2lvx: Difference between revisions

Latest revision as of 07:42, 9 October 2024

MRH domain of the Glucosidase II beta subunit from S. pombe

Structural highlights

2lvx is a 1 chain structure with sequence from Schizosaccharomyces pombe 972h-. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR, 20 models
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GLU2B_SCHPO Subunit of glucosidase 2, which cleaves sequentially the 2 innermost alpha-1,3-linked glucose residues from the Glc(2)Man(9)GlcNAc(2) oligosaccharide precursor of immature glycoproteins in the endoplasmic reticulum (ER). Specifically required for the cleavage of the final glucose. The subunit beta retains the catalytic subunit alpha in the ER.^[1] ^[2] ^[3]

Publication Abstract from PubMed

Here we report for the first time the three-dimensional structure of a mannose 6-phosphate receptor homology (MRH) domain present in a protein with enzymatic activity, glucosidase II (GII). GII is involved in glycoprotein folding in the endoplasmic reticulum. GII removes the two innermost glucose residues from the Glc3Man9GlcNAc2 transferred to nascent proteins and the glucose added by UDP-Glc:glycoprotein glucosyltransferase. GII is composed of a catalytic GIIalpha subunit and a regulatory GIIbeta subunit. GIIbeta participates in the endoplasmic reticulum localization of GIIalpha and mediates in vivo enhancement of N-glycan trimming by GII through its C-terminal MRH domain. We determined the structure of a functional GIIbeta MRH domain by NMR spectroscopy. It adopts a beta-barrel fold similar to that of other MRH domains, but its binding pocket is the most shallow known to date as it accommodates a single mannose residue. In addition, we identified a conserved residue outside the binding pocket (Trp-409) present in GIIbeta but not in other MRHs that influences GII glucose trimming activity.

Structure of the Lectin Mannose 6-Phosphate Receptor Homology (MRH) Domain of Glucosidase II, an Enzyme That Regulates Glycoprotein Folding Quality Control in the Endoplasmic Reticulum.,Olson LJ, Orsi R, Alculumbre SG, Peterson FC, Stigliano ID, Parodi AJ, D'Alessio C, Dahms NM J Biol Chem. 2013 Jun 7;288(23):16460-75. doi: 10.1074/jbc.M113.450239. Epub 2013, Apr 22. PMID:23609449^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ D'Alessio C, Fernandez F, Trombetta ES, Parodi AJ. Genetic evidence for the heterodimeric structure of glucosidase II. The effect of disrupting the subunit-encoding genes on glycoprotein folding. J Biol Chem. 1999 Sep 3;274(36):25899-905. PMID:10464333
↑ Stigliano ID, Caramelo JJ, Labriola CA, Parodi AJ, D'Alessio C. Glucosidase II beta subunit modulates N-glycan trimming in fission yeasts and mammals. Mol Biol Cell. 2009 Sep;20(17):3974-84. Epub 2009 Jul 15. PMID:19605557 doi:E09-04-0316
↑ Stigliano ID, Alculumbre SG, Labriola CA, Parodi AJ, D'Alessio C. Glucosidase II and N-glycan mannose content regulate the half-lives of monoglucosylated species in vivo. Mol Biol Cell. 2011 Jun 1;22(11):1810-23. doi: 10.1091/mbc.E11-01-0019. Epub 2011, Apr 6. PMID:21471007 doi:10.1091/mbc.E11-01-0019
↑ Olson LJ, Orsi R, Alculumbre SG, Peterson FC, Stigliano ID, Parodi AJ, D'Alessio C, Dahms NM. Structure of the Lectin Mannose 6-Phosphate Receptor Homology (MRH) Domain of Glucosidase II, an Enzyme That Regulates Glycoprotein Folding Quality Control in the Endoplasmic Reticulum. J Biol Chem. 2013 Jun 7;288(23):16460-75. doi: 10.1074/jbc.M113.450239. Epub 2013, Apr 22. PMID:23609449 doi:10.1074/jbc.M113.450239

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OCA

[1] D'Alessio C, Fernandez F, Trombetta ES, Parodi AJ. Genetic evidence for the heterodimeric structure of glucosidase II. The effect of disrupting the subunit-encoding genes on glycoprotein folding. J Biol Chem. 1999 Sep 3;274(36):25899-905. PMID:10464333

[2] Stigliano ID, Caramelo JJ, Labriola CA, Parodi AJ, D'Alessio C. Glucosidase II beta subunit modulates N-glycan trimming in fission yeasts and mammals. Mol Biol Cell. 2009 Sep;20(17):3974-84. Epub 2009 Jul 15. PMID:19605557 doi:E09-04-0316

[3] Stigliano ID, Alculumbre SG, Labriola CA, Parodi AJ, D'Alessio C. Glucosidase II and N-glycan mannose content regulate the half-lives of monoglucosylated species in vivo. Mol Biol Cell. 2011 Jun 1;22(11):1810-23. doi: 10.1091/mbc.E11-01-0019. Epub 2011, Apr 6. PMID:21471007 doi:10.1091/mbc.E11-01-0019

[4] Olson LJ, Orsi R, Alculumbre SG, Peterson FC, Stigliano ID, Parodi AJ, D'Alessio C, Dahms NM. Structure of the Lectin Mannose 6-Phosphate Receptor Homology (MRH) Domain of Glucosidase II, an Enzyme That Regulates Glycoprotein Folding Quality Control in the Endoplasmic Reticulum. J Biol Chem. 2013 Jun 7;288(23):16460-75. doi: 10.1074/jbc.M113.450239. Epub 2013, Apr 22. PMID:23609449 doi:10.1074/jbc.M113.450239

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[2]

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[4]

@@ Line 1: / Line 1: @@
 ==MRH domain of the Glucosidase II beta subunit from S. pombe==
-<StructureSection load='2lvx' size='340' side='right'caption='[[2lvx]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='2lvx' size='340' side='right'caption='[[2lvx]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2lvx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Fission_yeast Fission yeast]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LVX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LVX FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2lvx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe_972h- Schizosaccharomyces pombe 972h-]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LVX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LVX FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">gtb1, SPCC825.02 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284812 Fission yeast])</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR, 20 models</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Hydrolase Hydrolase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.84 3.2.1.84] </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=2lvx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lvx OCA], [https://pdbe.org/2lvx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lvx RCSB], [https://www.ebi.ac.uk/pdbsum/2lvx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lvx ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/GLU2B_SCHPO GLU2B_SCHPO]] Subunit of glucosidase 2, which cleaves sequentially the 2 innermost alpha-1,3-linked glucose residues from the Glc(2)Man(9)GlcNAc(2) oligosaccharide precursor of immature glycoproteins in the endoplasmic reticulum (ER). Specifically required for the cleavage of the final glucose. The subunit beta retains the catalytic subunit alpha in the ER.<ref>PMID:10464333</ref> <ref>PMID:19605557</ref> <ref>PMID:21471007</ref>
+[https://www.uniprot.org/uniprot/GLU2B_SCHPO GLU2B_SCHPO] Subunit of glucosidase 2, which cleaves sequentially the 2 innermost alpha-1,3-linked glucose residues from the Glc(2)Man(9)GlcNAc(2) oligosaccharide precursor of immature glycoproteins in the endoplasmic reticulum (ER). Specifically required for the cleavage of the final glucose. The subunit beta retains the catalytic subunit alpha in the ER.<ref>PMID:10464333</ref> <ref>PMID:19605557</ref> <ref>PMID:21471007</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 26: / Line 25: @@
 __TOC__
 </StructureSection>
-[[Category: Fission yeast]]
-[[Category: Hydrolase]]
 [[Category: Large Structures]]
-[[Category: Dahms, N M]]
+[[Category: Schizosaccharomyces pombe 972h-]]
-[[Category: Olson, L J]]
+[[Category: Dahms NM]]
-[[Category: Peterson, F C]]
+[[Category: Olson LJ]]
-[[Category: Glycobiology]]
+[[Category: Peterson FC]]
-[[Category: Lectin]]
-[[Category: Mrh domain]]
-[[Category: Protein folding]]
-[[Category: Sugar binding protein]]

2lvx: Difference between revisions

Latest revision as of 07:42, 9 October 2024

MRH domain of the Glucosidase II beta subunit from S. pombe

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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