic acid, an essential flagellar modification in Helicobacter pylori" - Journal of Biological Chemistry 281(13) (2006) 8907-8916
  

  Helicobacter pylori flagellin is heavily glycosylated with the novel sialic acid-like nonulosonate, pseudaminic acid (Pse). The glycosylation process is essential for assembly of functional flagellar filaments and consequent bacterial motility. Because motility is a key virulence factor for this and other important pathogens, the Pse biosynthetic pathway offers potential for novel therapeutic targets. From recent NMR analyses, we determined that the conversion of UDP-α-D-Glc-NAc to the central intermediate in the pathway, UDP-4-amino-4,6-dideoxy-β-L-AltNAc, proceeds by formation of UDP-2-acetamido-2,6-dideoxy-β-L-arabino-4-hexulose by the dehydratase/epimerase PseB (HP0840) followed with amino transfer by the aminotransferase, PseC (HP0366). The central role of PseC in the H. pylori Pse biosynthetic pathway prompted us to determine crystal structures of the native protein, its complexes with pyridoxal phosphate alone and in combination with the UDP-4-amino-4,6-dideoxy-β-L-AltNAc product, the latter being converted to the external aldimine form in the active site of the enzyme. In the binding site, the AltNAc sugar ring adopts a (4)C(1) chair conformation, which is different from the predominant (1)C(4) form found in solution. The enzyme forms a homodimer where each monomer contributes to the active site, and these structures have permitted the identification of key residues involved in stabilization, and possibly catalysis, of the β-L-arabino intermediate during the amino transfer reaction. The essential role of Lys(183) in the catalytic event was confirmed by site-directed mutagenesis. This work presents for the first time a nucleotide-sugar aminotransferase co-crystallized with its natural ligand, and, in conjunction with the recent functional characterization of this enzyme, these results will assist in elucidating the aminotransferase reaction mechanism within the Pse biosynthetic pathway.

  biosynthesis, pseudaminic acid, Helicobacter pylori, Flagellin, aminotransferase, PseC

  NCBI PubMed ID: 16421095
  Publication DOI: 10.1074/jbc.M512987200
  Journal NLM ID: 2985121R
  Publisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
  Correspondence: Martin.Young@nrc-cnrc.gc.ca
  Institutions: Institute for Biological Sciences, National Research Council, Ottawa, Ontario K1A 0R6, Biotechnology Research, Institute, National Research Council, Montreal, Quebec H4P 2R2, Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
  Methods: NMR-2D, NMR, SDS-PAGE, genetic methods, biochemical methods, capillary electrophoresis (CE), crystallization
  
   
  
  Helicobacter pylori 26695/1061
  CSDB ID 20218 (all data & tools)
• Article ID: 3404
  Guerry P, Ewing CP, Schoenhofen IC, Logan SM "Protein glycosylation in Campylobacter jejuni: partial suppression of pglF by mutation of pseC" - Journal of Bacteriology 189(18) (2007) 6731-6733
  

  Campylobacter jejuni has systems for N- and O-linked protein glycosylation. Although biochemical evidence demonstrated that a pseC mutant in the O-linked pathway accumulated the product of pglF in the N-linked pathway, analyses of transformation frequencies and glycosylation statuses of N-glycosylated proteins indicated a partial suppression of pglF by pseC

  biosynthesis, Bacterial Proteins, Campylobacter jejuni, glycosylation

  NCBI PubMed ID: 17631632
  Journal NLM ID: 2985120R
  Publisher: American Society for Microbiology
  Correspondence: guerryp@nmrc.navy.mil
  Institutions: Enteric Diseases Department, Naval Medical Research Center, 503 Robert Grant Ave., Silver Spring, MD 20910, USA
  Methods: PCR, serological methods, genetic methods
  
   
  
  Campylobacter jejuni
  CSDB ID 21963 (all data & tools)
• Article ID: 3506
  Liu B, Knirel YA, Feng L, Perepelov AV, Senchenkova SN, Wang Q, Reeves P, Wang L "Structure and genetics of Shigella O antigens" - FEMS Microbiology Reviews 32(4) (2008) 627-653
  

  This review covers the O antigens of the 46 serotypes of Shigella, but those of most Shigella flexneri are variants of one basic structure, leaving 34 Shigella distinct O antigens to review, together with their gene clusters. Several of the structures and gene clusters are reported for the first time and this is the first such group for which structures and DNA sequences have been determined for all O antigens. Shigella strains are in effect Escherichia coli with a specific mode of pathogenicity, and 18 of the 34 O antigens are also found in traditional E. coli. Three are very similar to E. coli O antigens and 13 are unique to Shigella strains. The O antigen of Shigella sonnei is quite atypical for E. coli and is thought to have transferred from Plesiomonas. The other 12 O antigens unique to Shigella strains have structures that are typical of E. coli, but there are considerably more anomalies in their gene clusters, probably reflecting recent modification of the structures. Having the complete set of structures and genes opens the way for experimental studies on the role of this diversity in pathogenicity.

  structure, O antigen, Shigella, O antigen gene cluster, O antigen diversity

  NCBI PubMed ID: 18422615
  Publication DOI: 10.1111/j.1574-6976.2008.00114.x
  Journal NLM ID: 8902526
  Publisher: Oxford University Press
  Correspondence: wanglei@nankai.edu.cn
  Institutions: TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China, TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China.
  Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, ESI-MS, serological methods, genetic methods, biochemical methods
  
   
  
  Shigella
  CSDB ID 23110 (all data & tools)
• Article ID: 3516
  McNally DJ, Schoenhofen IC, Houliston RS, Khieu NH, Whitfield DM, Logan SM, Jarrell HC, Brisson JR "CMP-Pseudaminic Acid is a Natural Potent Inhibitor of PseB, the First Enzyme of the Pseudaminic Acid Pathway in Campylobacter jejuni and Helicobacter pylori" - ChemMedChem 3(1) (2008) 55-59
  

  No abstract available

  Research, acid, Campylobacter, Campylobacter jejuni, NMR spectroscopy, pseudaminic acid, biological, Helicobacter pylori, enzyme, natural, pathway, Helicobacter, inhibitors, STD, STD NMR spectroscopy, potent

  NCBI PubMed ID: 17893902
  Journal NLM ID: 101259013
  Publisher: Wiley-VCH
  Correspondence: david.mcnally@nrc-cnrc.gc.ca
  Institutions: National Research Council of Canada-Institute for Biological Sciences, Ottawa ON, K1A 0R6, Canada, Fax: (+1) 613-952-9092
  Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, NMR-1D, genetic methods, biochemical methods, STD NMR
  
   
  
  Campylobacter jejuni, Helicobacter pylori
  CSDB ID 23133 (all data & tools)
• Article ID: 3767
  Rangarajan ES, Proteau A, Cui Q, Logan SM, Potetinova Z, Whitfield D, Purisima EO, Cygler M, Matte A, Sulea T, Schoenhofen IC "Structural and Functional Analysis of Campylobacter jejuni PseG: A UDP-sugar hydrolase from the pseudaminic acid biosynthetic pathway" - Journal of Biological Chemistry 284(31) (2009) 20989-21000
  

  Flagella of the bacteria Helicobacter pylori and Campylobacter jejuni are important virulence determinants, whose proper assembly and function are dependent upon glycosylation at multiple positions by sialic acid-like sugars, such as 5,7-diacetamido-3,5,7,9-tetradeoxy-l-glycero-l-manno-nonulosonic acid (pseudaminic acid (Pse)). The fourth enzymatic step in the pseudaminic acid pathway, the hydrolysis of UDP-2,4-diacetamido-2,4,6-trideoxy-β-L-altropyranose to generate 2,4-diacetamido-2,4,6-trideoxy-l-altropyranose, is performed by the nucleotide sugar hydrolase PseG. To better understand the molecular basis of the PseG catalytic reaction, we have determined the crystal structures of C. jejuni PseG in apo-form and as a complex with its UDP product at 1.8 and 1.85 A resolution, respectively. In addition, molecular modeling was utilized to provide insight into the structure of the PseG-substrate complex. This modeling identifies a His(17)-coordinated water molecule as the putative nucleophile and suggests the UDP-sugar substrate adopts a twist-boat conformation upon binding to PseG, enhancing the exposure of the anomeric bond cleaved and favoring inversion at C-1. Furthermore, based on these structures a series of amino acid substitution derivatives were constructed, altering residues within the active site, and each was kinetically characterized to examine its contribution to PseG catalysis. In conjunction with structural comparisons, the almost complete inactivation of the PseG H17F and H17L derivatives suggests that His(17) functions as an active site base, thereby activating the nucleophilic water molecule for attack of the anomeric C-O bond of the UDP-sugar. As the PseG structure reveals similarity to those of glycosyltransferase family-28 members, in particular that of Escherichia coli MurG, these findings may also be of relevance for the mechanistic understanding of this important enzyme family.

  Campylobacter jejuni, pseudaminic acid, crystal structure, Helicobacter pylori, glycosyltransferase, modeling, hydrolase, flagella

  NCBI PubMed ID: 19483088
  Journal NLM ID: 2985121R
  Publisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
  Correspondence: traian.sulea@nrc-cnrc.gc.ca; ian.schoenhofen@nrc-cnrc.gc.ca
  Institutions: From the Department of Biochemistry, McGill University, Montreal, Quebec H3G 1V6
  Methods: X-ray, SDS-PAGE, MD simulations, genetic methods, molecular modeling, CD, crystallization
  
   
  
  Campylobacter jejuni 11168
  CSDB ID 24189 (all data & tools)
• Article ID: 3824
  Brisson JR, Vinogradov E, McNally DJ, Khieu NH, Schoenhofen IC, Logan SM, Jarrell H "The application of NMR spectroscopy to functional glycomics" - Book: Methods in Molecular Biology (2010) Vol. 600, 155-173
  

  Glycomics which is the study of saccharides and genes responsible for their formation requires the continuous development of rapid and sensitive methods for the identification of glycan structures. It involves glycoanalysis which relies upon the development of methods for determining the structure and interactions of carbohydrates. For the application of functional glycomics to microbial virulence, carbohydrates and their associated metabolic and carbohydrate processing enzymes and respective genes can be identified and exploited as targets for drug discovery, glyco-engineering, vaccine design, and detection and diagnosis of diseases. Glycomics also encompasses the detailed understanding of carbohydrate-protein interactions and this knowledge can be applied to research efforts focused toward the development of vaccines and immunological therapies to alleviate infectious diseases.

  NMR, structural analysis, molecular modeling, polysaccharides, HR-MAS, Glycomics, glycans, glycoanalysis, protein–carbohydrate interactions

  NCBI PubMed ID: 19882127
  Publisher: Totowa, NJ: Humana Press
  Editors: Holst O, Walker JM, Beck A
  Institutions: Institute for Biological Sciences, National Research Council Canada, Ottawa, Ontario, Canada
  Methods: NMR
  
   
  
  Helicobacter pylori, Campylobacter jejuni
  CSDB ID 25544 (all data & tools)
• Article ID: 4356
  Miyafusa T, Caaveiro JM, Tanaka Y, Tsumoto K "Crystal structure of the enzyme CapF of Staphylococcus aureus reveals a unique architecture composed of two functional domains" - Biochemical Journal 443(3) (2012) 671-680
  

  CP (capsular polysaccharide) is an important virulence factor during infections by the bacterium Staphylococcus aureus. The enzyme CapF is an attractive therapeutic candidate belonging to the biosynthetic route of CP of pathogenic strains of S. aureus. In the present study, we report two independent crystal structures of CapF in an open form of the apoenzyme. CapF is a homodimer displaying a characteristic dumb-bell-shaped architecture composed of two domains. The N-terminal domain (residues 1-252) adopts a Rossmann fold belonging to the short-chain dehydrogenase/reductase family of proteins. The C-terminal domain (residues 252-369) displays a standard cupin fold with a Zn2+ ion bound deep in the binding pocket of the beta-barrel. Functional and thermodynamic analyses indicated that each domain catalyses separate enzymatic reactions. The cupin domain is necessary for the C3-epimerization of UDP-4-hexulose. Meanwhile, the N-terminal domain catalyses the NADPH-dependent reduction of the intermediate species generated by the cupin domain. Analysis by ITC (isothermal titration calorimetry) revealed a fascinating thermodynamic switch governing the attachment and release of the coenzyme NADPH during each catalytic cycle. These observations suggested that the binding of coenzyme to CapF facilitates a disorder-to-order transition in the catalytic loop of the reductase (N-terminal) domain. We anticipate that the present study will improve the general understanding of the synthesis of CP in S. aureus and will aid in the design of new therapeutic agents against this pathogenic bacterium.

  capsular polysaccharide, crystal structure, Staphylococcus aureus, bifunctional enzyme, cupin fold, short-chain dehydrogenase/reductase

  NCBI PubMed ID: 22320426
  Publication DOI: 10.1042/BJ20112049
  Journal NLM ID: 2984726R
  Publisher: London, UK : Published by Portland Press on behalf of the Biochemical Society
  Correspondence: jmmc@ims.u-tokyo.ac.jp; tsumoto@ims.u-tokyo.ac.jp
  Institutions: Department of Medical Genome Science, School of Frontier Sciences, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
  Methods: genetic methods, biochemical methods, HPLC, colorimetry, crystallization, ITC
  
   
  
  Staphylococcus aureus
  CSDB ID 27254 (all data & tools)

Show legend Show as text

Structure type: monomer
Trivial name: UDP-4-keto-6-deoxy-L-AltNAc (UDP-2-acetamido-2,6-dideoxy-β-L-arabino-hex-4-ulose)

• Article ID: 4770
  Li Z, Hwang S, Ericson J, Bowler K, Bar-Peled M "Pen and Pal Are Nucleotide-Sugar Dehydratases That Convert UDP-GlcNAc to UDP-6-Deoxy-D-GlcNAc-5,6-ene and Then to UDP-4-Keto-6-deoxy-L-AltNAc for CMP-Pseudaminic Acid Synthesis in Bacillus thuringiensis" - Journal of Biological Chemistry 290(2) (2015) 691-704
  

  CMP-pseudaminic acid is a precursor required for the O-glycosylation of flagellin in some pathogenic Gram-negative bacteria, a process known to be critical in bacterial motility and infection. However, little is known about flagellin glycosylation in Gram-positive bacteria. Here, we identified and functionally characterized an operon, named Bti_pse, in Bacillus thuringiensis israelensis ATCC 35646, which encodes seven different enzymes that together convert UDP-GlcNAc to CMP-pseudaminic acid. In contrast, Gram-negative bacteria complete this reaction with six enzymes. The first enzyme, which we named Pen, converts UDP-D-GlcNAc to an uncommon UDP-sugar, UDP-6-deoxy-D-GlcNAc-5,6-ene. Pen contains strongly bound NADP+ and has distinct UDP-GlcNAc 4-oxidase, 5,6-dehydratase, and 4-reductase activities. The second enzyme, which we named Pal, converts UDP-6-deoxy-D-GlcNAc-5,6-ene to UDP-4-keto-6-deoxy-L-AltNAc. Pal is NAD+-dependent and has distinct UDP-6-deoxy-D-GlcNAc-5,6-ene 4-oxidase, 5,6-reductase, and 5-epimerase activities. We also show here using NMR spectroscopy and mass spectrometry that in B. thuringiensis, the enzymatic product of Pen and Pal, UDP-4-keto-6-deoxy-L-AltNAc, is converted to CMP-pseudaminic acid by the sequential activities of a C4?-transaminase (Pam), a 4-N-acetyltransferase (Pdi), a UDP-hydrolase (Phy), an enzyme (Ppa) that adds phosphoenolpyruvate to form pseudaminic acid, and finally a cytidylyltransferase that condenses CTP to generate CMP-pseudaminic acid. Knowledge of the distinct dehydratase-like enzymes Pen and Pal and their role in CMP-pseudaminic acid biosynthesis in Gram-positive bacteria provides a foundation to investigate the role of pseudaminic acid and flagellin glycosylation in Bacillus and their involvement in bacterial motility and pathogenicity.

  pseudaminic acid, Bacillus, aminotransferase, CMP-pseudaminic acid, flagellin glycosylation, dehydratase, enzyme catalysis, bacterial metabolism, Bacillus thuringiensis, carbohydrate biosynthesis, glycobiology, UDP-GlcNAc

  NCBI PubMed ID: 25414257
  Publication DOI: 10.1074/jbc.M114.612747
  Journal NLM ID: 2985121R
  Publisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
  Correspondence: peled@ccrc.uga.edu
  Institutions: Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, From the Department of Plant Biology and Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
  Methods: 13C NMR, 1H NMR, gel filtration, NMR-2D, PCR, SDS-PAGE, DNA techniques, kinetics assays, NMR-1D, genetic methods, biochemical methods, HPLC, UV, enzymatic analysis, LC-ESI-MS/MS, HILIC-HPLC-UV, HILIC-ESI-MS
  
   
  
  Bacillus thuringiensis sv. israelensis ATCC 35646
  CSDB ID 30802 (all data & tools)