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3esw

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Revision as of 18:35, 25 December 2014

Complex of yeast PNGase with GlcNAc2-IAc.

Structural highlights

3esw is a 2 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
NonStd Res:
Gene:	PNG1, YPL096W (Saccharomyces cerevisiae), RAD23, SYGP-ORF29, YEL037C (Saccharomyces cerevisiae)
Activity:	Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase, with EC number 3.5.1.52
Resources:	FirstGlance, OCA, RCSB, PDBsum

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] [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.

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.

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

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3esw"

@@ Line 9: / Line 9: @@
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3esw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3esw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3esw RCSB], [http://www.ebi.ac.uk/pdbsum/3esw PDBsum]</span></td></tr>
 </table>
+== Function ==
+[[http://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>  [[http://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.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]

3esw

From Proteopedia

Revision as of 18:35, 25 December 2014

Complex of yeast PNGase with GlcNAc2-IAc.

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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