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Yi L, Zhu J, Li Q, Guan X, Cheng W, Xie Y, Zhao Y, Zhao S. Panax notoginseng stems and leaves affect microbial community and function in cecum of duzang pigs. Transl Anim Sci 2024; 8:txad142. [PMID: 38425544 PMCID: PMC10904106 DOI: 10.1093/tas/txad142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 01/09/2024] [Indexed: 03/02/2024] Open
Abstract
Panax notoginseng is a Chinese medicine with a long history in which stems and leaves are the wastes of processing Panax notoginseng and have not been effectively utilized. The effects of diets containing Panax notoginseng stems and leaves on the cecal short-chain fatty acid (SCFA) concentration and microbiome of independent pigs were studied. Diets containing Panax notoginseng stems and leaves did not affect the concentration of SCFA in the cecal contents of Duzang pigs but affected the microbial composition and diversity. Firmicutes, Proteobacteria, and Bacteroidetes dominate in the cecal of Duzang pigs. Feeding Duzang pigs with a 10% Panax notoginseng stems and leaves diet increases the abundance of Lactobacillus, Christensenellaceae R-7 group, and Akkermansia in the cecal. We found 14 genera positively associated with acetate, and they were Lactobacillus, Ruminococcaceae UCG 005, Ruminiclostridium 6; Escherichia Shigella and Family XIII AD3011 group showed negative correlations. Solobacterium, Desulfovibrio, and Erysipelatoclostridium were positively associated with propionate. Campylobacter, Clostridium sensu stricto 11, and Angelakisella were positively associated with butyrate. In conclusion, Panax notoginseng stems and leaves could affect the cecal microbial community and functional composition of Duzang pigs. Panax notoginseng stems and leaves reduce the enrichment of lipopolysaccharide biosynthetic pathway of the cecal microbiome, which may have a positive effect on intestinal health. The higher abundance of GH25 family in Duzang pig's cecal microbiome of fed Panax notoginseng stems and leaves diet. This increase may be the reason for the microbial diversity decrease.
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Affiliation(s)
- Lanlan Yi
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Yunnan 650201, China
| | - Junhong Zhu
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Yunnan 650201, China
| | - Qiuyan Li
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Yunnan 650201, China
| | - Xuancheng Guan
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Yunnan 650201, China
| | - Wenjie Cheng
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Yunnan 650201, China
| | - Yuxiao Xie
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Yunnan 650201, China
- College of Biology and Agriculture, Zunyi Normal University, Guizhou 563006, China
| | - Yanguang Zhao
- Shanghai Academy of Science Technology, Shanghai Lab. Animal Research Center, Shanghai 201203, China
| | - Sumei Zhao
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Yunnan 650201, China
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2
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Sobala ŁF. Evolution and phylogenetic distribution of endo-α-mannosidase. Glycobiology 2023; 33:687-699. [PMID: 37202179 PMCID: PMC11025385 DOI: 10.1093/glycob/cwad041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 05/20/2023] Open
Abstract
While glycans underlie many biological processes, such as protein folding, cell adhesion, and cell-cell recognition, deep evolution of glycosylation machinery remains an understudied topic. N-linked glycosylation is a conserved process in which mannosidases are key trimming enzymes. One of them is the glycoprotein endo-α-1,2-mannosidase which participates in the initial trimming of mannose moieties from an N-linked glycan inside the cis-Golgi. It is unique as the only endo-acting mannosidase found in this organelle. Relatively little is known about its origins and evolutionary history; so far it was reported to occur only in vertebrates. In this work, a taxon-rich bioinformatic survey to unravel the evolutionary history of this enzyme, including all major eukaryotic clades and a wide representation of animals, is presented. The endomannosidase was found to be more widely distributed in animals and other eukaryotes. The protein motif changes in context of the canonical animal enzyme were tracked. Additionally, the data show the two canonical vertebrate endomannosidase genes, MANEA and MANEAL, arose at the second round of the two vertebrate genome duplications and one more vertebrate paralog, CMANEAL, is uncovered. Finally, a framework where N-glycosylation co-evolved with complex multicellularity is described. A better understanding of the evolution of core glycosylation pathways is pivotal to understanding biology of eukaryotes in general, and the Golgi apparatus in particular. This systematic analysis of the endomannosidase evolution is one step toward this goal.
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Affiliation(s)
- Łukasz F Sobala
- Laboratory of Glycobiology, Hirszfeld Institute of Immunology and Experimental Therapy, Weigla 12, 53-114 Wroclaw, Poland
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3
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Kołaczkowski BM, Moroz OV, Blagova E, Davies GJ, Møller MS, Meyer AS, Westh P, Jensen K, Wilson KS, Krogh KBRM. Structural and functional characterization of a multi-domain GH92 α-1,2-mannosidase from Neobacillus novalis. Acta Crystallogr D Struct Biol 2023; 79:387-400. [PMID: 37071393 PMCID: PMC10167667 DOI: 10.1107/s2059798323001663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/23/2023] [Indexed: 04/19/2023] Open
Abstract
Many secreted eukaryotic proteins are N-glycosylated with oligosaccharides composed of a high-mannose N-glycan core and, in the specific case of yeast cell-wall proteins, an extended α-1,6-mannan backbone carrying a number of α-1,2- and α-1,3-mannose substituents of varying lengths. α-Mannosidases from CAZy family GH92 release terminal mannose residues from these N-glycans, providing access for the α-endomannanases, which then degrade the α-mannan backbone. Most characterized GH92 α-mannosidases consist of a single catalytic domain, while a few have extra domains including putative carbohydrate-binding modules (CBMs). To date, neither the function nor the structure of a multi-domain GH92 α-mannosidase CBM has been characterized. Here, the biochemical investigation and crystal structure of the full-length five-domain GH92 α-1,2-mannosidase from Neobacillus novalis (NnGH92) with mannoimidazole bound in the active site and an additional mannoimidazole bound to the N-terminal CBM32 are reported. The structure of the catalytic domain is very similar to that reported for the GH92 α-mannosidase Bt3990 from Bacteroides thetaiotaomicron, with the substrate-binding site being highly conserved. The function of the CBM32s and other NnGH92 domains was investigated by their sequential deletion and suggested that whilst their binding to the catalytic domain was crucial for the overall structural integrity of the enzyme, they appear to have little impact on the binding affinity to the yeast α-mannan substrate. These new findings provide a better understanding of how to select and optimize other multi-domain bacterial GH92 α-mannosidases for the degradation of yeast α-mannan or mannose-rich glycans.
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Affiliation(s)
- Bartłomiej M. Kołaczkowski
- Department of Science and Environment, Roskilde University, Universitetsvej 1, Building 28, 4000 Roskilde, Denmark
- Novozymes A/S, Biologiens Vej 2, 2800 Kongens Lyngby, Denmark
| | - Olga V. Moroz
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Elena Blagova
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Gideon J. Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Marie Sofie Møller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 224, 2800 Kongens Lyngby, Denmark
| | - Anne S. Meyer
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 224, 2800 Kongens Lyngby, Denmark
| | - Peter Westh
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 224, 2800 Kongens Lyngby, Denmark
| | - Kenneth Jensen
- Novozymes A/S, Biologiens Vej 2, 2800 Kongens Lyngby, Denmark
| | - Keith S. Wilson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
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4
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Burchill L, Males A, Kaur A, Davies GJ, Williams SJ. Structure, Function and Mechanism of N‐Glycan Processing Enzymes:
endo
‐α‐1,2‐Mannanase and
endo
‐α‐1,2‐Mannosidase. Isr J Chem 2022. [DOI: 10.1002/ijch.202200067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Laura Burchill
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute University of Melbourne Parkville Victoria Australia 3010
| | - Alexandra Males
- Department of Chemistry University of York York YO10 5DD United Kingdom
| | - Arashdeep Kaur
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute University of Melbourne Parkville Victoria Australia 3010
| | - Gideon J. Davies
- Department of Chemistry University of York York YO10 5DD United Kingdom
| | - Spencer J. Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute University of Melbourne Parkville Victoria Australia 3010
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5
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Structure of human endo-α-1,2-mannosidase (MANEA), an antiviral host-glycosylation target. Proc Natl Acad Sci U S A 2020; 117:29595-29601. [PMID: 33154157 PMCID: PMC7703563 DOI: 10.1073/pnas.2013620117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Mammalian protein N-linked glycosylation is critical for glycoprotein folding, quality control, trafficking, recognition, and function. N-linked glycans are synthesized from Glc3Man9GlcNAc2 precursors that are trimmed and modified in the endoplasmic reticulum (ER) and Golgi apparatus by glycoside hydrolases and glycosyltransferases. Endo-α-1,2-mannosidase (MANEA) is the sole endo-acting glycoside hydrolase involved in N-glycan trimming and is located within the Golgi, where it allows ER-escaped glycoproteins to bypass the classical N-glycosylation trimming pathway involving ER glucosidases I and II. There is considerable interest in the use of small molecules that disrupt N-linked glycosylation as therapeutic agents for diseases such as cancer and viral infection. Here we report the structure of the catalytic domain of human MANEA and complexes with substrate-derived inhibitors, which provide insight into dynamic loop movements that occur on substrate binding. We reveal structural features of the human enzyme that explain its substrate preference and the mechanistic basis for catalysis. These structures have inspired the development of new inhibitors that disrupt host protein N-glycan processing of viral glycans and reduce the infectivity of bovine viral diarrhea and dengue viruses in cellular models. These results may contribute to efforts aimed at developing broad-spectrum antiviral agents and help provide a more in-depth understanding of the biology of mammalian glycosylation.
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6
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Sobala L, Speciale G, Zhu S, Raich L, Sannikova N, Thompson AJ, Hakki Z, Lu D, Shamsi Kazem Abadi S, Lewis AR, Rojas-Cervellera V, Bernardo-Seisdedos G, Zhang Y, Millet O, Jiménez-Barbero J, Bennet AJ, Sollogoub M, Rovira C, Davies GJ, Williams SJ. An Epoxide Intermediate in Glycosidase Catalysis. ACS CENTRAL SCIENCE 2020; 6:760-770. [PMID: 32490192 PMCID: PMC7256955 DOI: 10.1021/acscentsci.0c00111] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Indexed: 05/18/2023]
Abstract
Retaining glycoside hydrolases cleave their substrates through stereochemical retention at the anomeric position. Typically, this involves two-step mechanisms using either an enzymatic nucleophile via a covalent glycosyl enzyme intermediate or neighboring-group participation by a substrate-borne 2-acetamido neighboring group via an oxazoline intermediate; no enzymatic mechanism with participation of the sugar 2-hydroxyl has been reported. Here, we detail structural, computational, and kinetic evidence for neighboring-group participation by a mannose 2-hydroxyl in glycoside hydrolase family 99 endo-α-1,2-mannanases. We present a series of crystallographic snapshots of key species along the reaction coordinate: a Michaelis complex with a tetrasaccharide substrate; complexes with intermediate mimics, a sugar-shaped cyclitol β-1,2-aziridine and β-1,2-epoxide; and a product complex. The 1,2-epoxide intermediate mimic displayed hydrolytic and transfer reactivity analogous to that expected for the 1,2-anhydro sugar intermediate supporting its catalytic equivalence. Quantum mechanics/molecular mechanics modeling of the reaction coordinate predicted a reaction pathway through a 1,2-anhydro sugar via a transition state in an unusual flattened, envelope (E 3) conformation. Kinetic isotope effects (k cat/K M) for anomeric-2H and anomeric-13C support an oxocarbenium ion-like transition state, and that for C2-18O (1.052 ± 0.006) directly implicates nucleophilic participation by the C2-hydroxyl. Collectively, these data substantiate this unprecedented and long-imagined enzymatic mechanism.
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Affiliation(s)
- Lukasz
F. Sobala
- York
Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Gaetano Speciale
- School
of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Sha Zhu
- Sorbonne
Université, CNRS, Institut Parisien de Chimie Moléculaire,
UMR 8232, 4 place Jussieu, 75005 Paris, France
| | - Lluís Raich
- Departament
de Química Inorgànica
i Orgànica (Secció de Química Orgànica) &
Institut de Química
Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí
i Franquès 1, 08028 Barcelona, Spain
| | - Natalia Sannikova
- Department
of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Andrew J. Thompson
- York
Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Zalihe Hakki
- School
of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Dan Lu
- Sorbonne
Université, CNRS, Institut Parisien de Chimie Moléculaire,
UMR 8232, 4 place Jussieu, 75005 Paris, France
| | - Saeideh Shamsi Kazem Abadi
- Department
of Biochemistry and Molecular Biology, Simon
Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Andrew R. Lewis
- Department
of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Víctor Rojas-Cervellera
- Departament
de Química Inorgànica
i Orgànica (Secció de Química Orgànica) &
Institut de Química
Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí
i Franquès 1, 08028 Barcelona, Spain
| | - Ganeko Bernardo-Seisdedos
- Molecular
Recognition and Host−Pathogen Interactions, CIC bioGUNE, Basque Research Technology Alliance (BRTA), Bizkaia Technology Park, Building
800, 48160 Derio, Spain
| | - Yongmin Zhang
- Sorbonne
Université, CNRS, Institut Parisien de Chimie Moléculaire,
UMR 8232, 4 place Jussieu, 75005 Paris, France
| | - Oscar Millet
- Molecular
Recognition and Host−Pathogen Interactions, CIC bioGUNE, Basque Research Technology Alliance (BRTA), Bizkaia Technology Park, Building
800, 48160 Derio, Spain
| | - Jesús Jiménez-Barbero
- Ikerbasque,
Basque Foundation for Science, Marıá Dıáz de Haro 3, 48013 Bilbao, Spain
- Molecular
Recognition and Host−Pathogen Interactions, CIC bioGUNE, Basque Research Technology Alliance (BRTA), Bizkaia Technology Park, Building
800, 48160 Derio, Spain
| | - Andrew J. Bennet
- Department
of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
- Department
of Biochemistry and Molecular Biology, Simon
Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
- E-mail:
| | - Matthieu Sollogoub
- Sorbonne
Université, CNRS, Institut Parisien de Chimie Moléculaire,
UMR 8232, 4 place Jussieu, 75005 Paris, France
- E-mail:
| | - Carme Rovira
- Departament
de Química Inorgànica
i Orgànica (Secció de Química Orgànica) &
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), Pg. Lluís Companys
23, 08010 Barcelona, Spain
- E-mail:
| | - Gideon J. Davies
- York
Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
- E-mail:
| | - Spencer J. Williams
- School
of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
- E-mail:
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7
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Vocadlo DJ. A Shut-and-Open Case: An Epoxide Intermediate Spotted in the Reaction Coordinate of a Family of Glycoside Hydrolases. ACS CENTRAL SCIENCE 2020; 6:619-621. [PMID: 32490180 PMCID: PMC7256941 DOI: 10.1021/acscentsci.0c00482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Affiliation(s)
- David J. Vocadlo
- Department of
Chemistry and Department of Molecular
Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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8
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Rovira C, Males A, Davies GJ, Williams SJ. Mannosidase mechanism: at the intersection of conformation and catalysis. Curr Opin Struct Biol 2019; 62:79-92. [PMID: 31891872 DOI: 10.1016/j.sbi.2019.11.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/06/2019] [Accepted: 11/15/2019] [Indexed: 12/17/2022]
Abstract
Mannosidases are a diverse group of enzymes that are important in the biological processing of mannose-containing polysaccharides and complex glycoconjugates. They are found in 12 of the >160 sequence-based glycosidase families. We discuss evidence that nature has evolved a small set of common mechanisms that unite almost all of these mannosidase families. Broadly, mannosidases (and the closely related rhamnosidases) perform catalysis through just two conformations of the oxocarbenium ion-like transition state: a B2,5 (or enantiomeric 2,5B) boat and a 3H4 half-chair. This extends to a new family (GT108) of GDPMan-dependent β-1,2-mannosyltransferases/phosphorylases that perform mannosyl transfer through a boat conformation as well as some mannosidases that are metalloenzymes and require divalent cations for catalysis. Yet, among this commonality lies diversity. New evidence shows that one unique family (GH99) of mannosidases use an unusual mechanism involving anchimeric assistance via a 1,2-anhydro sugar (epoxide) intermediate.
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Affiliation(s)
- Carme Rovira
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) & 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), Pg. Lluís Companys 23, 08010 Barcelona, Spain.
| | - Alexandra Males
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Gideon J Davies
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Spencer J Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.
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9
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Sano K, Kuribara T, Ishii N, Kuroiwa A, Yoshihara T, Tobita S, Totani K, Matsuo I. Fluorescence Quenching-based Assay for Measuring Golgi endo-α-Mannosidase. Chem Asian J 2019; 14:1965-1969. [PMID: 30884161 DOI: 10.1002/asia.201900240] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/13/2019] [Indexed: 11/11/2022]
Abstract
Golgi endo-α-mannosidase (G-EM) catalyzes an alternative deglucosylation process for N-glycans and plays important roles in the post-endoplasmic reticulum (ER) quality control pathway. To understand the post-ER quality control mechanism, we synthesized a tetrasaccharide probe for the detection of the hydrolytic activity of G-EM based on a fluorescence quenching assay. The probe was labeled with an N-methylanthraniloyl group as a reporter dye at the non-reducing end and a 2,4-dinitrophenyl group as a quencher at the reducing end. This probe is hydrolyzed to disaccharide derivatives by G-EM, resulting in increased fluorescence intensity. Thus, the fluorescence signal is directly proportional to the amount of disaccharide derivative present, allowing the G-EM activity to be evaluated easily and quantitatively.
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Affiliation(s)
- Kanae Sano
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan), (IM
| | - Taiki Kuribara
- Department of Materials and Life Science, Seikei University, 3-3-1 Kichijoji-kitamachi, Musashino, Tokyo, 180-8633, Japan
| | - Nozomi Ishii
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan), (IM
| | - Ayumi Kuroiwa
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan), (IM
| | - Toshitada Yoshihara
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan), (IM
| | - Seiji Tobita
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan), (IM
| | - Kiichiro Totani
- Department of Materials and Life Science, Seikei University, 3-3-1 Kichijoji-kitamachi, Musashino, Tokyo, 180-8633, Japan
| | - Ichiro Matsuo
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan), (IM
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10
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Lu D, Zhu S, Sobala LF, Bernardo-Seisdedos G, Millet O, Zhang Y, Jiménez-Barbero J, Davies GJ, Sollogoub M. From 1,4-Disaccharide to 1,3-Glycosyl Carbasugar: Synthesis of a Bespoke Inhibitor of Family GH99 Endo-α-mannosidase. Org Lett 2018; 20:7488-7492. [PMID: 30427198 DOI: 10.1021/acs.orglett.8b03260] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding the enzyme reaction mechanism can lead to the design of enzyme inhibitors. A Claisen rearrangement was used to allow conversion of an α-1,4-disaccharide into an α-1,3-linked glycosyl carbasugar to target the endo-α-mannosidase from the GH99 glycosidase family, which, unusually, is believed to act through a 1,2-anhydrosugar "epoxide" intermediate. Using NMR and X-ray crystallography, it is shown that glucosyl carbasugar α-aziridines can act as reasonably potent endo-α-mannosidase inhibitors, likely by virtue of their shape mimicry and the interactions of the aziridine nitrogen with the conserved catalytic acid/base of the enzyme active site.
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Affiliation(s)
- Dan Lu
- Sorbonne Université , CNRS, Institut Parisien de Chimie Moléculaire, UMR 8232 , 4 place Jussieu , 75005 Paris , France
| | - Sha Zhu
- Sorbonne Université , CNRS, Institut Parisien de Chimie Moléculaire, UMR 8232 , 4 place Jussieu , 75005 Paris , France
| | - Lukasz F Sobala
- York Structural Biology Laboratory, Department of Chemistry , University of York , York YO10 5DD , U.K
| | | | | | - Yongmin Zhang
- Sorbonne Université , CNRS, Institut Parisien de Chimie Moléculaire, UMR 8232 , 4 place Jussieu , 75005 Paris , France
| | - Jesus Jiménez-Barbero
- Ikerbasque, Basque Foundation for Science , Maria Diaz de Haro 3 , 48013 Bilbao , Spain
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry , University of York , York YO10 5DD , U.K
| | - Matthieu Sollogoub
- Sorbonne Université , CNRS, Institut Parisien de Chimie Moléculaire, UMR 8232 , 4 place Jussieu , 75005 Paris , France
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11
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Schröder SP, Kallemeijn WW, Debets MF, Hansen T, Sobala LF, Hakki Z, Williams SJ, Beenakker TJM, Aerts JMFG, van der Marel GA, Codée JDC, Davies GJ, Overkleeft HS. Spiro-epoxyglycosides as Activity-Based Probes for Glycoside Hydrolase Family 99 Endomannosidase/Endomannanase. Chemistry 2018; 24:9983-9992. [PMID: 29797675 PMCID: PMC6055899 DOI: 10.1002/chem.201801902] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 05/23/2018] [Indexed: 11/06/2022]
Abstract
N-Glycans direct protein function, stability, folding and targeting, and influence immunogenicity. While most glycosidases that process N-glycans cleave a single sugar residue at a time, enzymes from glycoside hydrolase family 99 are endo-acting enzymes that cleave within complex N-glycans. Eukaryotic Golgi endo-1,2-α-mannosidase cleaves glucose-substituted mannose within immature glucosylated high-mannose N-glycans in the secretory pathway. Certain bacteria within the human gut microbiota produce endo-1,2-α-mannanase, which cleaves related structures within fungal mannan, as part of nutrient acquisition. An unconventional mechanism of catalysis was proposed for enzymes of this family, hinted at by crystal structures of imino/azasugars complexed within the active site. Based on this mechanism, we developed the synthesis of two glycosides bearing a spiro-epoxide at C-2 as electrophilic trap, to covalently bind a mechanistically important, conserved GH99 catalytic residue. The spiro-epoxyglycosides are equipped with a fluorescent tag, and following incubation with recombinant enzyme, allow concentration, time and pH dependent visualization of the bound enzyme using gel electrophoresis.
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Affiliation(s)
- Sybrin P. Schröder
- Department of Bioorganic ChemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Wouter W. Kallemeijn
- Department of Medical BiochemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Marjoke F. Debets
- Department of Bioorganic ChemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Thomas Hansen
- Department of Bioorganic ChemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Lukasz F. Sobala
- Department of Chemistry, York Structural Biology LaboratoryUniversity of YorkHeslingtonYorkYO10 5DDUK
| | - Zalihe Hakki
- School of Chemistry and Bio21 Molecular Science and Biotechnology InstituteUniversity of MelbourneParkvilleVictoriaAustralia
| | - Spencer J. Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology InstituteUniversity of MelbourneParkvilleVictoriaAustralia
| | - Thomas J. M. Beenakker
- Department of Bioorganic ChemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Johannes M. F. G. Aerts
- Department of Medical BiochemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Gijsbert A. van der Marel
- Department of Bioorganic ChemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Jeroen D. C. Codée
- Department of Bioorganic ChemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Gideon J. Davies
- Department of Chemistry, York Structural Biology LaboratoryUniversity of YorkHeslingtonYorkYO10 5DDUK
| | - Herman S. Overkleeft
- Department of Bioorganic ChemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
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12
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Fernandes PZ, Petricevic M, Sobala L, Davies GJ, Williams SJ. Exploration of Strategies for Mechanism-Based Inhibitor Design for Family GH99 endo-α-1,2-Mannanases. Chemistry 2018; 24:7464-7473. [PMID: 29508463 PMCID: PMC6001782 DOI: 10.1002/chem.201800435] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Indexed: 11/06/2022]
Abstract
endo-α-1,2-Mannosidases and -mannanases, members of glycoside hydrolase family 99 (GH99), cleave α-Glc/Man-1,3-α-Man-OR structures within mammalian N-linked glycans and fungal α-mannan, respectively. They are proposed to act through a two-step mechanism involving a 1,2-anhydrosugar "epoxide" intermediate incorporating two conserved catalytic carboxylates. In the first step, one carboxylate acts as a general base to deprotonate the 2-hydroxy group adjacent to the fissile glycosidic bond, and the other provides general acid assistance to the departure of the aglycon. We report herein the synthesis of two inhibitors designed to interact with either the general base (α-mannosyl-1,3-(2-aminodeoxymannojirimycin), Man2NH2 DMJ) or the general acid (α-mannosyl-1,3-mannoimidazole, ManManIm). Modest affinities were observed for an endo-α-1,2-mannanase from Bacteroides thetaiotaomicron. Structural studies revealed that Man2NH2 DMJ binds like other iminosugar inhibitors, which suggests that the poor inhibition shown by this compound is not a result of a failure to achieve the expected interaction with the general base, but rather the reduction in basicity of the endocyclic nitrogen caused by introduction of a vicinal, protonated amine at C2. ManManIm binds with the imidazole headgroup distorted downwards, a result of an unfavourable interaction with a conserved active site tyrosine. This study has identified important limitations associated with mechanism-inspired inhibitor design for GH99 enzymes.
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Affiliation(s)
- Pearl Z. Fernandes
- School of ChemistryBio21 Molecular Science and Biotechnology InstituteUniversity of MelbourneParkvilleVic3010Australia
| | - Marija Petricevic
- School of ChemistryBio21 Molecular Science and Biotechnology InstituteUniversity of MelbourneParkvilleVic3010Australia
| | - Lukasz Sobala
- York Structural Biology LaboratoryDepartment of ChemistryUniversity of YorkHeslingtonYO10 5DDUK
| | - Gideon J. Davies
- York Structural Biology LaboratoryDepartment of ChemistryUniversity of YorkHeslingtonYO10 5DDUK
| | - Spencer J. Williams
- School of ChemistryBio21 Molecular Science and Biotechnology InstituteUniversity of MelbourneParkvilleVic3010Australia
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13
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De Moliner F, Knox K, Reinders A, Ward JM, McLaughlin PJ, Oparka K, Vendrell M. Probing binding specificity of the sucrose transporter AtSUC2 with fluorescent coumarin glucosides. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:2473-2482. [PMID: 29506213 PMCID: PMC5920547 DOI: 10.1093/jxb/ery075] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 02/19/2018] [Indexed: 05/18/2023]
Abstract
The phloem sucrose transporter, AtSUC2, is promiscuous with respect to substrate recognition, transporting a range of glucosides in addition to sucrose, including naturally occurring coumarin glucosides. We used the inherent fluorescence of coumarin glucosides to probe the specificity of AtSUC2 for its substrates, and determined the structure-activity relationships that confer phloem transport in vivo using Arabidopsis seedlings. In addition to natural coumarin glucosides, we synthesized new compounds to identify key structural features that specify recognition by AtSUC2. Our analysis of the structure-activity relationship revealed that the presence of a free hydroxyl group on the coumarin moiety is essential for binding by AtSUC2 and subsequent phloem mobility. Structural modeling of the AtSUC2 substrate-binding pocket explains some important structural requirements for the interaction of coumarin glucosides with the AtSUC2 transporter.
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Affiliation(s)
- Fabio De Moliner
- MRC/UoE Centre for Inflammation Research, Queen’s Medical Research Institute, University of Edinburgh, UK
| | - Kirsten Knox
- Institute of Molecular Plant Sciences, Max Born Crescent, University of Edinburgh, UK
| | - Anke Reinders
- Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
| | - John M Ward
- Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
| | - Paul J McLaughlin
- Institute of Quantitative Biology, Biochemistry and Biotechnology, Max Born Crescent, University of Edinburgh, UK
| | - Karl Oparka
- Institute of Molecular Plant Sciences, Max Born Crescent, University of Edinburgh, UK
- Correspondence: or
| | - Marc Vendrell
- MRC/UoE Centre for Inflammation Research, Queen’s Medical Research Institute, University of Edinburgh, UK
- Correspondence: or
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14
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Liu YF, Liao CT, Chiang YC, Li CE, Hsiao YM. WxcX is involved in bacterial attachment and virulence in Xanthomonas campestris pv. campestris. J Basic Microbiol 2018; 58:403-413. [PMID: 29504631 DOI: 10.1002/jobm.201700591] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 02/06/2018] [Accepted: 02/07/2018] [Indexed: 11/08/2022]
Abstract
Xanthomonas campestris pv. campestris (Xcc) is the causative agent of black rot in crucifers. Here, one EZ-Tn5 transposon mutant of Xcc, altered in bacterial attachment, was isolated. Further analysis revealed that the transposon was inserted in the wxcX gene (encodes a hypothetical protein) of the transposon mutant. Sequence analysis revealed that WxcX is highly conserved in Xanthomonas, but none has been characterized. In this study, it was indicated that mutation of wxcX resulted in enhanced bacterial attachment, reduced virulence on the host cabbage, and increased sensitivity to sodium dodecyl sulfate. The affected phenotypes of the wxcX mutant could be complemented to wild-type levels by the intact wxcX gene. Site-directed mutagenesis revealed that E408 and E411 are critical amino acid residues for WxcX function in bacterial attachment. Taken together, our results demonstrate the roles of wxcX in attachment, virulence, and tolerance to sodium dodecyl sulfate in Xanthomonas for the first time.
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Affiliation(s)
- Yu-Fan Liu
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan.,Division of Allergy, Department of Pediatrics, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Chao-Tsai Liao
- Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung, Taiwan
| | - Ying-Chuan Chiang
- Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung, Taiwan
| | - Chih-En Li
- Graduate Institute of Biotechnology and Biomedical Engineering, Central Taiwan University of Science and Technology, Taichung, Taiwan
| | - Yi-Min Hsiao
- Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung, Taiwan
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15
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Robb CS, Mystkowska AA, Hehemann JH. Crystal structure of a marine glycoside hydrolase family 99-related protein lacking catalytic machinery. Protein Sci 2017; 26:2445-2450. [PMID: 28884852 DOI: 10.1002/pro.3291] [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: 07/19/2017] [Revised: 09/05/2017] [Accepted: 09/06/2017] [Indexed: 11/10/2022]
Abstract
Algal polysaccharides of diverse structures are one of the most abundant carbon resources for heterotrophic, marine bacteria with coevolved digestive enzymes. A putative sulfo-mannan polysaccharide utilization locus, which is conserved in marine flavobacteria, contains an unusual GH99-like protein that lacks the conserved catalytic residues of glycoside hydrolase family 99. Using X-ray crystallography, we structurally characterized this protein from the marine flavobacterium Ochrovirga pacifica to help elucidate its molecular function. The structure reveals the absence of potential catalytic residues for polysaccharide hydrolysis, which-together with additional structural features-suggests this protein may be noncatalytic and involved in carbohydrate binding.
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Affiliation(s)
- Craig S Robb
- Center for Marine Environmental Sciences, University of Bremen (MARUM), Bremen, 28359, Germany.,Max Planck-Institute for Marine Microbiology, Bremen, 28359, Germany
| | - Agata Anna Mystkowska
- Center for Marine Environmental Sciences, University of Bremen (MARUM), Bremen, 28359, Germany.,Max Planck-Institute for Marine Microbiology, Bremen, 28359, Germany
| | - Jan-Hendrik Hehemann
- Center for Marine Environmental Sciences, University of Bremen (MARUM), Bremen, 28359, Germany.,Max Planck-Institute for Marine Microbiology, Bremen, 28359, Germany
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16
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Petricevic M, Sobala LF, Fernandes PZ, Raich L, Thompson AJ, Bernardo-Seisdedos G, Millet O, Zhu S, Sollogoub M, Jiménez-Barbero J, Rovira C, Davies GJ, Williams SJ. Contribution of Shape and Charge to the Inhibition of a Family GH99 endo-α-1,2-Mannanase. J Am Chem Soc 2017; 139:1089-1097. [PMID: 27992199 PMCID: PMC5269645 DOI: 10.1021/jacs.6b10075] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Inhibitor
design incorporating features of the reaction coordinate
and transition-state structure has emerged as a powerful approach
for the development of enzyme inhibitors. Such inhibitors find use
as mechanistic probes, chemical biology tools, and therapeutics. Endo-α-1,2-mannosidases and endo-α-1,2-mannanases,
members of glycoside hydrolase family 99 (GH99), are interesting targets
for inhibitor development as they play key roles in N-glycan maturation
and microbiotal yeast mannan degradation, respectively. These enzymes
are proposed to act via a 1,2-anhydrosugar “epoxide”
mechanism that proceeds through an unusual conformational itinerary.
Here, we explore how shape and charge contribute to binding of diverse
inhibitors of these enzymes. We report the synthesis of neutral dideoxy,
glucal and cyclohexenyl disaccharide inhibitors, their binding to
GH99 endo-α-1,2-mannanases, and their structural
analysis by X-ray crystallography. Quantum mechanical calculations
of the free energy landscapes reveal how the neutral inhibitors provide
shape but not charge mimicry of the proposed intermediate and transition
state structures. Building upon the knowledge of shape and charge
contributions to inhibition of family GH99 enzymes, we design and
synthesize α-Man-1,3-noeuromycin, which is revealed to be the
most potent inhibitor (KD 13 nM for Bacteroides xylanisolvens GH99 enzyme) of these enzymes
yet reported. This work reveals how shape and charge mimicry of transition
state features can enable the rational design of potent inhibitors.
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Affiliation(s)
- Marija Petricevic
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne , Parkville 3010, Australia
| | - Lukasz F Sobala
- York Structural Biology Laboratory, Department of Chemistry, University of York , York YO10 5DD, United Kingdom
| | - Pearl Z Fernandes
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne , Parkville 3010, Australia
| | - Lluís Raich
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona , Martí i Franquès 1, 08028 Barcelona, Spain
| | - Andrew J Thompson
- York Structural Biology Laboratory, Department of Chemistry, University of York , York YO10 5DD, United Kingdom
| | - Ganeko Bernardo-Seisdedos
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, Building 800, 48160 Derio, Spain
| | - Oscar Millet
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, Building 800, 48160 Derio, Spain
| | - Sha Zhu
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Institut Parisien de Chimie Moléculaire (IPCM), UMR 8232, 4, place Jussieu, 75005 Paris, France
| | - Matthieu Sollogoub
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Institut Parisien de Chimie Moléculaire (IPCM), UMR 8232, 4, place Jussieu, 75005 Paris, France
| | - Jesús Jiménez-Barbero
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, Building 800, 48160 Derio, Spain.,Ikerbasque, Basque Foundation for Science, Marı́a Dı́az de Haro 3, 48013 Bilbao, Spain
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) & 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) , Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York , York YO10 5DD, United Kingdom
| | - Spencer J Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne , Parkville 3010, Australia
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