2d5u: Difference between revisions

Latest revision as of 11:34, 22 May 2024

Solution structure of the N-terminal portion of the PUB domain of mouse peptide:N-glycanase

Structural highlights

2d5u is a 1 chain structure with sequence from Mus musculus. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NGLY1_MOUSE 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.^[1] ^[2] ^[3]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

↑ Park H, Suzuki T, Lennarz WJ. Identification of proteins that interact with mammalian peptide:N-glycanase and implicate this hydrolase in the proteasome-dependent pathway for protein degradation. Proc Natl Acad Sci U S A. 2001 Sep 25;98(20):11163-8. Epub 2001 Sep 18. PMID:11562482 doi:https://dx.doi.org/10.1073/pnas.201393498
↑ 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:https://dx.doi.org/10.1093/emboj/cdg107
↑ Katiyar S, Li G, Lennarz WJ. A complex between peptide:N-glycanase and two proteasome-linked proteins suggests a mechanism for the degradation of misfolded glycoproteins. Proc Natl Acad Sci U S A. 2004 Sep 21;101(38):13774-9. Epub 2004 Sep 9. PMID:15358861 doi:https://dx.doi.org/10.1073/pnas.0405663101

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Park H, Suzuki T, Lennarz WJ. Identification of proteins that interact with mammalian peptide:N-glycanase and implicate this hydrolase in the proteasome-dependent pathway for protein degradation. Proc Natl Acad Sci U S A. 2001 Sep 25;98(20):11163-8. Epub 2001 Sep 18. PMID:11562482 doi:https://dx.doi.org/10.1073/pnas.201393498

[2] 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:https://dx.doi.org/10.1093/emboj/cdg107

[3] Katiyar S, Li G, Lennarz WJ. A complex between peptide:N-glycanase and two proteasome-linked proteins suggests a mechanism for the degradation of misfolded glycoproteins. Proc Natl Acad Sci U S A. 2004 Sep 21;101(38):13774-9. Epub 2004 Sep 9. PMID:15358861 doi:https://dx.doi.org/10.1073/pnas.0405663101

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
-[[Image:2d5u.gif|left|200px]]
- {{Structure
+==Solution structure of the N-terminal portion of the PUB domain of mouse peptide:N-glycanase==
-|PDB= 2d5u |SIZE=350|CAPTION= <scene name='initialview01'>2d5u</scene>
+<StructureSection load='2d5u' size='340' side='right'caption='[[2d5u]]' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND=
+<table><tr><td colspan='2'>[[2d5u]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D5U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D5U FirstGlance]. <br>
-|ACTIVITY= <span class='plainlinks'>[http://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 [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.52 3.5.1.52] </span>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-|GENE=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2d5u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d5u OCA], [https://pdbe.org/2d5u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d5u RCSB], [https://www.ebi.ac.uk/pdbsum/2d5u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d5u ProSAT]</span></td></tr>
-|DOMAIN=
+</table>
-|RELATEDENTRY=
+== Function ==
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2d5u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d5u OCA], [http://www.ebi.ac.uk/pdbsum/2d5u PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2d5u RCSB]</span>
+[https://www.uniprot.org/uniprot/NGLY1_MOUSE NGLY1_MOUSE] 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.<ref>PMID:11562482</ref> <ref>PMID:12606569</ref> <ref>PMID:15358861</ref>
-}}
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d5/2d5u_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2d5u ConSurf].
+<div style="clear:both"></div>
-'''Solution structure of the N-terminal portion of the PUB domain of mouse peptide:N-glycanase'''
+==See Also==
+*[[Peptide N-glycanase|Peptide N-glycanase]]
+== References ==
-==About this Structure==
+<references/>
-D5U is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D5U OCA].
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Mus musculus]]
-[[Category: Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase]]
+[[Category: Hirao T]]
-[[Category: Single protein]]
+[[Category: Kato K]]
-[[Category: Hirao, T.]]
+[[Category: Sasakawa H]]
-[[Category: Kato, K.]]
+[[Category: Suzuki T]]
-[[Category: Sasakawa, H.]]
+[[Category: Yamaguchi Y]]
-[[Category: Suzuki, T.]]
-[[Category: Yamaguchi, Y.]]
-[[Category: pngase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:30:37 2008''

2d5u: Difference between revisions

Latest revision as of 11:34, 22 May 2024

Solution structure of the N-terminal portion of the PUB domain of mouse peptide:N-glycanase

Structural highlights

Function

Evolutionary Conservation

See Also

References

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