1
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Paparella A, Cahill SM, Aboulache BL, Schramm VL. Clostridioides difficile TcdB Toxin Glucosylates Rho GTPase by an S Ni Mechanism and Ion Pair Transition State. ACS Chem Biol 2022; 17:2507-2518. [PMID: 36038138 PMCID: PMC9486934 DOI: 10.1021/acschembio.2c00408] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Toxins TcdA and TcdB from Clostridioides difficile glucosylate human colon Rho GTPases. TcdA and TcdB glucosylation of RhoGTPases results in cytoskeletal changes, causing cell rounding and loss of intestinal integrity. Clostridial toxins TcdA and TcdB are proposed to catalyze glucosylation of Rho GTPases with retention of stereochemistry from UDP-glucose. We used kinetic isotope effects to analyze the mechanisms and transition-state structures of the glucohydrolase and glucosyltransferase activities of TcdB. TcdB catalyzes Rho GTPase glucosylation with retention of stereochemistry, while hydrolysis of UDP-glucose by TcdB causes inversion of stereochemistry. Kinetic analysis revealed TcdB glucosylation via the formation of a ternary complex with no intermediate, supporting an SNi mechanism with nucleophilic attack and leaving group departure occurring on the same face of the glucose ring. Kinetic isotope effects combined with quantum mechanical calculations revealed that the transition states of both glucohydrolase and glucosyltransferase activities of TcdB are highly dissociative. Specifically, the TcdB glucosyltransferase reaction proceeds via an SNi mechanism with the formation of a distinct oxocarbenium phosphate ion pair transition state where the glycosidic bond to the UDP leaving group breaks prior to attack of the threonine nucleophile from Rho GTPase.
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2
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Kok K, Zwiers KC, Boot RG, Overkleeft HS, Aerts JMFG, Artola M. Fabry Disease: Molecular Basis, Pathophysiology, Diagnostics and Potential Therapeutic Directions. Biomolecules 2021; 11:271. [PMID: 33673160 PMCID: PMC7918333 DOI: 10.3390/biom11020271] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/05/2021] [Accepted: 02/06/2021] [Indexed: 02/06/2023] Open
Abstract
Fabry disease (FD) is a lysosomal storage disorder (LSD) characterized by the deficiency of α-galactosidase A (α-GalA) and the consequent accumulation of toxic metabolites such as globotriaosylceramide (Gb3) and globotriaosylsphingosine (lysoGb3). Early diagnosis and appropriate timely treatment of FD patients are crucial to prevent tissue damage and organ failure which no treatment can reverse. LSDs might profit from four main therapeutic strategies, but hitherto there is no cure. Among the therapeutic possibilities are intravenous administered enzyme replacement therapy (ERT), oral pharmacological chaperone therapy (PCT) or enzyme stabilizers, substrate reduction therapy (SRT) and the more recent gene/RNA therapy. Unfortunately, FD patients can only benefit from ERT and, since 2016, PCT, both always combined with supportive adjunctive and preventive therapies to clinically manage FD-related chronic renal, cardiac and neurological complications. Gene therapy for FD is currently studied and further strategies such as substrate reduction therapy (SRT) and novel PCTs are under investigation. In this review, we discuss the molecular basis of FD, the pathophysiology and diagnostic procedures, together with the current treatments and potential therapeutic avenues that FD patients could benefit from in the future.
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Affiliation(s)
- Ken Kok
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Kimberley C Zwiers
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Rolf G Boot
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Hermen S Overkleeft
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Johannes M F G Aerts
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Marta Artola
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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3
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Na L, Yu H, McArthur JB, Ghosh T, Asbell T, Chen X. Engineer P. multocida Heparosan Synthase 2 (PmHS2) for Size-Controlled Synthesis of Longer Heparosan Oligosaccharides. ACS Catal 2020; 10:6113-6118. [PMID: 33520345 PMCID: PMC7842274 DOI: 10.1021/acscatal.0c01231] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Pasteurella multocida heparosan synthase 2 (PmHS2) is a dual-function polysaccharide synthase having both α1-4-N-acetylglucosaminyltransferase (α1-4-GlcNAcT) and β1-4-glucuronyltransferase (β1-4-GlcAT) activities located in two separate catalytic domains. We found that removing PmHS2 N-terminal 80-amino acid residues improved enzyme stability and expression level while retaining its substrate promiscuity. We also identified the reverse glycosylation activities of PmHS2 which complicated its application in size-controlled synthesis of oligosaccharides longer than hexasaccharide. Engineered Δ80PmHS2 single-function-glycosyltransferase mutants Δ80PmHS2_D291N (α1-4-GlcNAcT lacking both forward and reverse β1-4-GlcAT activities) and Δ80PmHS2_D569N (β1-4-GlcAT lacking both forward and reverse α1-4-GlcNAcT activities) were designed and showed to minimize side product formation. They were successfully used in a sequential one-pot multienzyme (OPME) platform for size-controlled high-yield production of oligosaccharides up to decasaccharide. The study draws attention to the consideration of reverse glycosylation activities of glycosyltransferases, including polysaccharide synthases, when applying them in the synthesis of oligosaccharides and polysaccharides. The mutagenesis strategy has the potential to be extended to other multifunctional polysaccharide synthases with reverse glycosylation activities to generate catalysts with improved synthetic efficiency.
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Affiliation(s)
| | | | - John B. McArthur
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Tamashree Ghosh
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Thomas Asbell
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Xi Chen
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
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4
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Taujale R, Venkat A, Huang LC, Zhou Z, Yeung W, Rasheed KM, Li S, Edison AS, Moremen KW, Kannan N. Deep evolutionary analysis reveals the design principles of fold A glycosyltransferases. eLife 2020; 9:54532. [PMID: 32234211 PMCID: PMC7185993 DOI: 10.7554/elife.54532] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/31/2020] [Indexed: 12/26/2022] Open
Abstract
Glycosyltransferases (GTs) are prevalent across the tree of life and regulate nearly all aspects of cellular functions. The evolutionary basis for their complex and diverse modes of catalytic functions remain enigmatic. Here, based on deep mining of over half million GT-A fold sequences, we define a minimal core component shared among functionally diverse enzymes. We find that variations in the common core and emergence of hypervariable loops extending from the core contributed to GT-A diversity. We provide a phylogenetic framework relating diverse GT-A fold families for the first time and show that inverting and retaining mechanisms emerged multiple times independently during evolution. Using evolutionary information encoded in primary sequences, we trained a machine learning classifier to predict donor specificity with nearly 90% accuracy and deployed it for the annotation of understudied GTs. Our studies provide an evolutionary framework for investigating complex relationships connecting GT-A fold sequence, structure, function and regulation. Carbohydrates are one of the major groups of large biological molecules that regulate nearly all aspects of life. Yet, unlike DNA or proteins, carbohydrates are made without a template to follow. Instead, these molecules are built from a set of sugar-based building blocks by the intricate activities of a large and diverse family of enzymes known as glycosyltransferases. An incomplete understanding of how glycosyltransferases recognize and build diverse carbohydrates presents a major bottleneck in developing therapeutic strategies for diseases associated with abnormalities in these enzymes. It also limits efforts to engineer these enzymes for biotechnology applications and biofuel production. Taujale et al. have now used evolutionary approaches to map the evolution of a major subset of glycosyltransferases from species across the tree of life to understand how these enzymes evolved such precise mechanisms to build diverse carbohydrates. First, a minimal structural unit was defined based on being shared among a group of over half a million unique glycosyltransferase enzymes with different activities. Further analysis then showed that the diverse activities of these enzymes evolved through the accumulation of mutations within this structural unit, as well as in much more variable regions in the enzyme that extend from the minimal unit. Taujale et al. then built an extended family tree for this collection of glycosyltransferases and details of the evolutionary relationships between the enzymes helped them to create a machine learning framework that could predict which sugar-containing molecules were the raw materials for a given glycosyltransferase. This framework could make predictions with nearly 90% accuracy based only on information that can be deciphered from the gene for that enzyme. These findings will provide scientists with new hypotheses for investigating the complex relationships connecting the genetic information about glycosyltransferases with their structures and activities. Further refinement of the machine learning framework may eventually enable the design of enzymes with properties that are desirable for applications in biotechnology.
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Affiliation(s)
- Rahil Taujale
- Institute of Bioinformatics, University of Georgia, Athens, Georgia.,Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia
| | - Aarya Venkat
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia
| | - Liang-Chin Huang
- Institute of Bioinformatics, University of Georgia, Athens, Georgia
| | - Zhongliang Zhou
- Department of Computer Science, University of Georgia, Athens, Georgia
| | - Wayland Yeung
- Institute of Bioinformatics, University of Georgia, Athens, Georgia
| | - Khaled M Rasheed
- Department of Computer Science, University of Georgia, Athens, Georgia
| | - Sheng Li
- Department of Computer Science, University of Georgia, Athens, Georgia
| | - Arthur S Edison
- Institute of Bioinformatics, University of Georgia, Athens, Georgia.,Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia
| | - Kelley W Moremen
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, Georgia.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia
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5
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Esposito D, Günster RA, Martino L, El Omari K, Wagner A, Thurston TLM, Rittinger K. Structural basis for the glycosyltransferase activity of the Salmonella effector SseK3. J Biol Chem 2018; 293:5064-5078. [PMID: 29449376 PMCID: PMC5892559 DOI: 10.1074/jbc.ra118.001796] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 01/31/2018] [Indexed: 01/03/2023] Open
Abstract
The Salmonella-secreted effector SseK3 translocates into host cells, targeting innate immune responses, including NF-κB activation. SseK3 is a glycosyltransferase that transfers an N-acetylglucosamine (GlcNAc) moiety onto the guanidino group of a target arginine, modulating host cell function. However, a lack of structural information has precluded elucidation of the molecular mechanisms in arginine and GlcNAc selection. We report here the crystal structure of SseK3 in its apo form and in complex with hydrolyzed UDP-GlcNAc. SseK3 possesses the typical glycosyltransferase type-A (GT-A)-family fold and the metal-coordinating DXD motif essential for ligand binding and enzymatic activity. Several conserved residues were essential for arginine GlcNAcylation and SseK3-mediated inhibition of NF-κB activation. Isothermal titration calorimetry revealed SseK3's preference for manganese coordination. The pattern of interactions in the substrate-bound SseK3 structure explained the selection of the primary ligand. Structural rearrangement of the C-terminal residues upon ligand binding was crucial for SseK3's catalytic activity, and NMR analysis indicated that SseK3 has limited UDP-GlcNAc hydrolysis activity. The release of free N-acetyl α-d-glucosamine, and the presence of the same molecule in the SseK3 active site, classified it as a retaining glycosyltransferase. A glutamate residue in the active site suggested a double-inversion mechanism for the arginine N-glycosylation reaction. Homology models of SseK1, SseK2, and the Escherichia coli orthologue NleB1 reveal differences in the surface electrostatic charge distribution, possibly accounting for their diverse activities. This first structure of a retaining GT-A arginine N-glycosyltransferase provides an important step toward a better understanding of this enzyme class and their roles as bacterial effectors.
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Affiliation(s)
- Diego Esposito
- From the Molecular Structure of Cell Signalling Laboratory, Francis Crick Institute, 1 Midland Road, London NW1 1AT, United Kingdom
| | - Regina A Günster
- the Section of Microbiology, Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom, and
| | - Luigi Martino
- From the Molecular Structure of Cell Signalling Laboratory, Francis Crick Institute, 1 Midland Road, London NW1 1AT, United Kingdom
| | - Kamel El Omari
- the Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Didcot OX11 0DE, United Kingdom
| | - Armin Wagner
- the Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Didcot OX11 0DE, United Kingdom
| | - Teresa L M Thurston
- the Section of Microbiology, Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom, and
| | - Katrin Rittinger
- From the Molecular Structure of Cell Signalling Laboratory, Francis Crick Institute, 1 Midland Road, London NW1 1AT, United Kingdom,
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6
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Blackler RJ, Gagnon SML, Polakowski R, Rose NL, Zheng RB, Letts JA, Johal AR, Schuman B, Borisova SN, Palcic MM, Evans SV. Glycosyltransfer in mutants of putative catalytic residue Glu303 of the human ABO(H) A and B blood group glycosyltransferases GTA and GTB proceeds through a labile active site. Glycobiology 2018; 27:370-380. [PMID: 27979997 DOI: 10.1093/glycob/cww117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 11/16/2016] [Indexed: 11/14/2022] Open
Abstract
The homologous glycosyltransferases α-1,3-N-acetylgalactosaminyltransferase (GTA) and α-1,3-galactosyltransferase (GTB) carry out the final synthetic step of the closely related human ABO(H) blood group A and B antigens. The catalytic mechanism of these model retaining enzymes remains under debate, where Glu303 has been suggested to act as a putative nucleophile in a double displacement mechanism, a local dipole stabilizing the intermediate in an orthogonal associative mechanism or a general base to stabilize the reactive oxocarbenium ion-like intermediate in an SNi-like mechanism. Kinetic analysis of GTA and GTB point mutants E303C, E303D, E303Q and E303A shows that despite the enzymes having nearly identical sequences, the corresponding mutants of GTA/GTB have up to a 13-fold difference in their residual activities relative to wild type. High-resolution single crystal X-ray diffraction studies reveal, surprisingly, that the mutated Cys, Asp and Gln functional groups are no more than 0.8 Å further from the anomeric carbon of donor substrate compared to wild type. However, complicating the analysis is the observation that Glu303 itself plays a critical role in maintaining the stability of a strained "double-turn" in the active site through several hydrogen bonds, and any mutation other than E303Q leads to significantly higher thermal motion or even disorder in the substrate recognition pockets. Thus, there is a remarkable juxtaposition of the mutants E303C and E303D, which retain significant activity despite disrupted active site architecture, with GTB/E303Q, which maintains active site architecture but exhibits zero activity. These findings indicate that nucleophilicity at position 303 is more catalytically valuable than active site stability and highlight the mechanistic elasticity of these enzymes.
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Affiliation(s)
- Ryan J Blackler
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 3800, STN CSC, Victoria, BC, Canada
| | - Susannah M L Gagnon
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 3800, STN CSC, Victoria, BC, Canada
| | - Robert Polakowski
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Natisha L Rose
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Ruixiang B Zheng
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - James A Letts
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 3800, STN CSC, Victoria, BC, Canada
| | - Asha R Johal
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 3800, STN CSC, Victoria, BC, Canada
| | - Brock Schuman
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 3800, STN CSC, Victoria, BC, Canada
| | - Svetlana N Borisova
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 3800, STN CSC, Victoria, BC, Canada
| | - Monica M Palcic
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 3800, STN CSC, Victoria, BC, Canada
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Stephen V Evans
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 3800, STN CSC, Victoria, BC, Canada
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7
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Albesa-Jové D, Sainz-Polo MÁ, Marina A, Guerin ME. Structural Snapshots of α-1,3-Galactosyltransferase with Native Substrates: Insight into the Catalytic Mechanism of Retaining Glycosyltransferases. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- David Albesa-Jové
- Structural Biology Unit-CIC bioGUNE; Technological Park of Bizkaia-Ed 800; 48160 Derio Vizcaya Spain
| | - M. Ángela Sainz-Polo
- Structural Biology Unit-CIC bioGUNE; Technological Park of Bizkaia-Ed 800; 48160 Derio Vizcaya Spain
| | - Alberto Marina
- Structural Biology Unit-CIC bioGUNE; Technological Park of Bizkaia-Ed 800; 48160 Derio Vizcaya Spain
| | - Marcelo E. Guerin
- Structural Biology Unit-CIC bioGUNE; Technological Park of Bizkaia-Ed 800; 48160 Derio Vizcaya Spain
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8
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Albesa-Jové D, Sainz-Polo MÁ, Marina A, Guerin ME. Structural Snapshots of α-1,3-Galactosyltransferase with Native Substrates: Insight into the Catalytic Mechanism of Retaining Glycosyltransferases. Angew Chem Int Ed Engl 2017; 56:14853-14857. [DOI: 10.1002/anie.201707922] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 09/19/2017] [Indexed: 11/11/2022]
Affiliation(s)
- David Albesa-Jové
- Structural Biology Unit-CIC bioGUNE; Technological Park of Bizkaia-Ed 800; 48160 Derio Vizcaya Spain
| | - M. Ángela Sainz-Polo
- Structural Biology Unit-CIC bioGUNE; Technological Park of Bizkaia-Ed 800; 48160 Derio Vizcaya Spain
| | - Alberto Marina
- Structural Biology Unit-CIC bioGUNE; Technological Park of Bizkaia-Ed 800; 48160 Derio Vizcaya Spain
| | - Marcelo E. Guerin
- Structural Biology Unit-CIC bioGUNE; Technological Park of Bizkaia-Ed 800; 48160 Derio Vizcaya Spain
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9
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Abstract
The catalytic mechanism of retaining glycosyltransferases (ret-GTs) remains a controversial issue in glycobiology. By analogy to the well-established mechanism of retaining glycosidases, it was first suggested that ret-GTs follow a double-displacement mechanism. However, only family 6 GTs exhibit a putative nucleophile protein residue properly located in the active site to participate in catalysis, prompting some authors to suggest an unusual single-displacement mechanism [named as front-face or SNi (substitution nucleophilic internal)-like]. This mechanism has now received strong support, from both experiment and theory, for several GT families except family 6, for which a double-displacement reaction is predicted. In the last few years, we have uncovered the molecular mechanisms of several retaining GTs by means of quantum mechanics/molecular mechanics (QM/MM) metadynamics simulations, which we overview in the present work.
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10
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Culbertson AT, Smith AL, Cook MD, Zabotina OA. Truncations of xyloglucan xylosyltransferase 2 provide insights into the roles of the N- and C-terminus. PHYTOCHEMISTRY 2016; 128:12-19. [PMID: 27193738 DOI: 10.1016/j.phytochem.2016.03.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 03/04/2016] [Accepted: 03/30/2016] [Indexed: 06/05/2023]
Abstract
Xyloglucan is the most abundant hemicellulose in the primary cell wall of dicotyledonous plants. In Arabidopsis, three xyloglucan xylosyltransferases, XXT1, XXT2, and XXT5, participate in xylosylation of the xyloglucan backbone. Despite the importance of these enzymes, there is a lack of information on their structure and the critical residues required for substrate binding and transferase activity. In this study, the roles of different domains of XX2 in protein expression and catalytic activity were investigated by constructing a series of N- and C-terminal truncations. XXT2 with an N-terminal truncation of 31 amino acids after the predicted transmembrane domain showed the highest protein expression, but truncations of more than 31 residues decreased protein expression and catalytic activity. XXT2 constructs with C-terminal truncations showed increased protein expression but decreased activity, particularly for truncations of 44 or more amino acids. Site-directed mutagenesis was also used to investigate six positively charged residues near the C-terminus and found that four of the mutants showed decreased enzymatic activity. We conclude that the N- and C-termini of XXT2 have important roles in protein folding and enzymatic activity: the stem region (particularly the N-terminus of the catalytic domain) is critical for protein folding and the C-terminus is essential for enzymatic activity but not for protein folding.
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Affiliation(s)
- Alan T Culbertson
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Adrienne L Smith
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Matthew D Cook
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Olga A Zabotina
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA.
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11
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Abstract
The article reviews the significant contributions to, and the present status of, applications of computational methods for the characterization and prediction of protein-carbohydrate interactions. After a presentation of the specific features of carbohydrate modeling, along with a brief description of the experimental data and general features of carbohydrate-protein interactions, the survey provides a thorough coverage of the available computational methods and tools. At the quantum-mechanical level, the use of both molecular orbitals and density-functional theory is critically assessed. These are followed by a presentation and critical evaluation of the applications of semiempirical and empirical methods: QM/MM, molecular dynamics, free-energy calculations, metadynamics, molecular robotics, and others. The usefulness of molecular docking in structural glycobiology is evaluated by considering recent docking- validation studies on a range of protein targets. The range of applications of these theoretical methods provides insights into the structural, energetic, and mechanistic facets that occur in the course of the recognition processes. Selected examples are provided to exemplify the usefulness and the present limitations of these computational methods in their ability to assist in elucidation of the structural basis underlying the diverse function and biological roles of carbohydrates in their dialogue with proteins. These test cases cover the field of both carbohydrate biosynthesis and glycosyltransferases, as well as glycoside hydrolases. The phenomenon of (macro)molecular recognition is illustrated for the interactions of carbohydrates with such proteins as lectins, monoclonal antibodies, GAG-binding proteins, porins, and viruses.
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Affiliation(s)
- Serge Pérez
- Department of Molecular Pharmacochemistry, CNRS, University Grenoble-Alpes, Grenoble, France.
| | - Igor Tvaroška
- Department of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic; Department of Chemistry, Faculty of Natural Sciences, Constantine The Philosopher University, Nitra, Slovak Republic.
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12
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Gómez H, Mendoza F, Lluch JM, Masgrau L. QM/MM Studies Reveal How Substrate-Substrate and Enzyme-Substrate Interactions Modulate Retaining Glycosyltransferases Catalysis and Mechanism. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2015; 100:225-54. [PMID: 26415846 DOI: 10.1016/bs.apcsb.2015.06.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Glycosyltransferases (GTs) catalyze the biosynthesis of glycosidic linkages by transferring a monosaccharide from a nucleotide sugar donor to an acceptor substrate, and they do that with exquisite regio- and stereospecificity. Retaining GTs act with retention of the configuration at the anomeric carbon of the transferred sugar. Their chemical mechanism has been under debate for long as conclusive experimental data to confirm the mechanism have been elusive. In the past years, quantum mechanical/molecular mechanical (QM/MM) calculations have shed light on the mechanistic discussion. Here, we review the work carried out in our group investigating three of these retaining enzymes (LgtC, α3GalT, and GalNAc-T2). Our results support the controversial front-side attack mechanism as the general mechanism for most retaining GTs. The latest structural data are in agreement with these findings. QM/MM calculations have revealed how enzyme-substrate and substrate-substrate interactions modulate the transfer reaction catalyzed by these enzymes. Moreover, they provide an explanation on why in some cases a strong nucleophilic residue is found on the β-face of the sugar, opening the door to a shift toward a double-displacement mechanism.
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Affiliation(s)
- Hansel Gómez
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain; Departament de Química, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain.
| | - Fernanda Mendoza
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain; Departament de Química, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - José M Lluch
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain; Departament de Química, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Laura Masgrau
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
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13
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Ardèvol A, Rovira C. Reaction Mechanisms in Carbohydrate-Active Enzymes: Glycoside Hydrolases and Glycosyltransferases. Insights from ab Initio Quantum Mechanics/Molecular Mechanics Dynamic Simulations. J Am Chem Soc 2015; 137:7528-47. [DOI: 10.1021/jacs.5b01156] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Albert Ardèvol
- Departament
de Química Orgànica and Institut de Química Teòrica
i Computacional (IQTCUB), Universitat de Barcelona, Martí
i Franquès 1, 08028 Barcelona, Spain
| | - Carme Rovira
- Departament
de Química Orgànica and Institut de Química Teòrica
i Computacional (IQTCUB), Universitat de Barcelona, Martí
i Franquès 1, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08018 Barcelona, Spain
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14
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Tvaroška I. Atomistic insight into the catalytic mechanism of glycosyltransferases by combined quantum mechanics/molecular mechanics (QM/MM) methods. Carbohydr Res 2015; 403:38-47. [DOI: 10.1016/j.carres.2014.06.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 06/12/2014] [Accepted: 06/16/2014] [Indexed: 01/17/2023]
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15
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Cao JS, Qi F, Lu CY, Gu YC, Zhu LW. Effects of interfering RNA of α-1,3-galactosyltransferase and nuclear factor-kappa B on cardiac xenotransplantation. Transpl Immunol 2014; 31:173-82. [PMID: 25128705 DOI: 10.1016/j.trim.2014.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 07/24/2014] [Accepted: 07/24/2014] [Indexed: 10/24/2022]
Abstract
BACKGROUND Both α1,3-galactosyltransferase (α1,3GT) and nuclear factor kappa B (NF-κB) play an important role in the immune response of xenotransplantation. The purpose of this study is to investigate the effect of RNAi of α1,3GT and NF-κB on xenotransplantation. METHODS Lentiviral vectors with shRNA focusing on α1, 3GT and RelA were constructed. The effect of RNAi on α1, 3GT and RelA was examined in vitro and in vivo. Additionally, we established a mouse-to-rat heterotopic cardiac xenotransplantatic model (donor hearts transplanted to the right side of the neck in rat) using a modified cuff technique. The survival time of donor hearts in each group was monitored. The expressions of α1, 3GT and RelA mRNA, Galα1,3Gal antigen, and RelA protein were detected by RT-PCR, immunofluorescence, and Western blot respectively. The expressions of C3, IgM, IgG, NK, macrophages, ICAM-1 on donor hearts were examined by immunohistochemistry. RESULTS High titer lentiviral vectors carrying α1, 3GT and RelA shRNA plasmids had a high and stable transfection rate on EOMA in vitro. In vivo, heart tissue showed a much stronger GFP expression and significant decrease in target gene mRNA expression and protein expression in shRNA interfering groups (p < 0.01). The survival time of α1,3GTi-3 and dual lentiviral vector groups was significantly longer than other groups. The mRNA expression levels of α1,3GT and RelA, as well as Galα(1,3)Gal and RelA proteins, in α1,3GTi-3, RelAi-3, and dual lentiviral vector groups were downregulated and compared to other groups (p < 0.01). The depositions of C3, IgM, IgG in α1,3GTi-3 group and dual lentiviral vector group were less than other groups (p < 0.01). The infiltration of NK, macrophages and ICAM-1 in α1,3GTi-3 group and dual lentiviral vector group was more than other groups (p < 0.01), but the infiltration of NK, macrophages and ICAM-1 in dual lentiviral vector group was less than α1,3GTi-3 group (p < 0.01). CONCLUSIONS Our results indicate that RNAi technology with lentiviral vectors is an effective method to transmit exogenous genes into living bodies and stably inhibit the expression of target genes. Moreover, siRNA targeting the α1,3GT gene was found to control the immune process and obviously prolong the survival time of donors, whereas knocking down NF-κB alone showed no differences. However, the RNAi of NF-κB can make the infiltration of macrophages and natural killer cells decrease, and the expression of ICAM-1 in the xenografts also decreases, contributing to the restraining of AVR.
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Affiliation(s)
- Ji Sen Cao
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Feng Qi
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, China.
| | - Cheng Yu Lu
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Ya Chuan Gu
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Li Wei Zhu
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, China
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16
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Gómez H, Rojas R, Patel D, Tabak LA, Lluch JM, Masgrau L. A computational and experimental study of O-glycosylation. Catalysis by human UDP-GalNAc polypeptide:GalNAc transferase-T2. Org Biomol Chem 2014; 12:2645-55. [PMID: 24643241 PMCID: PMC4744471 DOI: 10.1039/c3ob42569j] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
It is estimated that >50% of proteins are glycosylated with sugar tags that can modulate protein activity through what has been called the sugar code. Here we present the first QM/MM calculations of human GalNAc-T2, a retaining glycosyltransferase, which initiates the biosynthesis of mucin-type O-glycans. Importantly, we have characterized a hydrogen bond between the β-phosphate of UDP and the backbone amide group from the Thr7 of the sugar acceptor (EA2 peptide) that promotes catalysis and that we propose could be a general catalytic strategy used in peptide O-glycosylation by retaining glycosyltransferases. Additional important substrate-substrate interactions have been identified, for example, between the β-phosphate of UDP with the attacking hydroxyl group from the acceptor substrate and with the substituent at the C2' position of the transferred sugar. Our results support a front-side attack mechanism for this enzyme, with a barrier height of ~20 kcal mol(-1) at the QM(M05-2X/TZVP//BP86/SVP)/CHARMM22 level, in reasonable agreement with the experimental kinetic data. Experimental and in silico mutations show that transferase activity is very sensitive to changes in residues Glu334, Asn335 and Arg362. Additionally, our calculations for different donor substrates suggest that human GalNAc-T2 would be inactive if 2'-deoxy-Gal or 2'-oxymethyl-Gal were used, while UDP-Gal is confirmed as a valid sugar donor. Finally, the analysis herein presented highlights that both the substrate-substrate and the enzyme-substrate interactions are mainly concentrated on stabilizing the negative charge developing at the UDP leaving group as the transition state is approached, identifying this as a key aspect of retaining glycosyltransferases catalysis.
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Affiliation(s)
- Hansel Gómez
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Raúl Rojas
- Section on Biological Chemistry, National Institute of Dental and Craniofacial Research, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA
| | - Divya Patel
- Section on Biological Chemistry, National Institute of Dental and Craniofacial Research, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA
| | - Lawrence A. Tabak
- Section on Biological Chemistry, National Institute of Dental and Craniofacial Research, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA
| | - José M. Lluch
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Laura Masgrau
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
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17
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Pham TTK, Stinson B, Thiyagarajan N, Lizotte-Waniewski M, Brew K, Acharya KR. Structures of complexes of a metal-independent glycosyltransferase GT6 from Bacteroides ovatus with UDP-N-acetylgalactosamine (UDP-GalNAc) and its hydrolysis products. J Biol Chem 2014; 289:8041-50. [PMID: 24459149 PMCID: PMC3961637 DOI: 10.1074/jbc.m113.545384] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 01/22/2014] [Indexed: 11/20/2022] Open
Abstract
Mammalian members of glycosyltransferase family 6 (GT6) of the CAZy database have a GT-A fold containing a conserved Asp-X-Asp (DXD) sequence that binds an essential metal cofactor. Bacteroides ovatus GT6a represents a GT6 clade found in more than 30 Gram-negative bacteria that is similar in sequence to the catalytic domains of mammalian GT6, but has an Asn(95)-Ala-Asn(97) (NXN) sequence substituted for the DXD motif and metal-independent catalytic activity. Co-crystals of a low activity mutant of BoGT6a (E192Q) with UDP-GalNAc contained protein complexes with intact UDP-GalNAc and two forms with hydrolysis products (UDP plus GalNAc) representing an initial closed complex and later open form primed for product release. Two cationic residues near the C terminus of BoGT6a, Lys(231) and Arg(243), interact with the diphosphate moiety of UDP-GalNAc, but only Lys(231) interacts with the UDP product and may function in leaving group stabilization. The amide group of Asn(95), the first Asn of the NXN motif, interacts with the ribose moiety of the substrate. This metal-independent GT6 resembles its metal-dependent homologs in undergoing conformational changes on binding UDP-GalNAc that arise from structuring the C terminus to cover this substrate. It appears that in the GT6 family, the metal cofactor functions specifically in binding the UDP moiety in the donor substrate and transition state, actions that can be efficiently performed by components of the polypeptide chain.
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Affiliation(s)
- Tram T. K. Pham
- From the Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom and
| | - Brittany Stinson
- the Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida 33431
| | - Nethaji Thiyagarajan
- From the Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom and
| | - Michelle Lizotte-Waniewski
- the Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida 33431
| | - Keith Brew
- the Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida 33431
| | - K. Ravi Acharya
- From the Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom and
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18
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Tedaldi L, Wagner GK. Beyond substrate analogues: new inhibitor chemotypes for glycosyltransferases. MEDCHEMCOMM 2014. [DOI: 10.1039/c4md00086b] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
New inhibitor chemotypes for glycosyltransferases, which are not structurally derived from either donor or acceptor substrate, are being reviewed.
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Affiliation(s)
- Lauren Tedaldi
- Institute of Pharmaceutical Science
- School of Biomedical Sciences
- King's College London
- London
- UK
| | - Gerd K. Wagner
- Institute of Pharmaceutical Science
- School of Biomedical Sciences
- King's College London
- London
- UK
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19
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Fujihashi M, Ishida T, Kuroda S, Kotra LP, Pai EF, Miki K. Substrate distortion contributes to the catalysis of orotidine 5'-monophosphate decarboxylase. J Am Chem Soc 2013; 135:17432-43. [PMID: 24151964 PMCID: PMC3949427 DOI: 10.1021/ja408197k] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Orotidine 5'-monophosphate decarboxylase (ODCase) accelerates the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP) by 17 orders of magnitude. Eight new crystal structures with ligand analogues combined with computational analyses of the enzyme's short-lived intermediates and the intrinsic electronic energies to distort the substrate and other ligands improve our understanding of the still controversially discussed reaction mechanism. In their respective complexes, 6-methyl-UMP displays significant distortion of its methyl substituent bond, 6-amino-UMP shows the competition between the K72 and C6 substituents for a position close to D70, and the methyl and ethyl esters of OMP both induce rotation of the carboxylate group substituent out of the plane of the pyrimidine ring. Molecular dynamics and quantum mechanics/molecular mechanics computations of the enzyme-substrate complex also show the bond between the carboxylate group and the pyrimidine ring to be distorted, with the distortion contributing a 10-15% decrease of the ΔΔG(⧧) value. These results are consistent with ODCase using both substrate distortion and transition-state stabilization, primarily exerted by K72, in its catalysis of the OMP decarboxylation reaction.
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Affiliation(s)
- Masahiro Fujihashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Toyokazu Ishida
- Nanosystem Research Institute (NRI), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 2, 1-1-1 Umezono, Tsukuba 305-8568, Japan
| | - Shingo Kuroda
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Lakshmi P. Kotra
- Center for Molecular Design and Preformulations and Division of Cell & Molecular Biology, Toronto General Research Institute/University Health Network, Toronto, ON, Canada M5G 1L7
- Departments of Pharmaceutical Sciences and Chemistry, McLaughlin Center for Molecular Medicine, University of Toronto, Canada M5S 3M2
| | - Emil F. Pai
- Center for Molecular Design and Preformulations and Division of Cell & Molecular Biology, Toronto General Research Institute/University Health Network, Toronto, ON, Canada M5G 1L7
- The Campbell Family Cancer Research Institute, Ontario Cancer Institute/University Health Network & Departments of Biochemistry, Medical Biophysics, and Molecular Genetics, University of Toronto, Toronto, ON, Canada M5G 1L7
| | - Kunio Miki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
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20
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Rojas-Cervellera V, Ardèvol A, Boero M, Planas A, Rovira C. Formation of a covalent glycosyl-enzyme species in a retaining glycosyltransferase. Chemistry 2013; 19:14018-23. [PMID: 24108590 DOI: 10.1002/chem.201302898] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Indexed: 01/11/2023]
Abstract
Elusive glycosyl-enzyme adduct: Using classical MD simulations and QM/MM metadynamics, the long-time sought glycosyl-enzyme covalent intermediate of a retaining glycosyltransferase, with a putative nucleophile residue in the active site, has been trapped (MD=molecular dynamics; QM/MM=quantum mechanics/molecular mechanics).
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Affiliation(s)
- Víctor Rojas-Cervellera
- Departament de Química Orgànica and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Diagonal 647, 08028 Barcelona (Spain)
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21
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Thiyagarajan N, Pham TTK, Stinson B, Sundriyal A, Tumbale P, Lizotte-Waniewski M, Brew K, Acharya KR. Structure of a metal-independent bacterial glycosyltransferase that catalyzes the synthesis of histo-blood group A antigen. Sci Rep 2012; 2:940. [PMID: 23230506 PMCID: PMC3516806 DOI: 10.1038/srep00940] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 11/16/2012] [Indexed: 11/09/2022] Open
Abstract
Histo-blood group antigens (HBGAs) are a source of antigenic variation between individuals that modulates resistance and susceptibility to pathogens and is a barrier to the spread of enveloped viruses. HBGAs are also produced by a few prokaryotes where they are synthesized by glycosyltransferases (GTs) related to human HBGA synthases. Here we report the first structure of a bacterial GT of this family, from an intestinal resident, Bacteroides ovatus. Unlike its mammalian homologues and other GTs with similar folds, this protein lacks a metal-binding Asp-X-Asp motif and is fully active in the absence of divalent metal ions, yet is strikingly similar in structure and in its interactions with substrates to structurally characterized mammalian metal-dependent mammalian homologues. This shows how an apparently major divergence in catalytic properties can be accommodated by minor structural adjustments and illustrates the structural underpinnings of horizontal transfer of a functional gene from prokaryotes to vertebrates.
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Affiliation(s)
- Nethaji Thiyagarajan
- Department of Biology and Biochemistry, University of Bath , Claverton Down, Bath BA2 7AY, UK
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22
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Sakono M, Seko A, Takeda Y, Hachisu M, Ito Y. Biophysical properties of UDP-glucose:glycoprotein glucosyltransferase, a folding sensor enzyme in the ER, delineated by synthetic probes. Biochem Biophys Res Commun 2012; 426:504-10. [PMID: 22960071 DOI: 10.1016/j.bbrc.2012.08.112] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Accepted: 08/23/2012] [Indexed: 12/19/2022]
Abstract
UDP-glucose:glycoprotein glucosyltransferase plays a key role in glycoprotein quality control in the endoplasmic reticulum, by virtue of its ability to discriminate folding states. Although lines of evidence have clarified the ability of UGGT to recognize a partially unfolded protein, its mechanistic rationale has been obscure. In this study, the substrate recognition mechanism of UGGT was studied using synthetic substrate of UGGT. Although UGGT has high extent of surface hydrophobicity, it clearly lacks property of typical molecular chaperones. Furthermore, it was revealed that the addition of the substrate caused secondary structure change of UGGT in a dose-dependent manner, resulting that the K(d) value of the UGGT-substrate interaction was estimated from theoretical formula based on 1:1 complexation between UGGT and the acceptor substrate. Moreover, the kinetic analysis of glucosyltransferase activity of UGGT elucidated Michaelis constant K(m) correctly.
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Affiliation(s)
- Masafumi Sakono
- Japan Science and Technology Agency (JST), ERATO, Ito Glycotrilogy Project, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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23
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Jambal I, Kefurt K, Hlaváčková M, Moravcová J. Synthesis of 2-fluoro and 4-fluoro galactopyranosyl phosphonate analogues of UDP-Gal. Carbohydr Res 2012; 360:31-9. [PMID: 22975276 DOI: 10.1016/j.carres.2012.07.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 07/13/2012] [Accepted: 07/17/2012] [Indexed: 12/01/2022]
Abstract
Two novel nonisosteric UDP-Gal analogues, (2-deoxy-2-fluoro- and 4-deoxy-4-fluoro-α-D-galactopyranosyl) phosphonoyl phosphates, were synthesized by optimized multistep procedures starting from 3,4,6-tri-O-benzyl-D-galactal and allyl 2,3,6-tri-O-benzyl-α-D-glucopyranoside, respectively. The key steps were a Michaelis-Arbuzov reaction of respective deoxy-fluoro-D-galactopyranosyl acetate with triethyl phosphite followed by a Moffatt-Khorana coupling reaction with UMP-morpholidate. The structure of all new compounds was confirmed by NMR and mass spectroscopies..
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Affiliation(s)
- Irekhjargal Jambal
- Department of Chemistry of Natural Compounds, Institute of Chemical Technology Prague, Technická 5, Prague 166 28, Czech Republic
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24
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Urresti S, Albesa-Jové D, Schaeffer F, Pham HT, Kaur D, Gest P, van der Woerd MJ, Carreras-González A, López-Fernández S, Alzari PM, Brennan PJ, Jackson M, Guerin ME. Mechanistic insights into the retaining glucosyl-3-phosphoglycerate synthase from mycobacteria. J Biol Chem 2012; 287:24649-61. [PMID: 22637481 DOI: 10.1074/jbc.m112.368191] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Considerable progress has been made in recent years in our understanding of the structural basis of glycosyl transfer. Yet the nature and relevance of the conformational changes associated with substrate recognition and catalysis remain poorly understood. We have focused on the glucosyl-3-phosphoglycerate synthase (GpgS), a "retaining" enzyme, that initiates the biosynthetic pathway of methylglucose lipopolysaccharides in mycobacteria. Evidence is provided that GpgS displays an unusually broad metal ion specificity for a GT-A enzyme, with Mg(2+), Mn(2+), Ca(2+), Co(2+), and Fe(2+) assisting catalysis. In the crystal structure of the apo-form of GpgS, we have observed that a flexible loop adopts a double conformation L(A) and L(I) in the active site of both monomers of the protein dimer. Notably, the L(A) loop geometry corresponds to an active conformation and is conserved in two other relevant states of the enzyme, namely the GpgS·metal·nucleotide sugar donor and the GpgS·metal·nucleotide·acceptor-bound complexes, indicating that GpgS is intrinsically in a catalytically active conformation. The crystal structure of GpgS in the presence of Mn(2+)·UDP·phosphoglyceric acid revealed an alternate conformation for the nucleotide sugar β-phosphate, which likely occurs upon sugar transfer. Structural, biochemical, and biophysical data point to a crucial role of the β-phosphate in donor and acceptor substrate binding and catalysis. Altogether, our experimental data suggest a model wherein the catalytic site is essentially preformed, with a few conformational changes of lateral chain residues as the protein proceeds along the catalytic cycle. This model of action may be applicable to a broad range of GT-A glycosyltransferases.
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Affiliation(s)
- Saioa Urresti
- Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas-Universidad del País Vasco/Euskal Herriko Unibertsitatea, Barrio Sarriena s/n, Leioa, Bizkaia, 48940, Spain
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25
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Gómez H, Lluch JM, Masgrau L. Essential role of glutamate 317 in galactosyl transfer by α3GalT: a computational study. Carbohydr Res 2012; 356:204-8. [PMID: 22520506 DOI: 10.1016/j.carres.2012.03.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 03/15/2012] [Accepted: 03/23/2012] [Indexed: 11/17/2022]
Abstract
Retaining glycosyltransferases (ret-GTs) are the enzymes responsible for the biosynthesis of highly specific glycosidic bonds and have drawn the interest of the scientific community. The catalytic mechanism of such enzymes is not yet fully understood and its study remains a challenge for both experimental and theoretical researches. In the case of ret-GTs where a well defined nucleophilic agent is identified in the vicinity of the anomeric center, a double-displacement mechanism via a covalent enzyme-glycosyl intermediate is commonly assumed and has received some experimental support, although not direct and univocal evidence has been obtained so far. This is the case for α-(1→3)-galactosyltransferase (α3GalT), a ret-GT from Bos taurus where a glutamate (Glu317) is in suitable position to act as a nucleophile. Here we perform density functional theory (DFT) quantum mechanics/molecular mechanics (QM/MM) calculations on the full α3GalT enzyme to analyze the role of Glu317 in the catalytic process. This is done not only for the double-displacement mechanism, where the function of the nucleophile is obvious, but also in the scenario of a front-side attack mechanism (via an oxocarbenium ion-like transition state (S(N)i) or an ion-pair oxocarbenium intermediate (S(N)i-like)). Glu317 is found to be essential in both cases. For a front-side attack, this residue would have a key role in leaving group departure and consequent stabilization of the increasing positive charge at the anomeric center. This finding alerts on the interpretation of the mutagenesis data as both, the formation of a covalent intermediate and a S(N)i or a S(N)i-like mechanism 'assisted' by a nucleophile, could be consistent with experiment. In addition, it could explain why the covalent enzyme-glycosyl intermediate has never been isolated.
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Affiliation(s)
- Hansel Gómez
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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26
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Descroix K, Pesnot T, Yoshimura Y, Gehrke SS, Wakarchuk W, Palcic MM, Wagner GK. Inhibition of galactosyltransferases by a novel class of donor analogues. J Med Chem 2012; 55:2015-24. [PMID: 22356319 DOI: 10.1021/jm201154p] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Galactosyltransferases (GalT) are important molecular targets in a range of therapeutic areas, including infection, inflammation, and cancer. GalT inhibitors are therefore sought after as potential lead compounds for drug discovery. We have recently discovered a new class of GalT inhibitors with a novel mode of action. In this publication, we describe a series of analogues which provide insights, for the first time, into SAR for this new mode of GalT inhibition. We also report that a new C-glycoside, designed as a chemically stable analogue of the most potent inhibitor in this series, retains inhibitory activity against a panel of GalTs. Initial results from cellular studies suggest that despite their polarity, these sugar-nucleotides are taken up by HL-60 cells. Results from molecular modeling studies with a representative bacterial GalT provide a rationale for the differences in bioactivity observed in this series. These findings may provide a blueprint for the rational development of new GalT inhibitors with improved potency.
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Affiliation(s)
- Karine Descroix
- School of Pharmacy, University of East Anglia, Norwich NR4 7TJ, UK
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27
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Lee SS, Hong SY, Errey JC, Izumi A, Davies GJ, Davis BG. Mechanistic evidence for a front-side, SNi-type reaction in a retaining glycosyltransferase. Nat Chem Biol 2011; 7:631-8. [DOI: 10.1038/nchembio.628] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 06/10/2011] [Indexed: 01/14/2023]
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28
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Chinese hamster ovary cells can produce galactose-α-1,3-galactose antigens on proteins. Nat Biotechnol 2011; 28:1153-6. [PMID: 21057479 DOI: 10.1038/nbt1110-1153] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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29
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Pasek M, Ramakrishnan B, Boeggeman E, Manzoni M, Waybright TJ, Qasba PK. Bioconjugation and detection of lactosamine moiety using alpha1,3-galactosyltransferase mutants that transfer C2-modified galactose with a chemical handle. Bioconjug Chem 2010; 20:608-18. [PMID: 19245254 DOI: 10.1021/bc800534r] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Studies on wild-type and mutant glycosyltransferases have shown that they can transfer modified sugars with a versatile chemical handle, such as keto or azido group, that can be used for conjugation chemistry and detection of glycan residues on glycoconjugates. To detect the most prevalent glycan epitope, N-acetyllactosamine (LacNAc (Galbeta1-4GalNAcbeta)), we have mutated a bovine alpha1,3-galactosyltransferse (alpha3Gal-T)() enzyme which normally transfers Gal from UDP-Gal to the LacNAc acceptor, to transfer GalNAc or C2-modified galactose from their UDP derivatives. The alpha3Gal-T enzyme belongs to the alpha3Gal/GalNAc-T family that includes human blood group A and B glycosyltransferases, which transfer GalNAc and Gal, respectively, to the Gal moiety of the trisaccharide Fucalpha1-2Galbeta1-4GlcNAc. On the basis of the sequence and structure comparison of these enzymes, we have carried out rational mutation studies on the sugar donor-binding residues in bovine alpha3Gal-T at positions 280 to 282. A mutation of His280 to Leu/Thr/Ser/Ala or Gly and Ala281 and Ala282 to Gly resulted in the GalNAc transferase activity by the mutant alpha3Gal-T enzymes to 5-19% of their original Gal-T activity. We show that the mutants (280)SGG(282) and (280)AGG(282) with the highest GalNAc-T activity can also transfer modified sugars such as 2-keto-galactose or GalNAz from their respective UDP-sugar derivatives to LacNAc moiety present at the nonreducing end of glycans of asialofetuin, thus enabling the detection of LacNAc moiety of glycoproteins and glycolipids by a chemiluminescence method.
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Affiliation(s)
- Marta Pasek
- Structural Glycobiology Section, Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA
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30
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Brew K, Tumbale P, Acharya KR. Family 6 glycosyltransferases in vertebrates and bacteria: inactivation and horizontal gene transfer may enhance mutualism between vertebrates and bacteria. J Biol Chem 2010; 285:37121-7. [PMID: 20870714 DOI: 10.1074/jbc.r110.176248] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Glycosyltransferases (GTs) control the synthesis and structures of glycans. Inactivation and intense allelic variation in members of the GT6 family generate species-specific and individual variations in carbohydrate structures, including histo-blood group oligosaccharides, resulting in anti-glycan antibodies that target glycan-decorated pathogens. GT6 genes are ubiquitous in vertebrates but are otherwise rare, existing in a few bacteria, one protozoan, and cyanophages, suggesting lateral gene transfer. Prokaryotic GT6 genes correspond to one exon of vertebrate genes, yet their translated protein sequences are strikingly similar. Bacterial and phage GT6 genes influence the surface chemistry of bacteria, affecting their interactions, including those with vertebrate hosts.
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Affiliation(s)
- Keith Brew
- Department of Basic Science, College of Medicine, Florida Atlantic University, Boca Raton, Florida 33431, USA.
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Schuman B, Persson M, Landry RC, Polakowski R, Weadge JT, Seto NOL, Borisova SN, Palcic MM, Evans SV. Cysteine-to-serine mutants dramatically reorder the active site of human ABO(H) blood group B glycosyltransferase without affecting activity: structural insights into cooperative substrate binding. J Mol Biol 2010; 402:399-411. [PMID: 20655926 PMCID: PMC3069981 DOI: 10.1016/j.jmb.2010.07.036] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Revised: 07/15/2010] [Accepted: 07/18/2010] [Indexed: 11/29/2022]
Abstract
A common feature in the structures of GT-A-fold-type glycosyltransferases is a mobile polypeptide loop that has been observed to participate in substrate recognition and enclose the active site upon substrate binding. This is the case for the human ABO(H) blood group B glycosyltransferase GTB, where amino acid residues 177-195 display significantly higher levels of disorder in the unliganded state than in the fully liganded state. Structural studies of mutant enzymes GTB/C80S/C196S and GTB/C80S/C196S/C209S at resolutions ranging from 1.93 to 1.40 A display the opposite trend, where the unliganded structures show nearly complete ordering of the mobile loop residues that is lost upon substrate binding. In the liganded states of the mutant structures, while the UDP moiety of the donor molecule is observed to bind in the expected location, the galactose moiety is observed to bind in a conformation significantly different from that observed for the wild-type chimeric structures. Although this would be expected to impede catalytic turnover, the kinetics of the transfer reaction are largely unaffected. These structures demonstrate that the enzymes bind the donor in a conformation more similar to the dominant solution rotamer and facilitate its gyration into the catalytically competent form. Further, by preventing active-site closure, these structures provide a basis for recently observed cooperativity in substrate binding. Finally, the mutation of C80S introduces a fully occupied UDP binding site at the enzyme dimer interface that is observed to be dependent on the binding of H antigen acceptor analog.
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Affiliation(s)
- Brock Schuman
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 3800, STN CSC, Petch Building, Victoria, BC, Canada V8W 3P6
| | - Mattias Persson
- Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-200 Valby, Denmark
| | - Roxanne C. Landry
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5
| | - Robert Polakowski
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Joel T. Weadge
- Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-200 Valby, Denmark
| | - Nina O. L. Seto
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 3800, STN CSC, Petch Building, Victoria, BC, Canada V8W 3P6
- Institute for Biological Sciences, National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario, Canada K1A 0R6
| | - Svetlana N. Borisova
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 3800, STN CSC, Petch Building, Victoria, BC, Canada V8W 3P6
| | - Monica M. Palcic
- Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-200 Valby, Denmark
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Stephen V. Evans
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 3800, STN CSC, Petch Building, Victoria, BC, Canada V8W 3P6
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5
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Gonçalves S, Borges N, Esteves AM, Victor BL, Soares CM, Santos H, Matias PM. Structural analysis of Thermus thermophilus HB27 mannosyl-3-phosphoglycerate synthase provides evidence for a second catalytic metal ion and new insight into the retaining mechanism of glycosyltransferases. J Biol Chem 2010; 285:17857-68. [PMID: 20356840 PMCID: PMC2878549 DOI: 10.1074/jbc.m109.095976] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Revised: 03/17/2010] [Indexed: 11/06/2022] Open
Abstract
Mannosyl-3-phosphoglycerate synthase is a glycosyltransferase involved in the two-step synthetic pathway of mannosylglycerate, a compatible solute that accumulates in response to salt and/or heat stresses in many microorganisms thriving in hot environments. The three-dimensional structure of mannosyl-3-phosphoglycerate synthase from Thermus thermophilus HB27 in its binary complex form, with GDP-alpha-D-mannose and Mg(2+), shows a second metal binding site, about 6 A away from the mannose moiety. Kinetic and mutagenesis studies have shown that this metal site plays a role in catalysis. Additionally, Asp(167) in the DXD motif is found within van der Waals contact distance of the C1' atom in the mannopyranose ring, suggesting its action as a catalytic nucleophile, either in the formation of a glycosyl-enzyme intermediate according to the double-displacement S(N)2 reaction mechanism or in the stabilization of the oxocarbenium ion-like intermediate according to the D(N)*A(Nss) (S(N)i-like) reaction mechanism. We propose that either mechanism may occur in retaining glycosyltransferases with a GT-A fold, and, based on the gathered structural information, we identified an extended structural signature toward a common scaffold between the inverting and retaining glycosyltransferases.
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Affiliation(s)
- Susana Gonçalves
- From the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
| | - Nuno Borges
- From the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
| | - Ana M. Esteves
- From the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
| | - Bruno L. Victor
- From the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
| | - Cláudio M. Soares
- From the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
| | - Helena Santos
- From the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
| | - Pedro M. Matias
- From the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
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33
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Molecular mechanism of elongation factor 1A inhibition by a Legionella pneumophila glycosyltransferase. Biochem J 2010; 426:281-92. [PMID: 20030628 DOI: 10.1042/bj20091351] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Legionnaires' disease is caused by a lethal colonization of alveolar macrophages with the Gram-negative bacterium Legionella pneumophila. LpGT (L. pneumophila glucosyltransferase; also known as Lgt1) has recently been identified as a virulence factor, shutting down protein synthesis in the human cell by specific glucosylation of EF1A (elongation factor 1A), using an unknown mode of substrate recognition and a retaining mechanism for glycosyl transfer. We have determined the crystal structure of LpGT in complex with substrates, revealing a GT-A fold with two unusual protruding domains. Through structure-guided mutagenesis of LpGT, several residues essential for binding of the UDP-glucose-donor and EF1A-acceptor substrates were identified, which also affected L. pneumophila virulence as demonstrated by microinjection studies. Together, these results suggested that a positively charged EF1A loop binds to a negatively charged conserved groove on the LpGT structure, and that two asparagine residues are essential for catalysis. Furthermore, we showed that two further L. pneumophila glycosyltransferases possessed the conserved UDP-glucose-binding sites and EF1A-binding grooves, and are, like LpGT, translocated into the macrophage through the Icm/Dot (intracellular multiplication/defect in organelle trafficking) system.
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Tumbale P, Brew K. Characterization of a metal-independent CAZy family 6 glycosyltransferase from Bacteroides ovatus. J Biol Chem 2009; 284:25126-34. [PMID: 19622749 DOI: 10.1074/jbc.m109.033878] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The myriad functions of complex carbohydrates include modulating interactions between bacteria and their eukaryotic hosts. In humans and other vertebrates, variations in the activity of glycosyltransferases of CAZy family 6 generate antigenic variation between individuals and species that facilitates resistance to pathogens. The well characterized vertebrate glycosyltransferases of this family are multidomain membrane proteins with C-terminal catalytic domains. Genes for proteins homologous with their catalytic domains are found in at least nine species of anaerobic commensal bacteria and a cyanophage. Although the bacterial proteins are strikingly similar in sequence to the catalytic domains of their eukaryotic relatives, a metal-binding Asp-X-Asp sequence, present in a wide array of metal ion-dependent glycosyltransferases, is replaced by Asn-X-Asn. We have cloned and expressed one of these proteins from Bacteroides ovatus, a bacterium that is linked to inflammatory bowel disease. Functional characterization shows it to be a metal-independent glycosyltransferase with a 200-fold preference for UDP-GalNAc as substrate relative to UDP-Gal. It efficiently catalyzes the synthesis of oligosaccharides similar to human blood group A and may participate in the synthesis of the bacterial O-antigen. The kinetics for GalNAc transfer to 2'-fucosyl lactose are characteristic of a sequential mechanism, as observed previously for this family. Mutational studies indicate that despite the lack of a metal cofactor, there are pronounced similarities in structure-function relationships between the bacterial and vertebrate family 6 glycosyltransferases. These two groups appear to provide an example of horizontal gene transfer involving vertebrates and prokaryotes.
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Affiliation(s)
- Percy Tumbale
- Department of Basic Science, Charles E. Schmidt College of Biomedical Science, Florida Atlantic University, Boca Raton, Florida 33431, USA
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35
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Buschiazzo A, Alzari PM. Structural insights into sialic acid enzymology. Curr Opin Chem Biol 2008; 12:565-72. [DOI: 10.1016/j.cbpa.2008.06.017] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2008] [Accepted: 06/17/2008] [Indexed: 01/27/2023]
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Tumbale P, Jamaluddin H, Thiyagarajan N, Acharya KR, Brew K. Screening a limited structure-based library identifies UDP-GalNAc-specific mutants of alpha-1,3-galactosyltransferase. Glycobiology 2008; 18:1036-43. [PMID: 18782853 DOI: 10.1093/glycob/cwn083] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Complex glycans have important roles in biological recognition processes and considerable pharmaceutical potential. The synthesis of novel glycans can be facilitated by engineering glycosyltransferases to modify their substrate specificities. The choice of sites to modify requires the knowledge of the structures of enzyme-substrate complexes while the complexity of protein structures necessitates the exploration of a large array of multisite mutations. The retaining glycosyltransferase, alpha-1,3-galactosyltransferase (alpha3GT), which catalyzes the synthesis of the alpha-Gal epitope, has strict specificity for UDP-galactose as a donor substrate. Based on the structure of a complex of UDP-galactose with alpha3GT, the specificity for the galactose moiety can be partly attributed to residues that interact with the galactose 2-OH group, particularly His280 and Ala282. With the goal of engineering a variant of bovine alpha3GT with GalNAc transferase activity, we constructed a limited library of 456 alpha3GT mutants containing 19 alternative amino acids at position 280, two each at 281 and 282 and six at position 283. Clones (1500) were screened by assaying partially purified bacterially expressed variants for GalNAc transferase activity. Mutants with the highest levels of GalNAc transferase activity, AGGL or GGGL, had substitutions at all four sites. The AGGL mutant had slightly superior GalNAc transferase activity amounting to about 3% of the activity of the wild-type enzyme with UDP-Gal. This mutant had a low activity with UDP-Gal; its crystallographic structure suggests that the smaller side chains at residues 280-282 form a pocket to accommodate the larger acetamido group of GalNAc. Mutational studies indicate that Leu283 is important for stability in this mutant.
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Affiliation(s)
- Percy Tumbale
- Department of Biomedical Science, College of Biomedical Science, Florida Atlantic University, Glades Road, Boca Raton, FL 33431, USA
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Lairson LL, Henrissat B, Davies GJ, Withers SG. Glycosyltransferases: structures, functions, and mechanisms. Annu Rev Biochem 2008; 77:521-55. [PMID: 18518825 DOI: 10.1146/annurev.biochem.76.061005.092322] [Citation(s) in RCA: 1382] [Impact Index Per Article: 86.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Glycosyltransferases catalyze glycosidic bond formation using sugar donors containing a nucleoside phosphate or a lipid phosphate leaving group. Only two structural folds, GT-A and GT-B, have been identified for the nucleotide sugar-dependent enzymes, but other folds are now appearing for the soluble domains of lipid phosphosugar-dependent glycosyl transferases. Structural and kinetic studies have provided new insights. Inverting glycosyltransferases utilize a direct displacement S(N)2-like mechanism involving an enzymatic base catalyst. Leaving group departure in GT-A fold enzymes is typically facilitated via a coordinated divalent cation, whereas GT-B fold enzymes instead use positively charged side chains and/or hydroxyls and helix dipoles. The mechanism of retaining glycosyltransferases is less clear. The expected two-step double-displacement mechanism is rendered less likely by the lack of conserved architecture in the region where a catalytic nucleophile would be expected. A mechanism involving a short-lived oxocarbenium ion intermediate now seems the most likely, with the leaving phosphate serving as the base.
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Affiliation(s)
- L L Lairson
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada.
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38
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Tumbale P, Jamaluddin H, Thiyagarajan N, Brew K, Acharya KR. Structural basis of UDP-galactose binding by alpha-1,3-galactosyltransferase (alpha3GT): role of negative charge on aspartic acid 316 in structure and activity. Biochemistry 2008; 47:8711-8. [PMID: 18651752 DOI: 10.1021/bi800852a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
alpha-1,3-Galactosyltransferase (alpha3GT) catalyzes the transfer of galactose from UDP-galactose to form an alpha 1-3 link with beta-linked galactosides; it is part of a family of homologous retaining glycosyltransferases that includes the histo-blood group A and B glycosyltransferases, Forssman glycolipid synthase, iGb3 synthase, and some uncharacterized prokaryotic glycosyltransferases. In mammals, the presence or absence of active forms of these enzymes results in antigenic differences between individuals and species that modulate the interplay between the immune system and pathogens. The catalytic mechanism of alpha3GT is controversial, but the structure of an enzyme complex with the donor substrate could illuminate both this and the basis of donor substrate specificity. We report here the structure of the complex of a low-activity mutant alpha3GT with UDP-galactose (UDP-gal) exhibiting a bent configuration stabilized by interactions of the galactose with multiple residues in the enzyme including those in a highly conserved region (His315 to Ser318). Analysis of the properties of mutants containing substitutions for these residues shows that catalytic activity is strongly affected by His315 and Asp316. The negative charge of Asp316 is crucial for catalytic activity, and structural studies of two mutants show that its interaction with Arg202 is needed for an active site structure that facilitates the binding of UDP-gal in a catalytically competent conformation.
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Affiliation(s)
- Percy Tumbale
- Department of Biomedical Science, Florida Atlantic University, 777 Glades Road, Boca Raton, Florida 33431, USA
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Goedl C, Nidetzky B. The phosphate site of trehalose phosphorylase from Schizophyllum commune probed by site-directed mutagenesis and chemical rescue studies. FEBS J 2008. [DOI: 10.1111/j.1742-4658.2008.06254.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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40
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Mannerstedt K, Hindsgaul O. Synthesis and photolytic activation of 6''-O-2-nitrobenzyl uridine-5'-diphosphogalactose: a 'caged' UDP-Gal derivative. Carbohydr Res 2008; 343:875-81. [PMID: 18275942 DOI: 10.1016/j.carres.2008.01.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2007] [Revised: 01/14/2008] [Accepted: 01/17/2008] [Indexed: 10/22/2022]
Abstract
Placing an 2-nitrobenzyl group on O-6 of the galactosyl residue in uridine-5'-diphosphogalactose (UDP-Gal) gives 6''-O-2-nitrobenzyl-UDP-Gal that is shown to be inactive as a donor substrate for beta-(1-->4)-galactosyltransferase (GalT). On irradiation at 365 nm, the nitrobenzyl group is completely removed yielding native UDP-Gal that then transfers normally to produce the expected betaGal-(1-->4)-betaGlcNAc disaccharidic linkage. 6''-O-2-Nitrobenzyl-UDP-Gal thus fulfils the minimum requirements of a 'caged' UDP-Gal for application in time-resolved crystallographic studies of beta-(1-->4)-GalT.
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Affiliation(s)
- Karin Mannerstedt
- Carlsberg Laboratory, Gamle Carlsberg Vej 10, Valby, Copenhagen, Denmark
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Goedl C, Nidetzky B. The phosphate site of trehalose phosphorylase from Schizophyllum commune probed by site-directed mutagenesis and chemical rescue studies. FEBS J 2008; 275:903-13. [PMID: 18205830 DOI: 10.1111/j.1742-4658.2007.06254.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Schizophyllum communealpha,alpha-trehalose phosphorylase utilizes a glycosyltransferase-like catalytic mechanism to convert its disaccharide substrate into alpha-d-glucose 1-phosphate and alpha-d-glucose. Recruitment of phosphate by the free enzyme induces alpha,alpha-trehalose binding recognition and promotes the catalytic steps. Like the structurally related glycogen phosphorylase and other retaining glycosyltransferases of fold family GT-B, the trehalose phosphorylase contains an Arg507-XXXX-Lys512 consensus motif (where X is any amino acid) comprising key residues of its putative phosphate-binding sub-site. Loss of wild-type catalytic efficiency for reaction with phosphate (kcat/Km=21,000 m(-1).s(-1)) was dramatic (>or=10(7)-fold) in purified Arg507-->Ala (R507A) and Lys512-->Ala (K512A) enzymes, reflecting a corresponding change of comparable magnitude in kcat (Arg507) and Km (Lys512). External amine and guanidine derivatives selectively enhanced the activity of the K512A mutant and the R507A mutant respectively. Analysis of the pH dependence of chemical rescue of the K512A mutant by propargylamine suggested that unprotonated amine in combination with H2PO4-, the protonic form of phosphate presumably utilized in enzymatic catalysis, caused restoration of activity. Transition state-like inhibition of the wild-type enzyme A by vanadate in combination with alpha,alpha-trehalose (Ki=0.4 microm) was completely disrupted in the R507A mutant but only weakened in the K512A mutant (Ki=300 microm). Phosphate (50 mm) enhanced the basal hydrolase activity of the K512A mutant toward alpha,alpha-trehalose by 60% but caused its total suppression in wild-type and R507A enzymes. The results portray differential roles for the side chains of Lys512 and Arg507 in trehalose phosphorylase catalysis, reactant state binding of phosphate and selective stabilization of the transition state respectively.
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Affiliation(s)
- Christiane Goedl
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Austria
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Alfaro JA, Zheng RB, Persson M, Letts JA, Polakowski R, Bai Y, Borisova SN, Seto NOL, Lowary TL, Palcic MM, Evans SV. ABO(H) blood group A and B glycosyltransferases recognize substrate via specific conformational changes. J Biol Chem 2008; 283:10097-108. [PMID: 18192272 DOI: 10.1074/jbc.m708669200] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The final step in the enzymatic synthesis of the ABO(H) blood group A and B antigens is catalyzed by two closely related glycosyltransferases, an alpha-(1-->3)-N-acetylgalactosaminyltransferase (GTA) and an alpha-(1-->3)-galactosyltransferase (GTB). Of their 354 amino acid residues, GTA and GTB differ by only four "critical" residues. High resolution structures for GTB and the GTA/GTB chimeric enzymes GTB/G176R and GTB/G176R/G235S bound to a panel of donor and acceptor analog substrates reveal "open," "semi-closed," and "closed" conformations as the enzymes go from the unliganded to the liganded states. In the open form the internal polypeptide loop (amino acid residues 177-195) adjacent to the active site in the unliganded or H antigen-bound enzymes is composed of two alpha-helices spanning Arg(180)-Met(186) and Arg(188)-Asp(194), respectively. The semi-closed and closed forms of the enzymes are generated by binding of UDP or of UDP and H antigen analogs, respectively, and show that these helices merge to form a single distorted helical structure with alternating alpha-3(10)-alpha character that partially occludes the active site. The closed form is distinguished from the semi-closed form by the ordering of the final nine C-terminal residues through the formation of hydrogen bonds to both UDP and H antigen analogs. The semi-closed forms for various mutants generally show significantly more disorder than the open forms, whereas the closed forms display little or no disorder depending strongly on the identity of residue 176. Finally, the use of synthetic analogs reveals how H antigen acceptor binding can be critical in stabilizing the closed conformation. These structures demonstrate a delicately balanced substrate recognition mechanism and give insight on critical aspects of donor and acceptor specificity, on the order of substrate binding, and on the requirements for catalysis.
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Affiliation(s)
- Javier A Alfaro
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
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The Galalpha1,3Galbeta1,4GlcNAc-R (alpha-Gal) epitope: a carbohydrate of unique evolution and clinical relevance. Biochim Biophys Acta Gen Subj 2007; 1780:75-88. [PMID: 18047841 DOI: 10.1016/j.bbagen.2007.11.003] [Citation(s) in RCA: 307] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2007] [Revised: 11/10/2007] [Accepted: 11/13/2007] [Indexed: 11/22/2022]
Abstract
In 1985, we reported that a naturally occurring human antibody (anti-Gal), produced as the most abundant antibody (1% of immunoglobulins) throughout the life of all individuals, recognizes a carbohydrate epitope Galalpha1-3Galbeta1-4GlcNAc-R (the alpha-gal epitope). Since that time, an extensive literature has developed on discoveries related to the alpha-gal epitope and the anti-Gal antibody, including the barrier they form in xenotransplantation and their reciprocity in mammalian evolution. This review covers these topics and new avenues of clinical importance related to this unique antigen/antibody system (alpha-gal epitope/anti-Gal) in improving the efficacy of viral vaccines and in immunotherapy against cancer.
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