1
|
Vuksanovic N, Clasman JR, Imperiali B, Allen KN. Specificity determinants revealed by the structure of glycosyltransferase Campylobacter concisus PglA. Protein Sci 2024; 33:e4848. [PMID: 38019455 PMCID: PMC10731488 DOI: 10.1002/pro.4848] [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: 09/09/2023] [Revised: 11/23/2023] [Accepted: 11/25/2023] [Indexed: 11/30/2023]
Abstract
In selected Campylobacter species, the biosynthesis of N-linked glycoconjugates via the pgl pathway is essential for pathogenicity and survival. However, most of the membrane-associated GT-B fold glycosyltransferases responsible for diversifying glycans in this pathway have not been structurally characterized which hinders the understanding of the structural factors that govern substrate specificity and prediction of resulting glycan composition. Herein, we report the 1.8 Å resolution structure of Campylobacter concisus PglA, the glycosyltransferase responsible for the transfer of N-acetylgalatosamine (GalNAc) from uridine 5'-diphospho-N-acetylgalactosamine (UDP-GalNAc) to undecaprenyl-diphospho-N,N'-diacetylbacillosamine (UndPP-diNAcBac) in complex with the sugar donor GalNAc. This study identifies distinguishing characteristics that set PglA apart within the GT4 enzyme family. Computational docking of the structure in the membrane in comparison to homologs points to differences in interactions with the membrane-embedded acceptor and the structural analysis of the complex together with bioinformatics and site-directed mutagenesis identifies donor sugar binding motifs. Notably, E113, conserved solely among PglA enzymes, forms a hydrogen bond with the GalNAc C6″-OH. Mutagenesis of E113 reveals activity consistent with this role in substrate binding, rather than stabilization of the oxocarbenium ion transition state, a function sometimes ascribed to the corresponding residue in GT4 homologs. The bioinformatic analyses reveal a substrate-specificity motif, showing that Pro281 in a substrate binding loop of PglA directs configurational preference for GalNAc over GlcNAc. This proline is replaced by a conformationally flexible glycine, even in distant homologs, which favor substrates with the same stereochemistry at C4, such as glucose. The signature loop is conserved across all Campylobacter PglA enzymes, emphasizing its importance in substrate specificity.
Collapse
Affiliation(s)
| | | | - Barbara Imperiali
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Karen N. Allen
- Department of ChemistryBoston UniversityBostonMassachusettsUSA
| |
Collapse
|
2
|
Gheorghita AA, Wozniak DJ, Parsek MR, Howell PL. Pseudomonas aeruginosa biofilm exopolysaccharides: assembly, function, and degradation. FEMS Microbiol Rev 2023; 47:fuad060. [PMID: 37884397 PMCID: PMC10644985 DOI: 10.1093/femsre/fuad060] [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: 04/21/2023] [Revised: 10/04/2023] [Accepted: 10/25/2023] [Indexed: 10/28/2023] Open
Abstract
The biofilm matrix is a fortress; sheltering bacteria in a protective and nourishing barrier that allows for growth and adaptation to various surroundings. A variety of different components are found within the matrix including water, lipids, proteins, extracellular DNA, RNA, membrane vesicles, phages, and exopolysaccharides. As part of its biofilm matrix, Pseudomonas aeruginosa is genetically capable of producing three chemically distinct exopolysaccharides - alginate, Pel, and Psl - each of which has a distinct role in biofilm formation and immune evasion during infection. The polymers are produced by highly conserved mechanisms of secretion, involving many proteins that span both the inner and outer bacterial membranes. Experimentally determined structures, predictive modelling of proteins whose structures are yet to be solved, and structural homology comparisons give us insight into the molecular mechanisms of these secretion systems, from polymer synthesis to modification and export. Here, we review recent advances that enhance our understanding of P. aeruginosa multiprotein exopolysaccharide biosynthetic complexes, and how the glycoside hydrolases/lyases within these systems have been commandeered for antimicrobial applications.
Collapse
Affiliation(s)
- Andreea A Gheorghita
- Program in Molecular Medicine, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, 686 Bay St, Toronto, ON M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Medical Science Building, 1 King's College Cir, Toronto, ON M5S 1A8, Canada
| | - Daniel J Wozniak
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, 776 Biomedical Research Tower, 460 W 12th Ave, Columbus, OH 43210, United States
- Department of Microbiology, The Ohio State University College, Biological Sciences Bldg, 105, 484 W 12th Ave, Columbus, OH 43210, United States
| | - Matthew R Parsek
- Department of Microbiology, University of Washington, Health Sciences Bldg, 1705 NE Pacific St, Seattle, WA 98195-7735, United States
| | - P Lynne Howell
- Program in Molecular Medicine, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, 686 Bay St, Toronto, ON M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Medical Science Building, 1 King's College Cir, Toronto, ON M5S 1A8, Canada
| |
Collapse
|
3
|
Bloch JS, John A, Mao R, Mukherjee S, Boilevin J, Irobalieva RN, Darbre T, Scott NE, Reymond JL, Kossiakoff AA, Goddard-Borger ED, Locher KP. Structure, sequon recognition and mechanism of tryptophan C-mannosyltransferase. Nat Chem Biol 2023; 19:575-584. [PMID: 36604564 PMCID: PMC10154233 DOI: 10.1038/s41589-022-01219-9] [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: 06/22/2022] [Accepted: 10/28/2022] [Indexed: 01/07/2023]
Abstract
C-linked glycosylation is essential for the trafficking, folding and function of secretory and transmembrane proteins involved in cellular communication processes. The tryptophan C-mannosyltransferase (CMT) enzymes that install the modification attach a mannose to the first tryptophan of WxxW/C sequons in nascent polypeptide chains by an unknown mechanism. Here, we report cryogenic-electron microscopy structures of Caenorhabditis elegans CMT in four key states: apo, acceptor peptide-bound, donor-substrate analog-bound and as a trapped ternary complex with both peptide and a donor-substrate mimic bound. The structures indicate how the C-mannosylation sequon is recognized by this CMT and its paralogs, and how sequon binding triggers conformational activation of the donor substrate: a process relevant to all glycosyltransferase C superfamily enzymes. Our structural data further indicate that the CMTs adopt an unprecedented electrophilic aromatic substitution mechanism to enable the C-glycosylation of proteins. These results afford opportunities for understanding human disease and therapeutic targeting of specific CMT paralogs.
Collapse
Affiliation(s)
- Joël S Bloch
- Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland
- Laboratory of Molecular Neurobiology and Biophysics and Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Alan John
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Runyu Mao
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Somnath Mukherjee
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Jérémy Boilevin
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | | | - Tamis Darbre
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Nichollas E Scott
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Jean-Louis Reymond
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Ethan D Goddard-Borger
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.
| | - Kaspar P Locher
- Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland.
| |
Collapse
|
4
|
Ramírez AS, Boilevin J, Mehdipour AR, Hummer G, Darbre T, Reymond JL, Locher KP. Structural basis of the molecular ruler mechanism of a bacterial glycosyltransferase. Nat Commun 2018; 9:445. [PMID: 29386647 PMCID: PMC5792488 DOI: 10.1038/s41467-018-02880-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 01/02/2018] [Indexed: 11/09/2022] Open
Abstract
The membrane-associated, processive and retaining glycosyltransferase PglH from Campylobacter jejuni is part of the biosynthetic pathway of the lipid-linked oligosaccharide (LLO) that serves as the glycan donor in bacterial protein N-glycosylation. Using an unknown counting mechanism, PglH catalyzes the transfer of exactly three α1,4 N-acetylgalactosamine (GalNAc) units to the growing LLO precursor, GalNAc-α1,4-GalNAc-α1,3-Bac-α1-PP-undecaprenyl. Here, we present crystal structures of PglH in three distinct states, including a binary complex with UDP-GalNAc and two ternary complexes containing a chemo-enzymatically generated LLO analog and either UDP or synthetic, nonhydrolyzable UDP-CH2-GalNAc. PglH contains an amphipathic helix ("ruler helix") that has a dual role of facilitating membrane attachment and glycan counting. The ruler helix contains three positively charged side chains that can bind the pyrophosphate group of the LLO substrate and thus limit the addition of GalNAc units to three. These results, combined with molecular dynamics simulations, provide the mechanism of glycan counting by PglH.
Collapse
Affiliation(s)
- Ana S Ramírez
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH), CH-8093, Zürich, Switzerland
| | - Jérémy Boilevin
- Department of Chemistry and Biochemistry, University of Berne, CH-3012, Berne, Switzerland
| | - Ahmad Reza Mehdipour
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, DE-60438, Frankfurt, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, DE-60438, Frankfurt, Germany.,Institute of Biophysics, Goethe University, DE-60438, Frankfurt, Germany
| | - Tamis Darbre
- Department of Chemistry and Biochemistry, University of Berne, CH-3012, Berne, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Berne, CH-3012, Berne, Switzerland
| | - Kaspar P Locher
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH), CH-8093, Zürich, Switzerland.
| |
Collapse
|