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Fekry M, Dave KK, Badgujar D, Hamnevik E, Aurelius O, Dobritzsch D, Danielson UH. The Crystal Structure of Tyrosinase from Verrucomicrobium spinosum Reveals It to Be an Atypical Bacterial Tyrosinase. Biomolecules 2023; 13:1360. [PMID: 37759761 PMCID: PMC10526336 DOI: 10.3390/biom13091360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Tyrosinases belong to the type-III copper enzyme family, which is involved in melanin production in a wide range of organisms. Despite similar overall characteristics and functions, their structures, activities, substrate specificities and regulation vary. The tyrosinase from the bacterium Verrucomicrobium spinosum (vsTyr) is produced as a pre-pro-enzyme in which a C-terminal extension serves as an inactivation domain. It does not require a caddie protein for copper ion incorporation, which makes it similar to eukaryotic tyrosinases. To gain an understanding of the catalytic machinery and regulation of vsTyr activity, we determined the structure of the catalytically active "core domain" of vsTyr by X-ray crystallography. The analysis showed that vsTyr is an atypical bacterial tyrosinase not only because it is independent of a caddie protein but also because it shows the highest structural (and sequence) similarity to plant-derived members of the type-III copper enzyme family and is more closely related to fungal tyrosinases regarding active site features. By modelling the structure of the pre-pro-enzyme using AlphaFold, we observed that Phe453, located in the C-terminal extension, is appropriately positioned to function as a "gatekeeper" residue. Our findings raise questions concerning the evolutionary origin of vsTyr.
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Affiliation(s)
- Mostafa Fekry
- Department of Chemistry—BMC, Uppsala University, SE 751 23 Uppsala, Sweden; (M.F.); (K.K.D.); (D.B.); (E.H.); (D.D.)
- Biophysics Department, Faculty of Science, Cairo University, Giza 12613, Egypt
| | - Khyati K. Dave
- Department of Chemistry—BMC, Uppsala University, SE 751 23 Uppsala, Sweden; (M.F.); (K.K.D.); (D.B.); (E.H.); (D.D.)
| | - Dilip Badgujar
- Department of Chemistry—BMC, Uppsala University, SE 751 23 Uppsala, Sweden; (M.F.); (K.K.D.); (D.B.); (E.H.); (D.D.)
| | - Emil Hamnevik
- Department of Chemistry—BMC, Uppsala University, SE 751 23 Uppsala, Sweden; (M.F.); (K.K.D.); (D.B.); (E.H.); (D.D.)
| | | | - Doreen Dobritzsch
- Department of Chemistry—BMC, Uppsala University, SE 751 23 Uppsala, Sweden; (M.F.); (K.K.D.); (D.B.); (E.H.); (D.D.)
| | - U. Helena Danielson
- Department of Chemistry—BMC, Uppsala University, SE 751 23 Uppsala, Sweden; (M.F.); (K.K.D.); (D.B.); (E.H.); (D.D.)
- Science for Life Laboratory, Drug Discovery & Development Platform, Uppsala University, SE 751 23 Uppsala, Sweden
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Zhang L, Wang W, Yang Y, Zhu W, Li P, Wang S, Liu X. Site-specific, covalent immobilization of PNGase F on magnetic particles mediated by microbial transglutaminase. Anal Chim Acta 2023; 1250:340972. [PMID: 36898812 DOI: 10.1016/j.aca.2023.340972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 02/06/2023] [Accepted: 02/12/2023] [Indexed: 02/16/2023]
Abstract
In the workflow of global N-glycosylation analysis, endoglycosidase-mediated removal of glycans from glycoproteins is an essential and rate-limiting step. Peptide-N-glycosidase F (PNGase F) is the most appropriate and efficient endoglycosidase for the removal of N-glycans from glycoproteins prior to analysis. Due to the high demand for PNGase F in both basic and industrial research, convenient and efficient methods are urgently needed to generate PNGase F, preferably in the immobilized form to solid phases. However, there is no integrated approach to implement both efficient expression, and site-specific immobilization of PNGase F. Herein, efficient production of PNGase F with a glutamine tag in Escherichia coli and site-specific covalent immobilization of PNGase F with this special tag via microbial transglutaminase (MTG) is described. PNGase F was fused with a glutamine tag to facilitate the co-expression of proteins in the supernatant. The glutamine tag was covalently and site-specifically transformed to primary amine-containing magnetic particles, mediated by MTG, to immobilize PNGase F. Immobilized PNGase F could deglycosylate substrates with identical enzymatic performance to that of the soluble counterpart, and exhibit good reusability and thermal stability. Moreover, the immobilized PNGase F could also be applied to clinical samples, including serum and saliva.
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Affiliation(s)
- Liang Zhang
- Hubei Superior Discipline Group of Exercise and Brain Science from Hubei Provincial, Wuhan Sports University, Wuhan, 430079, China
| | - Wenhui Wang
- Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Yueqin Yang
- Exercise Immunology Center, Wuhan Sports University, Wuhan, 430079, China
| | - Wenjie Zhu
- Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Pengjie Li
- Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Song Wang
- Hubei Superior Discipline Group of Exercise and Brain Science from Hubei Provincial, Wuhan Sports University, Wuhan, 430079, China.
| | - Xin Liu
- Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
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Kashima T, Ishiwata A, Fujita K, Fushinobu S. Identification and structural basis of an enzyme that degrades oligosaccharides in caramel. Biophys Physicobiol 2023; 20:e200017. [PMID: 38496246 PMCID: PMC10941961 DOI: 10.2142/biophysico.bppb-v20.0017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/27/2023] [Indexed: 03/30/2023] Open
Abstract
Cooking with fire produces foods containing carbohydrates that are not naturally occurring, such as α-d-fructofuranoside found in caramel. Each of the hundreds of compounds produced by caramelization reactions is considered to possess its own characteristics. Various studies from the viewpoints of biology and biochemistry have been conducted to elucidate some of the scientific characteristics. Here, we review the composition of caramelized sugars and then describe the enzymatic studies that have been conducted and the physiological functions of the caramelized sugar components that have been elucidated. In particular, we recently identified a glycoside hydrolase (GH), GH172 difructose dianhydride I synthase/hydrolase (αFFase1), from oral and intestinal bacteria, which is implicated in the degradation of oligosaccharides in caramel. The structural basis of αFFase1 and its ligands provided many insights. This discovery opened the door to several research fields, including the structural and phylogenetic relationship between the GH172 family enzymes and viral capsid proteins and the degradation of cell membrane glycans of acid-fast bacteria by some αFFase1 homologs. This review article is an extended version of the Japanese article, Identification and Structural Basis of an Enzyme Degrading Oligosaccharides in Caramel, published in SEIBUTSU BUTSURI Vol. 62, p. 184-186 (2022).
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Affiliation(s)
- Toma Kashima
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Akihiro Ishiwata
- Cluster for Pioneering Research, RIKEN, Wako, Saitama 351-0198, Japan
| | - Kiyotaka Fujita
- Faculty of Agriculture, Kagoshima University, Korimoto, Kagoshima 890-0065, Japan
| | - Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
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Ji S, Tian X, Li X, She Q. Identification and structural analysis of a carbohydrate-binding module specific to alginate, a representative of a new family, CBM96. J Biol Chem 2023; 299:102854. [PMID: 36592931 PMCID: PMC9971899 DOI: 10.1016/j.jbc.2022.102854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 12/23/2022] [Accepted: 12/27/2022] [Indexed: 01/01/2023] Open
Abstract
Carbohydrate-binding modules (CBMs) are the noncatalytic modules that assist functions of the catalytic modules in carbohydrate-active enzymes, and they are usually discrete structural domains in larger multimodular enzymes. CBMs often occur in tandem in different alginate lyases belonging to the CBM families 13, 16, and 32. However, none of the currently known CBMs in alginate lyases specifically bind to an internal alginate chain. In our investigation of the multidomain alginate lyase Dp0100 carrying several ancillary domains, we identified an alginate-binding domain denoted TM6-N4 using protein truncation analysis. The structure of this CBM domain was determined at 1.35 Å resolution. TM6-N4 exhibited an overall β-sandwich fold architecture with two antiparallel β-sheets. We identified an extended binding groove in the CBM using site-directed mutagenesis, docking, and surface electrostatic potential analysis. Affinity analysis revealed that residues of Lys10, Lys22, Lys25, Lys27, Lys31, Arg36, and Tyr159 located on the bottom or the wall of the shallow groove are responsible for alginate binding, and isothermal titration calorimetry analyses indicated that the binding cleft consists of six subsites for sugar recognition. This substrate binding pattern is typical for type B CBM, and it represents the first CBM domain that specifically binds internal alginate chain. Phylogenetic analysis supports that TM6-N4 constitutes the founding member of a new CBM family denoted as CBM96. Our reported structure not only facilitates the investigation of the CBM-alginate ligand recognition mechanism but also inspires the utilization of the CBM domain in biotechnical applications.
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Affiliation(s)
- Shiqi Ji
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China.
| | - Xuhui Tian
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Xin Li
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Qunxin She
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China.
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Miao X, Wu J, Chen H, Lu G. Comprehensive Analysis of the Structure and Function of Peptide:N-Glycanase 1 and Relationship with Congenital Disorder of Deglycosylation. Nutrients 2022; 14:nu14091690. [PMID: 35565658 PMCID: PMC9102325 DOI: 10.3390/nu14091690] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 02/01/2023] Open
Abstract
The cytosolic PNGase (peptide:N-glycanase), also known as peptide-N4-(N-acetyl-β-glucosaminyl)-asparagine amidase, is a well-conserved deglycosylation enzyme (EC 3.5.1.52) which catalyzes the non-lysosomal hydrolysis of an N(4)-(acetyl-β-d-glucosaminyl) asparagine residue (Asn, N) into a N-acetyl-β-d-glucosaminyl-amine and a peptide containing an aspartate residue (Asp, D). This enzyme (NGLY1) plays an essential role in the clearance of misfolded or unassembled glycoproteins through a process named ER-associated degradation (ERAD). Accumulating evidence also points out that NGLY1 deficiency can cause an autosomal recessive (AR) human genetic disorder associated with abnormal development and congenital disorder of deglycosylation. In addition, the loss of NGLY1 can affect multiple cellular pathways, including but not limited to NFE2L1 pathway, Creb1/Atf1-AQP pathway, BMP pathway, AMPK pathway, and SLC12A2 ion transporter, which might be the underlying reasons for a constellation of clinical phenotypes of NGLY1 deficiency. The current comprehensive review uncovers the NGLY1’ssdetailed structure and its important roles for participation in ERAD, involvement in CDDG and potential treatment for NGLY1 deficiency.
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Affiliation(s)
- Xiangguang Miao
- Queen Mary School, Nanchang University, No. 1299 Xuefu Avenue, Honggutan New District, Nanchang 330036, China;
| | - Jin Wu
- Laboratory of Translational Medicine Research, Department of Pathology, Deyang People’s Hospital, No. 173 First Section of Taishanbei Road, Jingyang District, Deyang 618000, China;
- Deyang Key Laboratory of Tumor Molecular Research, No. 173 First Section of Taishanbei Road, Jingyang District, Deyang 618000, China
- Department of Molecular & Cellular Biology, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Hongping Chen
- Department of Histology and Embryology, Medical College of Nanchang University, Nanchang 330006, China
- Correspondence: (H.C.); (G.L.); Tel.: +86-188-0147-4087 (G.L.)
| | - Guanting Lu
- Laboratory of Translational Medicine Research, Department of Pathology, Deyang People’s Hospital, No. 173 First Section of Taishanbei Road, Jingyang District, Deyang 618000, China;
- Deyang Key Laboratory of Tumor Molecular Research, No. 173 First Section of Taishanbei Road, Jingyang District, Deyang 618000, China
- Correspondence: (H.C.); (G.L.); Tel.: +86-188-0147-4087 (G.L.)
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Kovács N, Farsang R, Szigeti M, Vonderviszt F, Jankovics H. Enhanced Recombinant Protein Production of Soluble, Highly Active and Immobilizable PNGase F. Mol Biotechnol 2022; 64:914-918. [PMID: 35244857 PMCID: PMC9259526 DOI: 10.1007/s12033-022-00464-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 02/11/2022] [Indexed: 11/30/2022]
Abstract
High resolution analysis of N-glycans can be performed after their endoglycosidase mediated removal from proteins. N-glycosidase F peptide (PNGase F) is one the most frequently used enzyme for this purpose. Because of the significant demand for PNGase F both in basic and applied research, rapid and inexpensive methods are of great demand for its large-scale production, preferably in immobilizable form to solid supports or surfaces. In this paper, we report on the high-yield production of N-terminal 6His-PNGase F enzyme in a bacterial Escherichia coli SHuffle expression system. The activity profile of the generated enzyme was compared to commercially available PNGase F enzymes, featuring higher activity for the former. The method described here is thus suitable for the cost-effective production of PNGase F in an active, immobilizable form.
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Affiliation(s)
- Noémi Kovács
- Bio-Nanosystems Laboratory, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, 10 Egyetem Street, Veszprém, 8200, Hungary
| | - Róbert Farsang
- Translational Glycomics Research Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, 10 Egyetem Street, Veszprém, 8200, Hungary
| | - Márton Szigeti
- Translational Glycomics Research Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, 10 Egyetem Street, Veszprém, 8200, Hungary
| | - Ferenc Vonderviszt
- Bio-Nanosystems Laboratory, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, 10 Egyetem Street, Veszprém, 8200, Hungary
| | - Hajnalka Jankovics
- Bio-Nanosystems Laboratory, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, 10 Egyetem Street, Veszprém, 8200, Hungary.
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Wardman JF, Rahfeld P, Liu F, Morgan-Lang C, Sim L, Hallam SJ, Withers SG. Discovery and Development of Promiscuous O-Glycan Hydrolases for Removal of Intact Sialyl T-Antigen. ACS Chem Biol 2021; 16:2004-2015. [PMID: 34309358 DOI: 10.1021/acschembio.1c00316] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Mucin-type O-glycosylation (O-glycosylation) is a common post-translational modification that confers distinct biophysical properties to proteins and plays crucial roles in intercellular signaling. Yet, despite the importance of O-glycans, relatively few tools exist for their analysis and modification. In particular, there is a need for enzymes that can cleave the wide range of O-glycan structures found on protein surfaces, to facilitate glycan profiling and editing. Through functional metagenomic screening of the human gut microbiome, we discovered endo-O-glycan hydrolases from CAZy family GH101 that are capable of slowly cleaving the intact sialyl T-antigen trisaccharide (a ubiquitous O-glycan structure in humans) in addition to their primary activity against the T-antigen disaccharide. We then further explored this sequence space through phylogenetic profiling and analysis of representative enzymes, revealing large differences in the levels of this promiscuous activity between enzymes within the family. Through structural and sequence analysis, we identified active site residues that modulate specificity. Through subsequent rational protein engineering, we improved the activity of an enzyme identified by phylogenetic profiling sufficiently that substantial removal of the intact sialyl T-antigen from proteins could be readily achieved. Our best sialyl T-antigen hydrolase mutant, SpGH101 Q868G, is further shown to function on a number of proteins, tissues, and cells. Access to this enzyme opens up improved methodologies for unraveling the glycan code.
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Affiliation(s)
- Jacob F. Wardman
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Peter Rahfeld
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Feng Liu
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Connor Morgan-Lang
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Lyann Sim
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Steven J. Hallam
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
- Genome Science and Technology Program, University of British Columbia, 2329 West Mall, Vancouver, British Columbia V6T 1Z4, Canada
- Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Stephen G. Withers
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
- Genome Science and Technology Program, University of British Columbia, 2329 West Mall, Vancouver, British Columbia V6T 1Z4, Canada
- ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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Bokhari H, Maryam A, Shahid R, Siddiqi AR. Oligosaccharyltransferase PglB of Campylobacter jejuni is a glycoprotein. World J Microbiol Biotechnol 2019; 36:9. [PMID: 31858269 DOI: 10.1007/s11274-019-2784-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 12/10/2019] [Indexed: 11/29/2022]
Abstract
Campylobacter jejuni is the one of the leading cause of bacterial food borne gastroenteritis. PglB, a glycosyltransferase, plays a crucial role of mediating glycosylation of numerous periplasmic proteins. It catalyzes N-glycosylation at the sequon D/E-X1-N-X2-S/T in its substrate proteins. Here we report that the PglB itself is a glycoprotein which self-glycosylates at N534 site in its DYNQS sequon by its own catalytic WWDYG motif. Site-directed mutagenesis, lectin Immunoblot, and mobility shift assays confirmed that the DYNQS is an N-glycosylation motif. PglB's N-glycosylation motif is structurally and functionally similar to its widely studied glycosylation substrate, the OMPH1. Its DYNQS motif forms a solvent-exposed crest. This motif is close to a cluster of polar and hydrophilic residues, which form a loop flanked by two α helices. This arrangement extremely apposite for auto-glycosylation at N534. This self-glycosylation ability of PglB could mediate C. jejuni's ability to colonize the intestinal epithelium. Further this capability may also bear significance for the development of novel conjugated vaccines and diagnostic tests.
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Affiliation(s)
- Habib Bokhari
- Department of Biosciences, COMSATS University, Islamabad, Chak Shazad Campus, Islamabad, Pakistan.
| | - Arooma Maryam
- Department of Biosciences, COMSATS University, Islamabad, Chak Shazad Campus, Islamabad, Pakistan
| | - Ramla Shahid
- Department of Biosciences, COMSATS University, Islamabad, Chak Shazad Campus, Islamabad, Pakistan
| | - Abdul Rauf Siddiqi
- Department of Biosciences, COMSATS University, Islamabad, Chak Shazad Campus, Islamabad, Pakistan
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Nakatsuji Y, Kobayashi Y, Takemoto Y. Direct Addition of Amides to Glycals Enabled by Solvation‐Insusceptible 2‐Haloazolium Salt Catalysis. Angew Chem Int Ed Engl 2019; 131:14253-14257. [DOI: 10.1002/ange.201907129] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Nakatsuji Y, Kobayashi Y, Takemoto Y. Direct Addition of Amides to Glycals Enabled by Solvation-Insusceptible 2-Haloazolium Salt Catalysis. Angew Chem Int Ed Engl 2019; 58:14115-14119. [PMID: 31392793 DOI: 10.1002/anie.201907129] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/24/2019] [Indexed: 01/12/2023]
Abstract
The direct 2-deoxyglycosylation of nucleophiles with glycals leads to biologically and pharmacologically important 2-deoxysugar compounds. Although the direct addition of hydroxyl and sulfonamide groups have been well developed, the direct 2-deoxyglycosylation of amide groups has not been reported to date. Herein, we show the first direct 2-deoxyglycosylation of amide groups using a newly designed Brønsted acid catalyst under mild conditions. Through mechanistic investigations, we discovered that the amide group can inhibit acid catalysts, and the inhibition has made the 2-deoxyglycosylation reaction difficult. Diffusion-ordered two-dimensional NMR spectroscopy analysis implied that the 2-chloroazolium salt catalyst was less likely to form aggregates with amides in comparison to other acid catalysts. The chlorine atom and the extended π-scaffold of the catalyst played a crucial role for this phenomenon. This relative insusceptibility to inhibition by amides is more responsible for the catalytic activity than the strength of the acidity.
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Affiliation(s)
- Yuya Nakatsuji
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Shimoadachi-cho, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Yusuke Kobayashi
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Shimoadachi-cho, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Yoshiji Takemoto
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Shimoadachi-cho, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan
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Wang T, Zheng SL, Liu L, Voglmeir J. Development of a colorimetric PNGase activity assay. Carbohydr Res 2019; 472:58-64. [PMID: 30476755 DOI: 10.1016/j.carres.2018.11.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/19/2018] [Accepted: 11/10/2018] [Indexed: 11/22/2022]
Abstract
PNGases are crucial targets and valuable tools in analyzing asparagine-linked carbohydrate moieties (N-glycans) of glycoproteins. Activity tests of PNGases have been little improved since their discovery four decades ago, and still rely on observing deglycosylation patterns of glycoproteins or glycopeptides using SDS-PAGE or HPLC analysis. These techniques cannot be easily adapted for automated sampling and high-throughput procedures. Herein, we describe a PNGase activity assay which relies on the conversion of WST-1, a yellowish, water-soluble tetrazolium dye (sodium 2-(4-Iodophenyl)-3-(4-nitro-phenyl)-5-(2,4-disulfophenyl)-2H-tetrazolate), into a blue formazan dye. In this work, we showed that WST-1 could be reduced by N-glycans, which were enzymatically released from glycoprotein substrates. After optimization of the assay conditions, the robustness of the method was challenged by quantifying the activity of various PNGase isoforms at different purification stages using a microwell plate reader. Furthermore, the assay could be used to obtain steady-state kinetics of PNGase H+ wild-type and mutant variants, which showed significant differences in their enzymatic reaction rates. The simplicity and robustness of this method might be of benefit for the detection of PNGase activity in routine applications of large amounts of samples.
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Masuda A, Xu J, Mitsudome T, Nagata Y, Morokuma D, Mon H, Banno Y, Kusakabe T, Lee JM. Mass Production of an Active Peptide-N-Glycosidase F Using Silkworm-Baculovirus Expression System. Mol Biotechnol 2015; 57:735-45. [DOI: 10.1007/s12033-015-9866-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Sun G, Yu X, Bao C, Wang L, Li M, Gan J, Qu D, Ma J, Chen L. Identification and characterization of a novel prokaryotic peptide: N-glycosidase from Elizabethkingia meningoseptica. J Biol Chem 2015; 290:7452-62. [PMID: 25614628 DOI: 10.1074/jbc.m114.605493] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Peptide:N-glycosidase (PNGase) F, the first PNGase identified in prokaryotic cells, catalyzes the removal of intact asparagine-linked oligosaccharide chains from glycoproteins and/or glycopeptides. Since its discovery in 1984, PNGase F has remained as the sole prokaryotic PNGase. Recently, a novel gene encoding a protein with a predicted PNGase domain was identified from a clinical isolate of Elizabethkingia meningoseptica. In this study, the candidate protein was expressed in vitro and was subjected to biochemical and structural analyses. The results revealed that it possesses PNGase activity and has substrate specificity different from that of PNGase F. The crystal structure of the protein was determined at 1.9 Å resolution. Structural comparison with PNGase F revealed a relatively larger glycan-binding groove in the catalytic domain and an additional bowl-like domain with unknown function at the N terminus of the candidate protein. These structural and functional analyses indicated that the candidate protein is a novel prokaryotic N-glycosidase. The protein has been named PNGase F-II.
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Affiliation(s)
- Guiqin Sun
- From the Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, Shanghai Medical College, Fudan University, Shanghai 200032, China, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Xiang Yu
- the State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Celimuge Bao
- From the Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Lei Wang
- From the Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Meng Li
- From the Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Jianhua Gan
- the Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China, and
| | - Di Qu
- From the Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Jinbiao Ma
- the State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China,
| | - Li Chen
- From the Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, Shanghai Medical College, Fudan University, Shanghai 200032, China,
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14
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Chen W, Smeekens JM, Wu R. Comprehensive Analysis of Protein N-Glycosylation Sites by Combining Chemical Deglycosylation with LC–MS. J Proteome Res 2014; 13:1466-73. [DOI: 10.1021/pr401000c] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Weixuan Chen
- School
of Chemistry and Biochemistry
and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Johanna M. Smeekens
- School
of Chemistry and Biochemistry
and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Ronghu Wu
- School
of Chemistry and Biochemistry
and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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15
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Noguère C, Larsson AM, Guyot JC, Bignon C. Fractional factorial approach combining 4 Escherichia coli strains, 3 culture media, 3 expression temperatures and 5 N-terminal fusion tags for screening the soluble expression of recombinant proteins. Protein Expr Purif 2012; 84:204-13. [DOI: 10.1016/j.pep.2012.05.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 05/30/2012] [Indexed: 11/24/2022]
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16
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Abstract
A method for exploring protein-protein interactions using hydrogen/deuterium exchange coupled to mass spectrometry is described. The method monitors the exchange of backbone (amide) hydrogens in solutions of deuterated water that primarily occur on portions of the protein exposed to solvent. In the presence of a protein binding partner, regions that experience reduced exchange are either part of the protein-protein interaction interface or undergo conformational changes to reduce accessibility to solvent. This method has the advantage of being used under physiological conditions with unmodified proteins. In this chapter, we describe an approach suitable for probing interactions among relatively large proteins using conventional mass spectrometry systems. The interaction between human transferrin and the Neisseria meningitidis receptor protein, transferrin binding protein B, provides a challenging system as an example.
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Affiliation(s)
- Jessmi M L Ling
- Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, AB, Canada.
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17
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Ling JML, Shima CH, Schriemer DC, Schryvers AB. Delineating the regions of human transferrin involved in interactions with transferrin binding protein B from Neisseria meningitidis. Mol Microbiol 2010; 77:1301-14. [DOI: 10.1111/j.1365-2958.2010.07289.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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Abstract
Cytoplasmic peptide:N-glycanase (PNGase) is an enzyme that removes N-glycans from misfolded glycoproteins. The function of cytoplasmic PNGase plays a significant role in the degradation of misfolded glycoproteins, which is critical for cell viability. Recently, we reported that haloacetoamidyl derivatives of high-mannose-type oligosaccharides selectively modify the catalytic cysteine of cytoplasmic PNGase and serve as its specific inhibitor. Interestingly, a drastically simplified chloroacetamidyl chitobiose derivative [(GlcNAc)(2)-ClAc] was also reactive to PNGase. In our work, it was conjugated to a hydrophobic fluorophore in order to render (GlcNAc)(2)-ClAc cells permeable. We demonstrated that this compound [BODIPY-(GlcNAc)(2)-ClAc] specifically binds to cytoplasmic PNGase from budding yeast (Png1). To date, only Z-VAD-fmk is known as an inhibitor of PNGase. BODIPY-(GlcNAc)(2)-ClAc and Z-VAD-fmk share the same binding site on Png1, while BODIPY-(GlcNAc)(2)-ClAc has markedly stronger inhibitory activity. The functional analysis of PNGase using Z-VAD-fmk should be carefully interpreted because of its intrinsic property as a caspase inhibitor. In sharp contrast, chloroacetamidyl chitobiose was not reactive to caspase. In addition, BODIPY-(GlcNAc)(2)-ClAc did not bind either chitobiose-binding lectins or PNGase from other sources. Moreover, fluorescent microscopy clearly showed that BODIPY-(GlcNAc)(2)-ClAc was efficiently introduced into cells. These results suggest that this compound could be an in vivo inhibitor of cytoplasmic PNGase.
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Affiliation(s)
- Shinya Hagihara
- RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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19
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Kwan EM, Boraston AB, McLean BW, Kilburn DG, Warren RAJ. N-Glycosidase-carbohydrate-binding module fusion proteins as immobilized enzymes for protein deglycosylation. Protein Eng Des Sel 2005; 18:497-501. [PMID: 16155117 DOI: 10.1093/protein/gzi055] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A carbohydrate-binding module (CBM) was fused to the N-termini of mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase (EndoF1) and peptide N-glycosidase F (PNGaseF), two glycosidases from Chryseobacterium meningosepticum that are used to remove N-linked glycans from glycoproteins. The fusion proteins CBM-EndoF1 and CBM-PNGaseF also carry a hexahistidine tag for purification by immobilized metal affinity chromatography after production by Escherichia coli. CBM-EndoF1 is as effective as native EndoF1 at deglycosylating RNaseB; the glycans released by both enzymes are identical. Like native PNGaseF, CBM-PNGaseF is active on denatured but not on native RNaseB. Both fusion proteins are as active on RNaseB when immobilized on cellulose as they are in solution. They retain activity in the immobilized state for at least 1 month at 4 degrees C. The hexahistidine tag can be removed with thrombin, leaving the CBM as the only affinity tag. The CBM can be removed with factor Xa if required.
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Affiliation(s)
- Emily M Kwan
- The Protein Engineering Network of Centres of Excellence, 750 Heritage Medical Research Centre, Edmonton, AB T6G 2S2, Canada
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20
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Guerranti R, Aguiyi JC, Ogueli IG, Onorati G, Neri S, Rosati F, Del Buono F, Lampariello R, Pagani R, Marinello E. Protection of Mucuna pruriens seeds against Echis carinatus venom is exerted through a multiform glycoprotein whose oligosaccharide chains are functional in this role. Biochem Biophys Res Commun 2004; 323:484-90. [PMID: 15369777 DOI: 10.1016/j.bbrc.2004.08.122] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2004] [Indexed: 10/26/2022]
Abstract
In a previous paper we demonstrated that extracts of Mucuna pruriens seeds (MPE) protect mice against Echis carinatus venom (EV) by an immunological mechanism. In this paper we demonstrate that the MPE immunogen generating the antibody that cross-reacts with the venom proteins is a multiform glycoprotein (gpMuc) whose immunogenic properties mainly reside in its glycan-chains. The glycoprotein was purified from the protein extract of M. pruriens seeds using Concanavalin A affinity chromatography. Using 2-D gel electrophoresis it separated into seven isoforms having MWs in the range from 20.3 to 28.7 kDa and pIs from 4.8 to 6.5. N-terminal sequencing of these spots revealed close similarity since all of them contained the consensus sequence DDREPV-DT found in soybean Kunitz-type trypsin inhibitor. We suggest that gpMuc contains both N- and O-glycans. Mild alkaline treatment but not PNGase F led to loss of reactivity, indicating that O-glycans are probably involved in the antigenicity of gpMuc.
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Affiliation(s)
- Roberto Guerranti
- Dipartimento di Medicina Interna, Scienze Endocrino-metaboliche e Biochimica, Università di Siena, Via A. Moro 2, 53100 Siena, Italy.
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21
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Loo T, Patchett ML, Norris GE, Lott JS. Using secretion to solve a solubility problem: high-yield expression in Escherichia coli and purification of the bacterial glycoamidase PNGase F. Protein Expr Purif 2002; 24:90-8. [PMID: 11812228 DOI: 10.1006/prep.2001.1555] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
PNGase F is a widely used deglycosidase, secreted in small amounts by the gram-negative bacterium Flavobacterium meningosepticum. We have designed a T7 promoter-based Escherichia coli expression system to provide a high-yield source of recombinant enzyme. When expressed intracellularly, the enzyme was produced in a largely insoluble state. However, when expressed as a fusion with the leader sequence from the ompA gene, hexahistidine-tagged PNGase F was efficiently processed and exported to the E. coli periplasm. Single-step purification using immobilized metal affinity chromatography yielded 8 mg of pure enzyme per liter of culture, which is fully active on a range of protein and peptide substrates.
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Affiliation(s)
- Trevor Loo
- Institute of Molecular Biosciences, Massey University, Private Bag 11-222, Palmerston North, New Zealand
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22
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Hernández P, Debray H, Jaekel H, Garfias Y, Jiménez Md MDC, Martínez-Cairo S, Zenteno E. Chemical characterization of the lectin from Amaranthus leucocarpus syn. hypocondriacus by 2-D proteome analysis. Glycoconj J 2001; 18:321-9. [PMID: 11788800 DOI: 10.1023/a:1013760915738] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In this work, we characterized chemically the N-acetyl-D-galactosamine specific lectin from Amaranthus leucocarpus syn hypocondriacus lectin (ALL). It is a dimeric glycoprotein composed by three isoforms with pl at 4.8, 4.9, and 5.2. Circular dichroism analysis indicated that the secondary structure of ALL contains 45% of \bibeta-sheet and 5% of \bialpha-helix. Amino acid sequence of the purified lectin and its isoforms was determined from peptides obtained after trypsin digestion by MALDI-TOF (Matrix assisted laser desorption ionization-time of flight). The tryptic peptides prepared from the purified lectin and the three isoforms showed different degrees (80 to 83%) of identity with the amino acid sequence belonging to a previously described high nutritional value protein from A. hypocondriacus not shown at the time to be a lectin. Furthermore, analysis of tryptic peptides obtained from ALL previously treated with peptide N-glycosidase, revealed a 93% identity with the aforementioned protein. Presence of N-glycosidically linked glycans of the oligomannosidic type and, in minor proportion, of the N-acetyllactosaminic type glycans was determined by affinity chromatography on immobilized Con A.
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Affiliation(s)
- P Hernández
- Departamento de Bioquímica, Instituto Nacional de Enfermedades Respiratorias, Tlalpan D.F., 14080, México
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23
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Xuan J, Tarentino AL, Grimwood BG, Plummer TH, Cui T, Guan C, Van Roey P. Crystal structure of glycosylasparaginase from Flavobacterium meningosepticum. Protein Sci 1998; 7:774-81. [PMID: 9541410 PMCID: PMC2143967 DOI: 10.1002/pro.5560070327] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The crystal structure of recombinant glycosylasparaginase from Flavobacterium meningosepticum has been determined at 2.32 angstroms resolution. This enzyme is a glycoamidase that cleaves the link between the asparagine and the N-acetylglucosamine of N-linked oligosaccharides and plays a major role in the degradation of glycoproteins. The three-dimensional structure of the bacterial enzyme is very similar to that of the human enzyme, although it lacks the four disulfide bridges found in the human enzyme. The main difference is the absence of a small random coil domain at the end of the alpha-chain that forms part of the substrate binding cleft and that has a role in the stabilization of the tetramer of the human enzyme. The bacterial glycosylasparaginase is observed as an (alphabeta)2-tetramer in the crystal, despite being a dimer in solution. The study of the structure of the bacterial enzyme allows further evaluation of the effects of disease-causing mutations in the human enzyme and confirms the suitability of the bacterial enzyme as a model for functional analysis.
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Affiliation(s)
- J Xuan
- Division of Molecular Medicine, Wadsworth Center, New York State Department of Health, Albany 12201, USA
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24
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Abstract
We describe here the structures of several new N-glycan oligosaccharides from horseradish peroxidase (HRP). Glycopeptides from HRP were digested with glycoamidase A (from sweet almond) to release the N-glycans. The oligosaccharides were reductively aminated with 2-aminopyridine, and separated by high-performance liquid chromatography on octadecylsilyl- and amide-silica columns for two-dimensional mapping (Tomiya et al., Anal. Biochem. 171, 73-90, 1988). The N-glycans were also analyzed by electrospray ionization mass spectrometry. Two different lots of HRP showed a considerable difference in their N-glycan composition.
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Affiliation(s)
- N Takahashi
- GlycoLab, Nakano Vinegar Co., Ltd., Handa City Aichi, Japan
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25
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Wang LX, Tang M, Suzuki T, Kitajima K, Inoue Y, Inoue S, Fan JQ, Lee YC. Combined Chemical and Enzymatic Synthesis of a C-Glycopeptide and Its Inhibitory Activity toward Glycoamidases. J Am Chem Soc 1997. [DOI: 10.1021/ja9712027] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lai-Xi Wang
- Contribution from the Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, and Department of Biophysics and Biochemistry, University of Tokyo, Tokyo 113, Japan
| | - Mei Tang
- Contribution from the Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, and Department of Biophysics and Biochemistry, University of Tokyo, Tokyo 113, Japan
| | - Tadashi Suzuki
- Contribution from the Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, and Department of Biophysics and Biochemistry, University of Tokyo, Tokyo 113, Japan
| | - Ken Kitajima
- Contribution from the Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, and Department of Biophysics and Biochemistry, University of Tokyo, Tokyo 113, Japan
| | - Yasuo Inoue
- Contribution from the Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, and Department of Biophysics and Biochemistry, University of Tokyo, Tokyo 113, Japan
| | - Sadako Inoue
- Contribution from the Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, and Department of Biophysics and Biochemistry, University of Tokyo, Tokyo 113, Japan
| | - Jian-Qiang Fan
- Contribution from the Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, and Department of Biophysics and Biochemistry, University of Tokyo, Tokyo 113, Japan
| | - Yuan C. Lee
- Contribution from the Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, and Department of Biophysics and Biochemistry, University of Tokyo, Tokyo 113, Japan
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26
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Abstract
Glycoamidases (peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase, EC 3.5.1.52; also known as peptide: N-glycanases (PNGases) release N-linked oligosaccharides from glycopeptides and/or glycoproteins by hydrolyzing the glycosylated beta-amide bond of the asparagine side chain. The most widely used glycoamidases are those from Flavobacterium meningosepticum (glycoamidase F or PNGase F) and almond emulsin (glycoamidase A or PNGase A). To study the substrate structure requirement of these enzymes systematically, we synthesized >30 glycopeptides containing cellobiose, lactose, GlcNAc, and di-N,N'-acetylchitobiose (CTB). The length of the peptide was varied from one to five amino acids, and glycosylamines were linked to either Asn or Gln located at different positions in the peptide, including NH2 and COOH termini. Neither enzyme could cleave cellobiose and lactose glycopeptides, indicating that the 2-acetamido group on the Asn-linked GlcNAc is important in the recognition by both glycoamidases A and F. GlcNAc peptides could be cleaved by both enzymes, albeit not as effectively as CTB glycopeptides. Neither enzyme requires the Asn-Xaa-(Ser/Thr) sequence (required for N-glycosylation) for activity. Glycoamidase A could even hydrolyze a Gln-bound CTB glycopeptide, whereas the action of glycoamidase F on this substrate is minimal. While glycoamidase A could act on CTB dipeptides, glycoamidase F preferred a tripeptide or longer. The Km and Vmax values of glycoamidase A for t-butoxycarbonyl-(CTB)-Asn-Ala-Ser-OMe were 2.1 mM and 0.66 micromol/min/mg, respectively. A natural glycodipeptide, Man9-GlcNAc2-Asn-Phe, was also completely hydrolyzed by glycoamidase A.
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Affiliation(s)
- J Q Fan
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland 21218, USA
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27
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Ftouhi-Paquin N, Hauer CR, Stack RF, Tarentino AL, Plummer TH. Molecular cloning, primary structure, and properties of a new glycoamidase from the fungus Aspergillus tubigensis. J Biol Chem 1997; 272:22960-5. [PMID: 9312552 DOI: 10.1074/jbc.272.36.22960] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
A new glycoamidase, peptide-N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase (PNGase) At, was discovered in the eukaryote Aspergillus tubigensis. The enzyme was purified to homogeneity, and the DNA sequence was determined by cloning in Escherichia coli. Over 80% of the deduced amino acid sequence was verified independently by Edman analysis and/or electrospray ionization-mass spectrometry of protease fragments of native PNGase At. This glycoamidase contains 12 potential asparagine-linked glycosylation sites, of which at least 9 sites are occupied with typical high mannose oligosaccharides. PNGase At consists of two non-identical glycosylated subunits that are derived from a single polypeptide gene precursor. Evidence is presented suggesting that autocatalysis is involved in subunit formation. PNGase At is an important new tool for analysis of asparagine-linked glycans; it can hydrolyze a broad range of glycopeptides, including those with core-linked alpha1-->6 or alpha1-->3 fucose, under conditions not favorable with existing glycoamidases.
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Affiliation(s)
- N Ftouhi-Paquin
- Division of Molecular Medicine, Wadsworth Center for Laboratories and Research, New York State Department of Health, Albany, New York 12201-0509, USA.
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28
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Abstract
Glycoproteins generally exist as populations of glycosylated variants (glycoforms) of a single polypeptide. Although the same glycosylation machinery is available to all proteins that enter the secretory pathway in a given cell, most glycoproteins emerge with characteristic glycosylation patterns and heterogeneous populations of glycans at each glycosylation site. The factors that control the composition of the glycoform populations and the role that heterogeneity plays in the function of glycoproteins are important questions for glycobiology. A full understanding of the implications of glycosylation for the structure and function of a protein can only be reached when a glycoprotein is viewed as a single entity. Individual glycoproteins, by virtue of their unique structures, can selectively control their own glycosylation by modulating interactions with the glycosylating enzymes in the cell. Examples include protein-specific glycosylation within the immunoglobulins and immunoglobulin superfamily and site-specific processing in ribonuclease, Thy-1, IgG, tissue plasminogen activator, and influenza A hemagglutinin. General roles for the range of sugars on glycoproteins such as the leukocyte antigens include orientating the molecules on the cell surface. A major role for specific sugars is in recognition by lectins, including chaperones involved in protein folding. In addition, the recognition of identical motifs in different glycans allows a heterogeneous population of glycoforms to participate in specific biological interactions.
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Affiliation(s)
- P M Rudd
- Department of Biochemistry, University of Oxford, U.K
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