2g9f: Difference between revisions

Latest revision as of 09:26, 14 February 2024

Crystal structure of intein-tagged mouse PNGase C-terminal domain

Structural highlights

2g9f is a 1 chain structure with sequence from Mus musculus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.9Å
Ligands:	CL, GOL
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:2g9f.jpg|left|200px]]<br /><applet load="2g9f" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="2g9f, resolution 1.90&Aring;" />
-'''Crystal structure of intein-tagged mouse PNGase C-terminal domain'''<br />
-==About this Structure==
+==Crystal structure of intein-tagged mouse PNGase C-terminal domain==
-G9F is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] with CL and GOL as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2G9F OCA].
+<StructureSection load='2g9f' size='340' side='right'caption='[[2g9f]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2g9f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2G9F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2G9F FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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=2g9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g9f OCA], [https://pdbe.org/2g9f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2g9f RCSB], [https://www.ebi.ac.uk/pdbsum/2g9f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2g9f ProSAT]</span></td></tr>
+</table>
+== Function ==
+[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/g9/2g9f_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=2g9f ConSurf].
+<div style="clear:both"></div>
+==See Also==
+*[[Peptide N-glycanase|Peptide N-glycanase]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Mus musculus]]
-[[Category: Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase]]
+[[Category: Lennarz WJ]]
-[[Category: Single protein]]
+[[Category: Li G]]
-[[Category: Lennarz, W.J.]]
+[[Category: Schindelin H]]
-[[Category: Li, G.]]
+[[Category: Wang L]]
-[[Category: Schindelin, H.]]
+[[Category: Zhao G]]
-[[Category: Wang, L.]]
+[[Category: Zhou X]]
-[[Category: Zhao, G.]]
-[[Category: Zhou, X.]]
-[[Category: CL]]
-[[Category: GOL]]
-[[Category: beta-sandwich]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 11:03:14 2007''

2g9f: Difference between revisions

Latest revision as of 09:26, 14 February 2024

Crystal structure of intein-tagged mouse PNGase C-terminal domain

Structural highlights

Function

Evolutionary Conservation

See Also

References

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