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| | <StructureSection load='3esw' size='340' side='right'caption='[[3esw]], [[Resolution|resolution]] 3.40Å' scene=''> | | <StructureSection load='3esw' size='340' side='right'caption='[[3esw]], [[Resolution|resolution]] 3.40Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3esw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ESW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ESW FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3esw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ESW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ESW FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.4Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=YCM:S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE'>YCM</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=YCM:S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE'>YCM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PNG1, YPL096W ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824]), RAD23, SYGP-ORF29, YEL037C ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine_amidase Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.52 3.5.1.52] </span></td></tr>
| + | |
| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3esw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3esw OCA], [https://pdbe.org/3esw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3esw RCSB], [https://www.ebi.ac.uk/pdbsum/3esw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3esw ProSAT]</span></td></tr> | | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3esw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3esw OCA], [https://pdbe.org/3esw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3esw RCSB], [https://www.ebi.ac.uk/pdbsum/3esw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3esw ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/PNG1_YEAST PNG1_YEAST]] Specifically deglycosylates the denatured form of N-linked glycoproteins in the cytoplasm and assists their proteasome-mediated degradation. Cleaves the beta-aspartyl-glucosamine (GlcNAc) of the glycan and the amide side chain of Asn, converting Asn to Asp. Prefers proteins containing high-mannose over those bearing complex type oligosaccharides. Can recognize misfolded proteins in the endoplasmic reticulum that are exported to the cytosol to be destroyed and deglycosylate them, while it has no activity toward native proteins. Deglycosylation is a prerequisite for subsequent proteasome-mediated degradation of some, but not all, misfolded glycoproteins. Involved in the formation of free oligosaccharide in cytosol.<ref>PMID:10831608</ref> <ref>PMID:12723970</ref> <ref>PMID:12606569</ref> <ref>PMID:14726951</ref> <ref>PMID:15670854</ref> <ref>PMID:16401726</ref> [[https://www.uniprot.org/uniprot/RAD23_YEAST RAD23_YEAST]] Plays a central role both in proteasomal degradation of misfolded proteins and DNA repair. Central component of a complex required to couple deglycosylation and proteasome-mediated degradation of misfolded proteins in the endoplasmic reticulum that are retrotranslocated in the cytosol. Involved in DNA excision repair. May play a part in DNA damage recognition and/or in altering chromatin structure to allow access by damage-processing enzymes.
| + | [https://www.uniprot.org/uniprot/PNG1_YEAST PNG1_YEAST] Specifically deglycosylates the denatured form of N-linked glycoproteins in the cytoplasm and assists their proteasome-mediated degradation. Cleaves the beta-aspartyl-glucosamine (GlcNAc) of the glycan and the amide side chain of Asn, converting Asn to Asp. Prefers proteins containing high-mannose over those bearing complex type oligosaccharides. Can recognize misfolded proteins in the endoplasmic reticulum that are exported to the cytosol to be destroyed and deglycosylate them, while it has no activity toward native proteins. Deglycosylation is a prerequisite for subsequent proteasome-mediated degradation of some, but not all, misfolded glycoproteins. Involved in the formation of free oligosaccharide in cytosol.<ref>PMID:10831608</ref> <ref>PMID:12723970</ref> <ref>PMID:12606569</ref> <ref>PMID:14726951</ref> <ref>PMID:15670854</ref> <ref>PMID:16401726</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 18824]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Lennarz, W J]] | + | [[Category: Saccharomyces cerevisiae]] |
| - | [[Category: Schindelin, H]] | + | [[Category: Lennarz WJ]] |
| - | [[Category: Zhao, G]] | + | [[Category: Schindelin H]] |
| - | [[Category: Zhou, X]] | + | [[Category: Zhao G]] |
| - | [[Category: Dna damage]]
| + | [[Category: Zhou X]] |
| - | [[Category: Dna repair]]
| + | |
| - | [[Category: Glycoproteins peptide:n-glycanase chitobiose]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Metal-binding]]
| + | |
| - | [[Category: Nucleus]]
| + | |
| - | [[Category: Phosphoprotein]]
| + | |
| - | [[Category: Ubl conjugation pathway]]
| + | |
| Structural highlights
Function
PNG1_YEAST Specifically deglycosylates the denatured form of N-linked glycoproteins in the cytoplasm and assists their proteasome-mediated degradation. Cleaves the beta-aspartyl-glucosamine (GlcNAc) of the glycan and the amide side chain of Asn, converting Asn to Asp. Prefers proteins containing high-mannose over those bearing complex type oligosaccharides. Can recognize misfolded proteins in the endoplasmic reticulum that are exported to the cytosol to be destroyed and deglycosylate them, while it has no activity toward native proteins. Deglycosylation is a prerequisite for subsequent proteasome-mediated degradation of some, but not all, misfolded glycoproteins. Involved in the formation of free oligosaccharide in cytosol.[1] [2] [3] [4] [5] [6]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Peptide:N-glycanase (PNGase) is an important component of the endoplasmic reticulum-associated protein degradation pathway in which it de-glycosylates misfolded glycoproteins, thus facilitating their proteasomal degradation. PNGase belongs to the transglutaminase superfamily and features a Cys, His, and Asp catalytic triad, which is essential for its enzymatic activity. An elongated substrate-binding groove centered on the active site Cys191 was visualized in the crystal structure of apo-PNGase, whereas its complex with Z-VAD-fmk, a peptide-based inhibitor of PNGase, revealed that the inhibitor occupied one end of the substrate-binding groove while being covalently linked to the active site Cys. Recently, haloacetamidyl-containing carbohydrate-based inhibitors of PNGase were developed and shown to specifically label the active site Cys. In this study, we describe the crystal structure of yeast PNGase in complex with N,N'-diacetylchitobiose (chitobiose). We found that the chitobiose binds on the side opposite to the peptide binding site with the active site Cys191 being located approximately midway between the carbohydrate and peptide binding sites. Mutagenesis studies confirm the critical role of the chitobiose-interacting residues in substrate binding and suggest that efficient oligosaccharide binding is required for PNGase activity. In addition, the N-terminus of a symmetry-related PNGase was found to bind to the proposed peptide-binding site of PNGase. Together with the bound chitobiose, this enables us to propose a model for glycoprotein binding to PNGase. Finally, deleting the C-terminal residues of yeast PNGase, which are disordered in all structures of this enzyme, results in a significant reduction in enzyme activity, indicating that these residues might be involved in binding of the mannose residues of the glycan chain.
Structural and mutational studies on the importance of oligosaccharide binding for the activity of yeast PNGase.,Zhao G, Li G, Zhou X, Matsuo I, Ito Y, Suzuki T, Lennarz WJ, Schindelin H Glycobiology. 2009 Feb;19(2):118-25. Epub 2008 Oct 14. PMID:18854368[7]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Suzuki T, Park H, Hollingsworth NM, Sternglanz R, Lennarz WJ. PNG1, a yeast gene encoding a highly conserved peptide:N-glycanase. J Cell Biol. 2000 May 29;149(5):1039-52. PMID:10831608
- ↑ Chantret I, Frenoy JP, Moore SE. Free-oligosaccharide control in the yeast Saccharomyces cerevisiae: roles for peptide:N-glycanase (Png1p) and vacuolar mannosidase (Ams1p). Biochem J. 2003 Aug 1;373(Pt 3):901-8. PMID:12723970 doi:http://dx.doi.org/10.1042/BJ20030384
- ↑ Hirsch C, Blom D, Ploegh HL. A role for N-glycanase in the cytosolic turnover of glycoproteins. EMBO J. 2003 Mar 3;22(5):1036-46. PMID:12606569 doi:http://dx.doi.org/10.1093/emboj/cdg107
- ↑ Hirsch C, Misaghi S, Blom D, Pacold ME, Ploegh HL. Yeast N-glycanase distinguishes between native and non-native glycoproteins. EMBO Rep. 2004 Feb;5(2):201-6. Epub 2004 Jan 9. PMID:14726951 doi:http://dx.doi.org/10.1038/sj.embor.7400066
- ↑ Joshi S, Katiyar S, Lennarz WJ. Misfolding of glycoproteins is a prerequisite for peptide: N-glycanase mediated deglycosylation. FEBS Lett. 2005 Jan 31;579(3):823-6. PMID:15670854 doi:http://dx.doi.org/S0014-5793(05)00016-5
- ↑ Kim I, Ahn J, Liu C, Tanabe K, Apodaca J, Suzuki T, Rao H. The Png1-Rad23 complex regulates glycoprotein turnover. J Cell Biol. 2006 Jan 16;172(2):211-9. Epub 2006 Jan 9. PMID:16401726 doi:http://dx.doi.org/jcb.200507149
- ↑ Zhao G, Li G, Zhou X, Matsuo I, Ito Y, Suzuki T, Lennarz WJ, Schindelin H. Structural and mutational studies on the importance of oligosaccharide binding for the activity of yeast PNGase. Glycobiology. 2009 Feb;19(2):118-25. Epub 2008 Oct 14. PMID:18854368 doi:10.1093/glycob/cwn108
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