Structural and Biochemical Investigation of PglF from Campylobacter jejuni Reveals a New Mechanism for a Member of the Short Chain Dehydrogenase/Reductase Superfamily
Abstract
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 thatmore »
- Authors:
-
[1]
- Univ. of Wisconsin, Madison, WI (United States)
- National Research Council Canada, Ottawa, ON (Canada)
- Univ. of Missouri, Columbia, MO (United States)
- Publication Date:
- Research Org.:
- Argonne National Laboratory (ANL), Argonne, IL (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH)
- OSTI Identifier:
- 1409106
- Grant/Contract Number:
- AC02-06CH11357; GM115921
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Biochemistry
- Additional Journal Information:
- Journal Volume: 56; Journal Issue: 45; Journal ID: ISSN 0006-2960
- Publisher:
- American Chemical Society (ACS)
- Country of Publication:
- United States
- Language:
- ENGLISH
- Subject:
- 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 59 BASIC BIOLOGICAL SCIENCES; hydroxyls; peptides and proteins; carbohydrates; monomers; chemical structure
Citation Formats
Riegert, Alexander S., Thoden, James B., Schoenhofen, Ian C., Watson, David C., Young, N. Martin, Tipton, Peter A., and Holden, Hazel M. Structural and Biochemical Investigation of PglF from Campylobacter jejuni Reveals a New Mechanism for a Member of the Short Chain Dehydrogenase/Reductase Superfamily. United States: N. p., 2017.
Web. doi:10.1021/acs.biochem.7b00910.
Riegert, Alexander S., Thoden, James B., Schoenhofen, Ian C., Watson, David C., Young, N. Martin, Tipton, Peter A., & Holden, Hazel M. Structural and Biochemical Investigation of PglF from Campylobacter jejuni Reveals a New Mechanism for a Member of the Short Chain Dehydrogenase/Reductase Superfamily. United States. https://doi.org/10.1021/acs.biochem.7b00910
Riegert, Alexander S., Thoden, James B., Schoenhofen, Ian C., Watson, David C., Young, N. Martin, Tipton, Peter A., and Holden, Hazel M. Fri .
"Structural and Biochemical Investigation of PglF from Campylobacter jejuni Reveals a New Mechanism for a Member of the Short Chain Dehydrogenase/Reductase Superfamily". United States. https://doi.org/10.1021/acs.biochem.7b00910. https://www.osti.gov/servlets/purl/1409106.
@article{osti_1409106,
title = {Structural and Biochemical Investigation of PglF from Campylobacter jejuni Reveals a New Mechanism for a Member of the Short Chain Dehydrogenase/Reductase Superfamily},
author = {Riegert, Alexander S. and Thoden, James B. and Schoenhofen, Ian C. and Watson, David C. and Young, N. Martin and Tipton, Peter A. and Holden, Hazel M.},
abstractNote = {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.},
doi = {10.1021/acs.biochem.7b00910},
journal = {Biochemistry},
number = 45,
volume = 56,
place = {United States},
year = {Fri Oct 20 00:00:00 EDT 2017},
month = {Fri Oct 20 00:00:00 EDT 2017}
}
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Works referenced in this record:
Carbohydrates in protein
journal, September 1938
- Neuberger, A.
- Biochemical Journal, Vol. 32, Issue 9
Protein glycosylation in bacteria: sweeter than ever
journal, October 2010
- Nothaft, Harald; Szymanski, Christine M.
- Nature Reviews Microbiology, Vol. 8, Issue 11
Bacterial Protein N -Glycosylation: New Perspectives and Applications
journal, January 2013
- Nothaft, Harald; Szymanski, Christine M.
- Journal of Biological Chemistry, Vol. 288, Issue 10
Campylobacter
and bacterial gastroenteritis
journal, September 2007
- Galanis, Eleni
- Canadian Medical Association Journal, Vol. 177, Issue 6
Evidence for a system of general protein glycosylation in Campylobacter jejuni
journal, June 1999
- Szymanski, Christine M.; Yao, Ruijin; Ewing, Cheryl P.
- Molecular Microbiology, Vol. 32, Issue 5
Structure of the N-Linked Glycan Present on Multiple Glycoproteins in the Gram-negative Bacterium, Campylobacter jejuni
journal, November 2002
- Young, N. Martin; Brisson, Jean-Robert; Kelly, John
- Journal of Biological Chemistry, Vol. 277, Issue 45
Structure of the external aldimine form of PglE, an aminotransferase required for N , N '-diacetylbacillosamine biosynthesis: Structure of the Aminotransferase PglE
journal, July 2015
- Riegert, Alexander S.; Young, N. Martin; Watson, David C.
- Protein Science, Vol. 24, Issue 10
Structure and Active Site Residues of PglD, an N -Acetyltransferase from the Bacillosamine Synthetic Pathway Required for N -Glycan Synthesis in Campylobacter jejuni ,
journal, January 2008
- Rangarajan, Erumbi S.; Ruane, Karen M.; Sulea, Traian
- Biochemistry, Vol. 47, Issue 7
Crystal Structure and Catalytic Mechanism of PglD from Campylobacter jejuni
journal, October 2008
- Olivier, Nelson B.; Imperiali, Barbara
- Journal of Biological Chemistry, Vol. 283, Issue 41
Functional Characterization of Dehydratase/Aminotransferase Pairs from Helicobacter and Campylobacter
journal, November 2005
- Schoenhofen, Ian C.; McNally, David J.; Vinogradov, Evgeny
- Journal of Biological Chemistry, Vol. 281, Issue 2
Mechanisms of enzymatic CO bond cleavages in deoxyhexose biosynthesis
journal, October 2002
- He, Xuemei; Liu, Hung-wen
- Current Opinion in Chemical Biology, Vol. 6, Issue 5
Short-chain dehydrogenases/reductases (SDRs): Coenzyme-based functional assignments in completed genomes
journal, September 2002
- Kallberg, Yvonne; Oppermann, Udo; Jörnvall, Hans
- European Journal of Biochemistry, Vol. 269, Issue 18
Short-chain dehydrogenase/reductase (SDR) relationships: A large family with eight clusters common to human, animal, and plant genomes
journal, March 2002
- Kallberg, Yvonne; Oppermann, Udo; Jörnvall, Hans
- Protein Science, Vol. 11, Issue 3
Short-chain dehydrogenases/reductases (SDR): the 2002 update
journal, February 2003
- Oppermann, Udo; Filling, Charlotta; Hult, Malin
- Chemico-Biological Interactions, Vol. 143-144
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
journal, November 2008
- Kavanagh, K. L.; Jörnvall, H.; Persson, B.
- Cellular and Molecular Life Sciences, Vol. 65, Issue 24
Classification of the short-chain dehydrogenase/reductase superfamily using hidden Markov models: SDR classification using HMM
journal, April 2010
- Kallberg, Yvonne; Oppermann, Udo; Persson, Bengt
- FEBS Journal, Vol. 277, Issue 10
Steroid dehydrogenase structures, mechanism of action, and disease
book, January 2000
- Duax, William L.; Ghosh, Debashis; Pletnev, Vladimir
- Vitamins & Hormones
Rational proteomics I. Fingerprint identification and cofactor specificity in the short-chain oxidoreductase (SCOR) enzyme family
journal, November 2003
- Duax, William L.; Pletnev, Vladimir; Addlagatta, Anthony
- Proteins: Structure, Function, and Genetics, Vol. 53, Issue 4
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
journal, February 2000
- Somoza, John R.; Menon, Saurabh; Schmidt, Holly
- Structure, Vol. 8, Issue 2
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
journal, March 2001
- Allard, Simon T. M.; Giraud, Marie-France; Whitfield, Chris
- Journal of Molecular Biology, Vol. 307, Issue 1
Dehydration Is Catalyzed by Glutamate-136 and Aspartic Acid-135 Active Site Residues in Escherichia coli dTDP-Glucose 4,6-Dehydratase †
journal, October 2001
- Gross, Jeffrey W.; Hegeman, Adrian D.; Gerratana, Barbara
- Biochemistry, Vol. 40, Issue 42
Probing Catalysis by Escherichia coli dTDP-Glucose-4,6-dehydratase: Identification and Preliminary Characterization of Functional Amino Acid Residues at the Active Site †
journal, June 2001
- Hegeman, Adrian D.; Gross, Jeffrey W.; Frey, Perry A.
- Biochemistry, Vol. 40, Issue 22
Toward a Structural Understanding of the Dehydratase Mechanism
journal, January 2002
- Allard, Simon T. M.; Beis, Konstantinos; Giraud, Marie-France
- Structure, Vol. 10, Issue 1
Concerted and Stepwise Dehydration Mechanisms Observed in Wild-Type and Mutated Escherichia coli dTDP-Glucose 4,6-Dehydratase †
journal, February 2002
- Hegeman, Adrian D.; Gross, Jeffrey W.; Frey, Perry A.
- Biochemistry, Vol. 41, Issue 8
Structure of the MUR1 GDP-Mannose 4,6-Dehydratase from Arabidopsis thaliana : Implications for Ligand Binding and Specificity
journal, December 2002
- Mulichak, Anne M.; Bonin, Christopher P.; Reiter, Wolf-Dieter
- Biochemistry, Vol. 41, Issue 52
The Structure of NADH in the Enzyme dTDP- d -glucose Dehydratase (RmlB)
journal, October 2003
- Beis, Konstantinos; Allard, Simon T. M.; Hegeman, Adrian D.
- Journal of the American Chemical Society, Vol. 125, Issue 39
High Resolution X-ray Structure of dTDP-Glucose 4,6-Dehydratase from Streptomyces venezuelae
journal, October 2003
- Allard, Simon T. M.; Cleland, W. W.; Holden, Hazel M.
- Journal of Biological Chemistry, Vol. 279, Issue 3
Crystal structure of a tetrameric GDP-D-mannose 4,6-dehydratase from a bacterial GDP-D-rhamnose biosynthetic pathway
journal, February 2004
- Webb, N. A.
- Protein Science, Vol. 13, Issue 2
Crystal Structure at 1.8 Å Resolution of CDP- d -Glucose 4,6-Dehydratase from Yersinia pseudotuberculosis † , ‡
journal, March 2004
- Vogan, Erik M.; Bellamacina, Cornelia; He, Xuemei
- Biochemistry, Vol. 43, Issue 11
Structure of CDP- D -glucose 4,6-dehydratase from Salmonella typhi complexed with CDP- D -xylose
journal, March 2005
- Koropatkin, Nicole M.; Holden, Hazel M.
- Acta Crystallographica Section D Biological Crystallography, Vol. 61, Issue 4
Quaternary assembly and crystal structure of GDP-d-mannose 4,6 dehydratase from Paramecium bursaria Chlorella virus
journal, January 2006
- Rosano, Camillo; Zuccotti, Simone; Sturla, Laura
- Biochemical and Biophysical Research Communications, Vol. 339, Issue 1
Mechanistic studies on PseB of pseudaminic acid biosynthesis: A UDP-N-acetylglucosamine 5-inverting 4,6-dehydratase
journal, December 2008
- Morrison, James P.; Schoenhofen, Ian C.; Tanner, Martin E.
- Bioorganic Chemistry, Vol. 36, Issue 6
Dynamic elements govern the catalytic activity of CapE, a capsular polysaccharide-synthesizing enzyme from Staphylococcus aureus
journal, October 2013
- Miyafusa, Takamitsu; Caaveiro, Jose M. M.; Tanaka, Yoshikazu
- FEBS Letters, Vol. 587, Issue 23
Crystal structure of the capsular polysaccharide synthesizing protein CapE of Staphylococcus aureus
journal, June 2013
- Miyafusa, Takamitsu; Caaveiro, Jose M. M.; Tanaka, Yoshikazu
- Bioscience Reports, Vol. 33, Issue 3
Structure-Function Studies of Two Novel UDP-GlcNAc C6 Dehydratases/C4 Reductases
journal, July 2002
- Creuzenet, Carole; Urbanic, Robert V.; Lam, Joseph S.
- Journal of Biological Chemistry, Vol. 277, Issue 30
Phaser crystallographic software
journal, July 2007
- McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
- Journal of Applied Crystallography, Vol. 40, Issue 4
Coot model-building tools for molecular graphics
journal, November 2004
- Emsley, Paul; Cowtan, Kevin
- Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132
Refinement of Macromolecular Structures by the Maximum-Likelihood Method
journal, May 1997
- Murshudov, G. N.; Vagin, A. A.; Dodson, E. J.
- Acta Crystallographica Section D Biological Crystallography, Vol. 53, Issue 3
[20] Processing of X-ray diffraction data collected in oscillation mode
book, January 1997
- Otwinowski, Zbyszek; Minor, Wladek
- Macromolecular Crystallography Part A, 307-326
Main-chain Bond Lengths and Bond Angles in Protein Structures
journal, June 1993
- Laskowski, Roman A.; Moss, David S.; Thornton, Janet M.
- Journal of Molecular Biology, Vol. 231, Issue 4
Epimerases: structure, function and mechanism
journal, October 2001
- Allard, S. T. M.; Giraud, M. -F.; Naismith, J. H.
- Cellular and Molecular Life Sciences, Vol. 58, Issue 11
Mechanistic Roles of Tyrosine 149 and Serine 124 in UDP-galactose 4-Epimerase from Escherichia coli
journal, September 1997
- Liu, Yijeng; Thoden, James B.; Kim, Jeongmin
- Biochemistry, Vol. 36, Issue 35
Crystallographic Evidence for Tyr 157 Functioning as the Active Site Base in Human UDP−Galactose 4-Epimerase † , ‡
journal, May 2000
- Thoden, James B.; Wohlers, Travis M.; Fridovich-Keil, Judith L.
- Biochemistry, Vol. 39, Issue 19
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Giant viruses of the Megavirinae subfamily possess biosynthetic pathways to produce rare bacterial-like sugars in a clade-specific manner
journal, January 2022
- Notaro, Anna; Poirot, Olivier; Garcin, Elsa D.
- microLife, Vol. 3