Structural and Biochemical Investigation of PglF from Campylobacter jejuni Reveals a New Mechanism for a Member of the Short Chain Dehydrogenase/Reductase Superfamily

Riegert, Alexander S.; Thoden, James B.; Schoenhofen, Ian C.; Watson, David C.; Young, N. Martin; Tipton, Peter A.; Holden, Hazel M.

doi:10.1021/acs.biochem.7b00910

Title: Structural and Biochemical Investigation of PglF from Campylobacter jejuni Reveals a New Mechanism for a Member of the Short Chain Dehydrogenase/Reductase Superfamily

Journal Article · Fri Oct 20 00:00:00 EDT 2017 · Biochemistry

DOI:https://doi.org/10.1021/acs.biochem.7b00910· OSTI ID:1409106

Riegert, Alexander S. ^[1]; Thoden, James B. ^[1]; Schoenhofen, Ian C. ^[2]; Watson, David C. ^[2]; Young, N. Martin ^[2]; Tipton, Peter A. ^[3];

^[1]

Univ. of Wisconsin, Madison, WI (United States)
National Research Council Canada, Ottawa, ON (Canada)
Univ. of Missouri, Columbia, MO (United States)

Within recent years it has become apparent that protein glycosylation is not limited to eukaryotes. Indeed, in Campylobacter jejuni, a Gram-negative bacterium, more than 60 of its proteins are known to be glycosylated. One of the sugars found in such glycosylated proteins is 2,4-diacetamido-2,4,6-trideoxy-α-d-glucopyranose, hereafter referred to as QuiNAc4NAc. The pathway for its biosynthesis, initiating with UDP-GlcNAc, requires three enzymes referred to as PglF, PglE, and PlgD. The focus of this investigation is on PglF, an NAD+-dependent sugar 4,6-dehydratase known to belong to the short chain dehydrogenase/reductase (SDR) superfamily. Specifically, PglF catalyzes the first step in the pathway, namely, the dehydration of UDP-GlcNAc to UDP-2-acetamido-2,6-dideoxy-α-d-xylo-hexos-4-ulose. Most members of the SDR superfamily contain a characteristic signature sequence of YXXXK where the conserved tyrosine functions as a catalytic acid or a base. Strikingly, in PglF, this residue is a methionine. Here we describe a detailed structural and functional investigation of PglF from C. jejuni. For this investigation five X-ray structures were determined to resolutions of 2.0 Å or better. In addition, kinetic analyses of the wild-type and site-directed variants were performed. Furthermore, on the basis of the data reported herein, a new catalytic mechanism for a SDR superfamily member is proposed that does not require the typically conserved tyrosine residue.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH)

Grant/Contract Number:: AC02-06CH11357; GM115921

OSTI ID:: 1409106

Journal Information:: Biochemistry, Vol. 56, Issue 45; ISSN 0006-2960

Publisher:: American Chemical Society (ACS)Copyright Statement

Country of Publication:: United States

Language:: ENGLISH

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Cited by: 17 works

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References (43)

Carbohydrates in protein Neuberger, A. Biochemical Journal, Vol. 32, Issue 9 https://doi.org/10.1042/bj0321435	journal	September 1938
Protein glycosylation in bacteria: sweeter than ever Nothaft, Harald; Szymanski, Christine M. Nature Reviews Microbiology, Vol. 8, Issue 11 https://doi.org/10.1038/nrmicro2383	journal	October 2010
Bacterial Protein N -Glycosylation: New Perspectives and Applications Nothaft, Harald; Szymanski, Christine M. Journal of Biological Chemistry, Vol. 288, Issue 10 https://doi.org/10.1074/jbc.R112.417857	journal	January 2013
Campylobacter and bacterial gastroenteritis Galanis, Eleni Canadian Medical Association Journal, Vol. 177, Issue 6 https://doi.org/10.1503/cmaj.070660	journal	September 2007
Evidence for a system of general protein glycosylation in Campylobacter jejuni Szymanski, Christine M.; Yao, Ruijin; Ewing, Cheryl P. Molecular Microbiology, Vol. 32, Issue 5 https://doi.org/10.1046/j.1365-2958.1999.01415.x	journal	June 1999
Structure of the N-Linked Glycan Present on Multiple Glycoproteins in the Gram-negative Bacterium, Campylobacter jejuni Young, N. Martin; Brisson, Jean-Robert; Kelly, John Journal of Biological Chemistry, Vol. 277, Issue 45 https://doi.org/10.1074/jbc.M206114200	journal	November 2002
Structure of the external aldimine form of PglE, an aminotransferase required for N , N '-diacetylbacillosamine biosynthesis: Structure of the Aminotransferase PglE Riegert, Alexander S.; Young, N. Martin; Watson, David C. Protein Science, Vol. 24, Issue 10 https://doi.org/10.1002/pro.2745	journal	July 2015
Structure and Active Site Residues of PglD, an N -Acetyltransferase from the Bacillosamine Synthetic Pathway Required for N -Glycan Synthesis in Campylobacter jejuni ^, Rangarajan, Erumbi S.; Ruane, Karen M.; Sulea, Traian Biochemistry, Vol. 47, Issue 7 https://doi.org/10.1021/bi702032r	journal	January 2008
Crystal Structure and Catalytic Mechanism of PglD from Campylobacter jejuni Olivier, Nelson B.; Imperiali, Barbara Journal of Biological Chemistry, Vol. 283, Issue 41 https://doi.org/10.1074/jbc.M801207200	journal	October 2008
Functional Characterization of Dehydratase/Aminotransferase Pairs from Helicobacter and Campylobacter Schoenhofen, Ian C.; McNally, David J.; Vinogradov, Evgeny Journal of Biological Chemistry, Vol. 281, Issue 2 https://doi.org/10.1074/jbc.M511021200	journal	November 2005
Mechanisms of enzymatic CO bond cleavages in deoxyhexose biosynthesis He, Xuemei; Liu, Hung-wen Current Opinion in Chemical Biology, Vol. 6, Issue 5 https://doi.org/10.1016/S1367-5931(02)00367-8	journal	October 2002
Short-chain dehydrogenases/reductases (SDRs): Coenzyme-based functional assignments in completed genomes Kallberg, Yvonne; Oppermann, Udo; Jörnvall, Hans European Journal of Biochemistry, Vol. 269, Issue 18 https://doi.org/10.1046/j.1432-1033.2002.03130.x	journal	September 2002
Short-chain dehydrogenase/reductase (SDR) relationships: A large family with eight clusters common to human, animal, and plant genomes Kallberg, Yvonne; Oppermann, Udo; Jörnvall, Hans Protein Science, Vol. 11, Issue 3 https://doi.org/10.1110/ps.26902	journal	March 2002
Short-chain dehydrogenases/reductases (SDR): the 2002 update Oppermann, Udo; Filling, Charlotta; Hult, Malin Chemico-Biological Interactions, Vol. 143-144 https://doi.org/10.1016/S0009-2797(02)00164-3	journal	February 2003
Medium- and short-chain dehydrogenase/reductase gene and protein families: The SDR superfamily: functional and structural diversity within a family of metabolic and regulatory enzymes Kavanagh, K. L.; Jörnvall, H.; Persson, B. Cellular and Molecular Life Sciences, Vol. 65, Issue 24 https://doi.org/10.1007/s00018-008-8588-y	journal	November 2008
Classification of the short-chain dehydrogenase/reductase superfamily using hidden Markov models: SDR classification using HMM Kallberg, Yvonne; Oppermann, Udo; Persson, Bengt FEBS Journal, Vol. 277, Issue 10 https://doi.org/10.1111/j.1742-4658.2010.07656.x	journal	April 2010
Steroid dehydrogenase structures, mechanism of action, and disease Duax, William L.; Ghosh, Debashis; Pletnev, Vladimir Vitamins & Hormones https://doi.org/10.1016/S0083-6729(00)58023-6	book	January 2000
Rational proteomics I. Fingerprint identification and cofactor specificity in the short-chain oxidoreductase (SCOR) enzyme family Duax, William L.; Pletnev, Vladimir; Addlagatta, Anthony Proteins: Structure, Function, and Genetics, Vol. 53, Issue 4 https://doi.org/10.1002/prot.10512	journal	November 2003
Structural and kinetic analysis of Escherichia coli GDP-mannose 4,6 dehydratase provides insights into the enzyme’s catalytic mechanism and regulation by GDP-fucose Somoza, John R.; Menon, Saurabh; Schmidt, Holly Structure, Vol. 8, Issue 2 https://doi.org/10.1016/S0969-2126(00)00088-5	journal	February 2000
The crystal structure of dTDP-d-glucose 4,6-dehydratase (RmlB) from Salmonella enterica serovar typhimurium, the second enzyme in the dTDP-l-rhamnose pathway Allard, Simon T. M.; Giraud, Marie-France; Whitfield, Chris Journal of Molecular Biology, Vol. 307, Issue 1 https://doi.org/10.1006/jmbi.2000.4470	journal	March 2001
Dehydration Is Catalyzed by Glutamate-136 and Aspartic Acid-135 Active Site Residues in Escherichia coli dTDP-Glucose 4,6-Dehydratase ^† Gross, Jeffrey W.; Hegeman, Adrian D.; Gerratana, Barbara Biochemistry, Vol. 40, Issue 42 https://doi.org/10.1021/bi011138c	journal	October 2001
Probing Catalysis by Escherichia coli dTDP-Glucose-4,6-dehydratase: Identification and Preliminary Characterization of Functional Amino Acid Residues at the Active Site ^† Hegeman, Adrian D.; Gross, Jeffrey W.; Frey, Perry A. Biochemistry, Vol. 40, Issue 22 https://doi.org/10.1021/bi010441a	journal	June 2001
Toward a Structural Understanding of the Dehydratase Mechanism Allard, Simon T. M.; Beis, Konstantinos; Giraud, Marie-France Structure, Vol. 10, Issue 1 https://doi.org/10.1016/S0969-2126(01)00694-3	journal	January 2002
Concerted and Stepwise Dehydration Mechanisms Observed in Wild-Type and Mutated Escherichia coli dTDP-Glucose 4,6-Dehydratase ^† Hegeman, Adrian D.; Gross, Jeffrey W.; Frey, Perry A. Biochemistry, Vol. 41, Issue 8 https://doi.org/10.1021/bi011748c	journal	February 2002
Structure of the MUR1 GDP-Mannose 4,6-Dehydratase from Arabidopsis thaliana : Implications for Ligand Binding and Specificity Mulichak, Anne M.; Bonin, Christopher P.; Reiter, Wolf-Dieter Biochemistry, Vol. 41, Issue 52 https://doi.org/10.1021/bi0266683	journal	December 2002
The Structure of NADH in the Enzyme dTDP- d -glucose Dehydratase (RmlB) Beis, Konstantinos; Allard, Simon T. M.; Hegeman, Adrian D. Journal of the American Chemical Society, Vol. 125, Issue 39 https://doi.org/10.1021/ja035796r	journal	October 2003
High Resolution X-ray Structure of dTDP-Glucose 4,6-Dehydratase from Streptomyces venezuelae Allard, Simon T. M.; Cleland, W. W.; Holden, Hazel M. Journal of Biological Chemistry, Vol. 279, Issue 3 https://doi.org/10.1074/jbc.M310134200	journal	October 2003
Crystal structure of a tetrameric GDP-D-mannose 4,6-dehydratase from a bacterial GDP-D-rhamnose biosynthetic pathway Webb, N. A. Protein Science, Vol. 13, Issue 2 https://doi.org/10.1110/ps.03393904	journal	February 2004
Crystal Structure at 1.8 Å Resolution of CDP- d -Glucose 4,6-Dehydratase from Yersinia pseudotuberculosis ^† ^, ^‡ Vogan, Erik M.; Bellamacina, Cornelia; He, Xuemei Biochemistry, Vol. 43, Issue 11 https://doi.org/10.1021/bi035547f	journal	March 2004
Structure of CDP- D -glucose 4,6-dehydratase from Salmonella typhi complexed with CDP- D -xylose Koropatkin, Nicole M.; Holden, Hazel M. Acta Crystallographica Section D Biological Crystallography, Vol. 61, Issue 4 https://doi.org/10.1107/S0907444904033876	journal	March 2005
Quaternary assembly and crystal structure of GDP-d-mannose 4,6 dehydratase from Paramecium bursaria Chlorella virus Rosano, Camillo; Zuccotti, Simone; Sturla, Laura Biochemical and Biophysical Research Communications, Vol. 339, Issue 1 https://doi.org/10.1016/j.bbrc.2005.11.009	journal	January 2006
Mechanistic studies on PseB of pseudaminic acid biosynthesis: A UDP-N-acetylglucosamine 5-inverting 4,6-dehydratase Morrison, James P.; Schoenhofen, Ian C.; Tanner, Martin E. Bioorganic Chemistry, Vol. 36, Issue 6 https://doi.org/10.1016/j.bioorg.2008.08.004	journal	December 2008
Dynamic elements govern the catalytic activity of CapE, a capsular polysaccharide-synthesizing enzyme from Staphylococcus aureus Miyafusa, Takamitsu; Caaveiro, Jose M. M.; Tanaka, Yoshikazu FEBS Letters, Vol. 587, Issue 23 https://doi.org/10.1016/j.febslet.2013.10.009	journal	October 2013
Crystal structure of the capsular polysaccharide synthesizing protein CapE of Staphylococcus aureus Miyafusa, Takamitsu; Caaveiro, Jose M. M.; Tanaka, Yoshikazu Bioscience Reports, Vol. 33, Issue 3 https://doi.org/10.1042/BSR20130017	journal	June 2013
Structure-Function Studies of Two Novel UDP-GlcNAc C6 Dehydratases/C4 Reductases Creuzenet, Carole; Urbanic, Robert V.; Lam, Joseph S. Journal of Biological Chemistry, Vol. 277, Issue 30 https://doi.org/10.1074/jbc.M202882200	journal	July 2002
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
Coot model-building tools for molecular graphics Emsley, Paul; Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132 https://doi.org/10.1107/S0907444904019158	journal	November 2004
Refinement of Macromolecular Structures by the Maximum-Likelihood Method Murshudov, G. N.; Vagin, A. A.; Dodson, E. J. Acta Crystallographica Section D Biological Crystallography, Vol. 53, Issue 3 https://doi.org/10.1107/S0907444996012255	journal	May 1997
[20] Processing of X-ray diffraction data collected in oscillation mode Otwinowski, Zbyszek; Minor, Wladek Macromolecular Crystallography Part A, 307-326 https://doi.org/10.1016/S0076-6879(97)76066-X	book	January 1997
Main-chain Bond Lengths and Bond Angles in Protein Structures Laskowski, Roman A.; Moss, David S.; Thornton, Janet M. Journal of Molecular Biology, Vol. 231, Issue 4 https://doi.org/10.1006/jmbi.1993.1351	journal	June 1993
Epimerases: structure, function and mechanism Allard, S. T. M.; Giraud, M. -F.; Naismith, J. H. Cellular and Molecular Life Sciences, Vol. 58, Issue 11 https://doi.org/10.1007/PL00000803	journal	October 2001
Mechanistic Roles of Tyrosine 149 and Serine 124 in UDP-galactose 4-Epimerase from Escherichia coli Liu, Yijeng; Thoden, James B.; Kim, Jeongmin Biochemistry, Vol. 36, Issue 35 https://doi.org/10.1021/bi970430a	journal	September 1997
Crystallographic Evidence for Tyr 157 Functioning as the Active Site Base in Human UDP−Galactose 4-Epimerase ^† ^, ^‡ Thoden, James B.; Wohlers, Travis M.; Fridovich-Keil, Judith L. Biochemistry, Vol. 39, Issue 19 https://doi.org/10.1021/bi000215l	journal	May 2000

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Title: Structural and Biochemical Investigation of PglF from Campylobacter jejuni Reveals a New Mechanism for a Member of the Short Chain Dehydrogenase/Reductase Superfamily

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