2b5e

From Proteopedia

(Difference between revisions)

Current revision

Crystal Structure of Yeast Protein Disulfide Isomerase

Structural highlights

2b5e is a 1 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.4Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PDI_YEAST Protein disulfide isomerase of ER lumen required for formation of disulfide bonds in secretory and cell-surface proteins and which unscrambles non-native disulfide bonds. Forms a complex with MNL1 to process unfolded protein-bound Man8GlcNAc2 oligosaccharides to Man7GlcNAc2, promoting degradation in unfolded protein response.^[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.

Publication Abstract from PubMed

Protein disulfide isomerase plays a key role in catalyzing the folding of secretory proteins. It features two catalytically inactive thioredoxin domains inserted between two catalytically active thioredoxin domains and an acidic C-terminal tail. The crystal structure of yeast PDI reveals that the four thioredoxin domains are arranged in the shape of a twisted "U" with the active sites facing each other across the long sides of the "U." The inside surface of the "U" is enriched in hydrophobic residues, thereby facilitating interactions with misfolded proteins. The domain arrangement, active site location, and surface features strikingly resemble the Escherichia coli DsbC and DsbG protein disulfide isomerases. Biochemical studies demonstrate that all domains of PDI, including the C-terminal tail, are required for full catalytic activity. The structure defines a framework for rationalizing the differences between the two active sites and their respective roles in catalyzing the formation and rearrangement of disulfide bonds.

The crystal structure of yeast protein disulfide isomerase suggests cooperativity between its active sites.,Tian G, Xiang S, Noiva R, Lennarz WJ, Schindelin H Cell. 2006 Jan 13;124(1):61-73. PMID:16413482^[4]

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

References

↑ Kimura T, Hosoda Y, Sato Y, Kitamura Y, Ikeda T, Horibe T, Kikuchi M. Interactions among yeast protein-disulfide isomerase proteins and endoplasmic reticulum chaperone proteins influence their activities. J Biol Chem. 2005 Sep 9;280(36):31438-41. Epub 2005 Jul 7. PMID:16002399 doi:http://dx.doi.org/10.1074/jbc.M503377200
↑ Clerc S, Hirsch C, Oggier DM, Deprez P, Jakob C, Sommer T, Aebi M. Htm1 protein generates the N-glycan signal for glycoprotein degradation in the endoplasmic reticulum. J Cell Biol. 2009 Jan 12;184(1):159-72. doi: 10.1083/jcb.200809198. Epub 2009 Jan, 5. PMID:19124653 doi:http://dx.doi.org/10.1083/jcb.200809198
↑ Gauss R, Kanehara K, Carvalho P, Ng DT, Aebi M. A complex of Pdi1p and the mannosidase Htm1p initiates clearance of unfolded glycoproteins from the endoplasmic reticulum. Mol Cell. 2011 Jun 24;42(6):782-93. doi: 10.1016/j.molcel.2011.04.027. PMID:21700223 doi:http://dx.doi.org/10.1016/j.molcel.2011.04.027
↑ Tian G, Xiang S, Noiva R, Lennarz WJ, Schindelin H. The crystal structure of yeast protein disulfide isomerase suggests cooperativity between its active sites. Cell. 2006 Jan 13;124(1):61-73. PMID:16413482 doi:10.1016/j.cell.2005.10.044

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/2b5e"

Categories: Large Structures | Saccharomyces cerevisiae | Schindelin H | Tian G

@@ Line 1: / Line 1: @@
 ==Crystal Structure of Yeast Protein Disulfide Isomerase==
-<StructureSection load='2b5e' size='340' side='right' caption='[[2b5e]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+<StructureSection load='2b5e' size='340' side='right'caption='[[2b5e]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2b5e]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B5E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2B5E FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2b5e]] is a 1 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=2B5E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2B5E FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><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]] 2.4&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1mek|1mek]], [[2bjx|2bjx]], [[2trx|2trx]], [[1eej|1eej]], [[1v57|1v57]], [[1a8y|1a8y]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PDI1, MFP1, TRG1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</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=2b5e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b5e OCA], [https://pdbe.org/2b5e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2b5e RCSB], [https://www.ebi.ac.uk/pdbsum/2b5e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2b5e ProSAT]</span></td></tr>
-<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Protein_disulfide-isomerase Protein disulfide-isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.4.1 5.3.4.1] </span></td></tr>
+</table>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2b5e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b5e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2b5e RCSB], [http://www.ebi.ac.uk/pdbsum/2b5e PDBsum]</span></td></tr>
+== Function ==
-<table>
+[https://www.uniprot.org/uniprot/PDI_YEAST PDI_YEAST] Protein disulfide isomerase of ER lumen required for formation of disulfide bonds in secretory and cell-surface proteins and which unscrambles non-native disulfide bonds. Forms a complex with MNL1 to process unfolded protein-bound Man8GlcNAc2 oligosaccharides to Man7GlcNAc2, promoting degradation in unfolded protein response.<ref>PMID:16002399</ref> <ref>PMID:19124653</ref> <ref>PMID:21700223</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/b5/2b5e_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b5/2b5e_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2b5e ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 27: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2b5e" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Protein disulfide-isomerase]]
+[[Category: Large Structures]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Schindelin, H.]]
+[[Category: Schindelin H]]
-[[Category: Tian, G.]]
+[[Category: Tian G]]
-[[Category: Isomerase]]
-[[Category: Protein disulfide isomerase]]

2b5e

From Proteopedia

Current revision

Crystal Structure of Yeast Protein Disulfide Isomerase

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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