1
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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: 40] [Impact Index Per Article: 10.0] [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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2
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Gagnon SML, Legg MSG, Polakowski R, Letts JA, Persson M, Lin S, Zheng RB, Rempel B, Schuman B, Haji-Ghassemi O, Borisova SN, Palcic MM, Evans SV. Conserved residues Arg188 and Asp302 are critical for active site organization and catalysis in human ABO(H) blood group A and B glycosyltransferases. Glycobiology 2018; 28:624-636. [PMID: 29873711 PMCID: PMC6054251 DOI: 10.1093/glycob/cwy051] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 06/05/2018] [Indexed: 01/02/2023] Open
Abstract
Homologous glycosyltransferases GTA and GTB perform the final step in human ABO(H) blood group A and B antigen synthesis by transferring the sugar moiety from donor UDP-GalNAc/UDP-Gal to the terminal H antigen disaccharide acceptor. Like other GT-A fold family 6 glycosyltransferases, GTA and GTB undergo major conformational changes in two mobile regions, the C-terminal tail and internal loop, to achieve the closed, catalytic state. These changes are known to establish a salt bridge network among conserved active site residues Arg188, Asp211 and Asp302, which move to accommodate a series of discrete donor conformations while promoting loop ordering and formation of the closed enzyme state. However, the individual significance of these residues in linking these processes remains unclear. Here, we report the kinetics and high-resolution structures of GTA/GTB mutants of residues 188 and 302. The structural data support a conserved salt bridge network critical to mobile polypeptide loop organization and stabilization of the catalytically competent donor conformation. Consistent with the X-ray crystal structures, the kinetic data suggest that disruption of this salt bridge network has a destabilizing effect on the transition state, emphasizing the importance of Arg188 and Asp302 in the glycosyltransfer reaction mechanism. The salt bridge network observed in GTA/GTB structures during substrate binding appears to be conserved not only among other Carbohydrate Active EnZyme family 6 glycosyltransferases but also within both retaining and inverting GT-A fold glycosyltransferases. Our findings augment recently published crystal structures, which have identified a correlation between donor substrate conformational changes and mobile loop ordering.
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Affiliation(s)
- Susannah M L Gagnon
- Department of Biochemistry & Microbiology, University of Victoria, STN CSC, Victoria, BC, Canada
| | - Max S G Legg
- Department of Biochemistry & Microbiology, University of Victoria, STN CSC, Victoria, BC, Canada
| | - Robert Polakowski
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - James A Letts
- Department of Biochemistry & Microbiology, University of Victoria, STN CSC, Victoria, BC, Canada
| | - Mattias Persson
- Carlsberg Laboratory, Gamle Carlsberg Vej 4-10, Copenhagen V, Denmark
| | - Shuangjun Lin
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | | | - Brian Rempel
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Brock Schuman
- Department of Biochemistry & Microbiology, University of Victoria, STN CSC, Victoria, BC, Canada
| | - Omid Haji-Ghassemi
- Department of Biochemistry & Microbiology, University of Victoria, STN CSC, Victoria, BC, Canada
| | - Svetlana N Borisova
- Department of Biochemistry & Microbiology, University of Victoria, STN CSC, Victoria, BC, Canada
| | - Monica M Palcic
- Department of Biochemistry & Microbiology, University of Victoria, STN CSC, Victoria, BC, Canada
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
- Carlsberg Laboratory, Gamle Carlsberg Vej 4-10, Copenhagen V, Denmark
| | - Stephen V Evans
- Department of Biochemistry & Microbiology, University of Victoria, STN CSC, Victoria, BC, Canada
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3
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Gagnon SML, Legg MSG, Sindhuwinata N, Letts JA, Johal AR, Schuman B, Borisova SN, Palcic MM, Peters T, Evans SV. High-resolution crystal structures and STD NMR mapping of human ABO(H) blood group glycosyltransferases in complex with trisaccharide reaction products suggest a molecular basis for product release. Glycobiology 2018; 27:966-977. [PMID: 28575295 DOI: 10.1093/glycob/cwx053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 05/31/2017] [Indexed: 11/12/2022] Open
Abstract
The human ABO(H) blood group A- and B-synthesizing glycosyltransferases GTA and GTB have been structurally characterized to high resolution in complex with their respective trisaccharide antigen products. These findings are particularly timely and relevant given the dearth of glycosyltransferase structures collected in complex with their saccharide reaction products. GTA and GTB utilize the same acceptor substrates, oligosaccharides terminating with α-l-Fucp-(1→2)-β-d-Galp-OR (where R is a glycolipid or glycoprotein), but use distinct UDP donor sugars, UDP-N-acetylgalactosamine and UDP-galactose, to generate the blood group A (α-l-Fucp-(1→2)[α-d-GalNAcp-(1→3)]-β-d-Galp-OR) and blood group B (α-l-Fucp-(1→2)[α-d-Galp-(1→3)]-β-d-Galp-OR) determinant structures, respectively. Structures of GTA and GTB in complex with their respective trisaccharide products reveal a conflict between the transferred sugar monosaccharide and the β-phosphate of the UDP donor. Mapping of the binding epitopes by saturation transfer difference NMR measurements yielded data consistent with the X-ray structural results. Taken together these data suggest a mechanism of product release where monosaccharide transfer to the H-antigen acceptor induces active site disorder and ejection of the UDP leaving group prior to trisaccharide egress.
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Affiliation(s)
- Susannah M L Gagnon
- Department of Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Max S G Legg
- Department of Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Nora Sindhuwinata
- Institute of Chemistry, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - James A Letts
- Department of Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Asha R Johal
- Department of Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Brock Schuman
- Department of Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Svetlana N Borisova
- Department of Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Monica M Palcic
- Department of Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6.,Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Thomas Peters
- Institute of Chemistry, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Stephen V Evans
- Department of Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
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4
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Harrus D, Kellokumpu S, Glumoff T. Crystal structures of eukaryote glycosyltransferases reveal biologically relevant enzyme homooligomers. Cell Mol Life Sci 2018; 75:833-848. [PMID: 28932871 PMCID: PMC11105277 DOI: 10.1007/s00018-017-2659-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 08/24/2017] [Accepted: 09/13/2017] [Indexed: 12/31/2022]
Abstract
Glycosyltransferases (GTases) transfer sugar moieties to proteins, lipids or existing glycan or polysaccharide molecules. GTases form an important group of enzymes in the Golgi, where the synthesis and modification of glycoproteins and glycolipids take place. Golgi GTases are almost invariably type II integral membrane proteins, with the C-terminal globular catalytic domain residing in the Golgi lumen. The enzymes themselves are divided into 103 families based on their sequence homology. There is an abundance of published crystal structures of GTase catalytic domains deposited in the Protein Data Bank (PDB). All of these represent either of the two main characteristic structural folds, GT-A or GT-B, or present a variation thereof. Since GTases can function as homomeric or heteromeric complexes in vivo, we have summarized the structural features of the dimerization interfaces in crystal structures of GTases, as well as considered the biochemical data available for these enzymes. For this review, we have considered all 898 GTase crystal structures in the Protein Data Bank and highlight the dimer formation characteristics of various GTases based on 24 selected structures.
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Affiliation(s)
- Deborah Harrus
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, PO Box 5400, 90014, Oulu, Finland
| | - Sakari Kellokumpu
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, PO Box 5400, 90014, Oulu, Finland
| | - Tuomo Glumoff
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, PO Box 5400, 90014, Oulu, Finland.
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5
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Grimm LL, Weissbach S, Flügge F, Begemann N, Palcic MM, Peters T. Protein NMR Studies of Substrate Binding to Human Blood Group A and B Glycosyltransferases. Chembiochem 2017; 18:1260-1269. [PMID: 28256109 DOI: 10.1002/cbic.201700025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Indexed: 12/31/2022]
Abstract
Donor and acceptor substrate binding to human blood group A and B glycosyltransferases (GTA, GTB) has been studied by a variety of protein NMR experiments. Prior crystallographic studies had shown these enzymes to adopt an open conformation in the absence of substrates. Binding either of the donor substrate UDP-Gal or of UDP induces a semiclosed conformation. In the presence of both donor and acceptor substrates, the enzymes shift towards a closed conformation with ordering of an internal loop and the C-terminal residues, which then completely cover the donor-binding pocket. Chemical-shift titrations of uniformly 2 H,15 N-labeled GTA or GTB with UDP affected about 20 % of all crosspeaks in 1 H,15 N TROSY-HSQC spectra, reflecting substantial plasticity of the enzymes. On the other hand, it is this conformational flexibility that impedes NH backbone assignments. Chemical-shift-perturbation experiments with δ1-[13 C]methyl-Ile-labeled samples revealed two Ile residues-Ile123 at the bottom of the UDP binding pocket, and Ile192 as part of the internal loop-that were significantly disturbed upon stepwise addition of UDP and H-disaccharide, also revealing long-range perturbations. Finally, methyl TROSY-based relaxation dispersion experiments do not reveal micro- to millisecond timescale motions. Although this study reveals substantial conformational plasticity of GTA and GTB, the matter of how binding of substrates shifts the enzymes into catalytically competent states remains enigmatic.
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Affiliation(s)
- Lena Lisbeth Grimm
- Institute of Chemistry, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Sophie Weissbach
- Institute of Chemistry, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Friedemann Flügge
- Institute of Chemistry, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Nora Begemann
- Institute of Chemistry, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Monica M Palcic
- Department of Biochemistry and Microbiology, University of Victoria, P. O. Box 3800, STN CSC, Victoria, BC, V8W 3P6, Canada
| | - Thomas Peters
- Institute of Chemistry, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
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6
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Gagnon SML, Meloncelli PJ, Zheng RB, Haji-Ghassemi O, Johal AR, Borisova SN, Lowary TL, Evans SV. High Resolution Structures of the Human ABO(H) Blood Group Enzymes in Complex with Donor Analogs Reveal That the Enzymes Utilize Multiple Donor Conformations to Bind Substrates in a Stepwise Manner. J Biol Chem 2015; 290:27040-27052. [PMID: 26374898 DOI: 10.1074/jbc.m115.682401] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Indexed: 11/06/2022] Open
Abstract
Homologous glycosyltransferases α-(1→3)-N-acetylgalactosaminyltransferase (GTA) and α-(1→3)-galactosyltransferase (GTB) catalyze the final step in ABO(H) blood group A and B antigen synthesis through sugar transfer from activated donor to the H antigen acceptor. These enzymes have a GT-A fold type with characteristic mobile polypeptide loops that cover the active site upon substrate binding and, despite intense investigation, many aspects of substrate specificity and catalysis remain unclear. The structures of GTA, GTB, and their chimeras have been determined to between 1.55 and 1.39 Å resolution in complex with natural donors UDP-Gal, UDP-Glc and, in an attempt to overcome one of the common problems associated with three-dimensional studies, the non-hydrolyzable donor analog UDP-phosphono-galactose (UDP-C-Gal). Whereas the uracil moieties of the donors are observed to maintain a constant location, the sugar moieties lie in four distinct conformations, varying from extended to the "tucked under" conformation associated with catalysis, each stabilized by different hydrogen bonding partners with the enzyme. Further, several structures show clear evidence that the donor sugar is disordered over two of the observed conformations and so provide evidence for stepwise insertion into the active site. Although the natural donors can both assume the tucked under conformation in complex with enzyme, UDP-C-Gal cannot. Whereas UDP-C-Gal was designed to be "isosteric" with natural donor, the small differences in structure imposed by changing the epimeric oxygen atom to carbon appear to render the enzyme incapable of binding the analog in the active conformation and so preclude its use as a substrate mimic in GTA and GTB.
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Affiliation(s)
- Susannah M L Gagnon
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada and
| | - Peter J Meloncelli
- the Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Ruixiang B Zheng
- the Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Omid Haji-Ghassemi
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada and
| | - Asha R Johal
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada and
| | - Svetlana N Borisova
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada and
| | - Todd L Lowary
- the Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Stephen V Evans
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada and.
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7
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Schuman B, Evans SV, Fyles TM. Geometric attributes of retaining glycosyltransferase enzymes favor an orthogonal mechanism. PLoS One 2013; 8:e71077. [PMID: 23936487 PMCID: PMC3731257 DOI: 10.1371/journal.pone.0071077] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 07/02/2013] [Indexed: 01/20/2023] Open
Abstract
Retaining glycosyltransferase enzymes retain the stereochemistry of the donor glycosidic linkage after transfer to an acceptor molecule. The mechanism these enzymes utilize to achieve retention of the anomeric stereochemistry has been a matter of much debate. Re-analysis of previously released structural data from retaining and inverting glycosyltransferases allows competing mechanistic proposals to be evaluated. The binding of metal-nucleotide-sugars between inverting and retaining enzymes is conformationally unique and requires the donor substrate to occupy two different orientations in the two types of glycosyltransferases. The available structures of retaining glycosyltransferases lack appropriately positioned enzymatic dipolar residues to initiate or stabilize the intermediates of a dissociative mechanism. Further, available structures show that the acceptor nucleophile and anomeric carbon of the donor sugar are in close proximity. Structural features support orthogonal (front-side) attack from a position lying ≤90° from the C1-O phosphate bond for retaining enzymes. These structural conclusions are consistent with the geometric conclusions of recent kinetic and computational studies.
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Affiliation(s)
- Brock Schuman
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Stephen V. Evans
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Thomas M. Fyles
- Department of Chemistry, University of Victoria, Victoria, British Columbia, Canada
- * E-mail:
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8
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Johal AR, Schuman B, Alfaro JA, Borisova S, Seto NOL, Evans SV. Sequence-dependent effects of cryoprotectants on the active sites of the human ABO(H) blood group A and B glycosyltransferases. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:268-76. [DOI: 10.1107/s0907444912001801] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Accepted: 01/15/2012] [Indexed: 11/10/2022]
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9
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Chang A, Singh S, Phillips GN, Thorson JS. Glycosyltransferase structural biology and its role in the design of catalysts for glycosylation. Curr Opin Biotechnol 2011; 22:800-8. [PMID: 21592771 DOI: 10.1016/j.copbio.2011.04.013] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2011] [Revised: 04/11/2011] [Accepted: 04/19/2011] [Indexed: 12/19/2022]
Abstract
Glycosyltransferases (GTs) are ubiquitous in nature and are required for the transfer of sugars to a variety of important biomolecules. This essential enzyme family has been a focus of attention from both the perspective of a potential drug target and a catalyst for the development of vaccines, biopharmaceuticals and small molecule therapeutics. This review attempts to consolidate the emerging lessons from Leloir (nucleotide-dependent) GT structural biology studies and recent applications of these fundamentals toward rational engineering of glycosylation catalysts.
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Affiliation(s)
- Aram Chang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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10
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Park S, Lippard SJ. Redox state-dependent interaction of HMGB1 and cisplatin-modified DNA. Biochemistry 2011; 50:2567-74. [PMID: 21355578 DOI: 10.1021/bi2000214] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
HMGB1, one of the most abundant nuclear proteins, has a strong binding affinity for cisplatin-modified DNA. It has been proposed that HMGB1 enhances the anticancer efficacy of cisplatin by shielding platinated DNA lesions from repair. Two cysteine residues in HMGB1 domain A form a reversible disulfide bond under mildly oxidizing conditions. The reduced domain A protein binds to a 25-bp DNA probe containing a central 1,2-d(GpG) intrastrand cross-link, the major platinum-DNA adduct, with a 10-fold greater binding affinity than the oxidized domain A. The binding affinities of singly and doubly mutated HMGB1 domain A, respectively deficient in one or both cysteine residues that form the disulfide bond, are unaffected by changes in external redox conditions. The redox-dependent nature of the binding of HMGB1 domain A to cisplatin-modified DNA suggests that formation of the intradomain disulfide bond induces a conformational change that disfavors binding to cisplatin-modified DNA. Hydroxyl radical footprinting analyses of wild-type domain A bound to platinated DNA under different redox conditions revealed identical cleavage patterns, implying that the asymmetric binding mode of the protein across from the platinated lesion is conserved irrespective of the redox state. The results of this study reveal that the cellular redox environment can influence the interaction of HMGB1 with the platinated DNA and suggest that the redox state of the A domain is a potential factor in regulating the role of the protein in modulating the activity of cisplatin as an anticancer drug.
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Affiliation(s)
- Semi Park
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United States
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11
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Schuman B, Fisher SZ, Kovalevsky A, Borisova SN, Palcic MM, Coates L, Langan P, Evans SV. Preliminary joint neutron time-of-flight and X-ray crystallographic study of human ABO(H) blood group A glycosyltransferase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:258-62. [PMID: 21301100 PMCID: PMC3034622 DOI: 10.1107/s1744309110051298] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Accepted: 12/07/2010] [Indexed: 05/30/2023]
Abstract
The biosyntheses of oligosaccharides and glycoconjugates are conducted by glycosyltransferases. These extraordinarily diverse and widespread enzymes catalyze the formation of glycosidic bonds through the transfer of a monosaccharide from a donor molecule to an acceptor molecule, with the stereochemistry about the anomeric carbon being either inverted or retained. Human ABO(H) blood group A α-1,3-N-acetylgalactosaminyltransferase (GTA) generates the corresponding antigen by the transfer of N-acetylgalactosamine from UDP-GalNAc to the blood group H antigen. To understand better how specific active-site-residue protons and hydrogen-bonding patterns affect substrate recognition and catalysis, neutron diffraction studies were initiated at the Protein Crystallography Station (PCS) at Los Alamos Neutron Science Center (LANSCE). A large single crystal was subjected to H/D exchange prior to data collection and time-of-flight neutron diffraction data were collected to 2.5 Å resolution at the PCS to ∼85% overall completeness, with complementary X-ray diffraction data collected from a crystal from the same drop and extending to 1.85 Å resolution. Here, the first successful neutron data collection from a glycosyltransferase is reported.
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Affiliation(s)
- B. Schuman
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 3800, STN CSC, Victoria, BC V8W 3P6, Canada
| | - S. Z. Fisher
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - A. Kovalevsky
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - S. N. Borisova
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 3800, STN CSC, Victoria, BC V8W 3P6, Canada
| | - M. M. Palcic
- Carlsberg Laboratory, Gamle Carlsberg Vej 10, 2500 Valby, Denmark
| | - L. Coates
- Neutron Scattering Science Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - P. Langan
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - S. V. Evans
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 3800, STN CSC, Victoria, BC V8W 3P6, Canada
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