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| | ==Solution structure of the b' domain of thermophilic fungal protein disulfide isomerase== | | ==Solution structure of the b' domain of thermophilic fungal protein disulfide isomerase== |
| - | <StructureSection load='2kp2' size='340' side='right' caption='[[2kp2]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''> | + | <StructureSection load='2kp2' size='340' side='right'caption='[[2kp2]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2kp2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_16454 Atcc 16454]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KP2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KP2 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2kp2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Humicola_insolens Humicola insolens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KP2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KP2 FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2kp1|2kp1]]</td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> |
| - | <tr id='activity'><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>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2kp2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kp2 OCA], [https://pdbe.org/2kp2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kp2 RCSB], [https://www.ebi.ac.uk/pdbsum/2kp2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kp2 ProSAT]</span></td></tr> |
| - | <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=2kp2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kp2 OCA], [http://pdbe.org/2kp2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2kp2 RCSB], [http://www.ebi.ac.uk/pdbsum/2kp2 PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PDI_HUMIN PDI_HUMIN]] Participates in the folding of proteins containing disulfide bonds, may be involved in glycosylation, prolyl hydroxylation and triglyceride transfer (By similarity). | + | [https://www.uniprot.org/uniprot/PDI_HUMIN PDI_HUMIN] Participates in the folding of proteins containing disulfide bonds, may be involved in glycosylation, prolyl hydroxylation and triglyceride transfer (By similarity). |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kp/2kp2_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kp/2kp2_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </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=2kp2 ConSurf]. |
| | <div style="clear:both"></div> | | <div style="clear:both"></div> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 16454]] | + | [[Category: Humicola insolens]] |
| - | [[Category: Protein disulfide-isomerase]] | + | [[Category: Large Structures]] |
| - | [[Category: Kato, K]] | + | [[Category: Kato K]] |
| - | [[Category: Serve, O]] | + | [[Category: Serve O]] |
| - | [[Category: Yamaguchi, Y]] | + | [[Category: Yamaguchi Y]] |
| - | [[Category: Disulfide bond]]
| + | |
| - | [[Category: Endoplasmic reticulum]]
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| - | [[Category: Isomerase]]
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| - | [[Category: Redox-active center]]
| + | |
| - | [[Category: Thioredoxin fold]]
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| Structural highlights
Function
PDI_HUMIN Participates in the folding of proteins containing disulfide bonds, may be involved in glycosylation, prolyl hydroxylation and triglyceride transfer (By similarity).
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 (PDI) is a major protein in the endoplasmic reticulum, operating as an essential folding catalyst and molecular chaperone for disulfide-containing proteins by catalyzing the formation, rearrangement, and breakage of their disulfide bridges. This enzyme has a modular structure with four thioredoxin-like domains, a, b, b', and a', along with a C-terminal extension. The homologous a and a' domains contain one cysteine pair in their active site directly involved in thiol-disulfide exchange reactions, while the b' domain putatively provides a primary binding site for unstructured regions of the substrate polypeptides. Here, we report a redox-dependent intramolecular rearrangement of the b' and a' domains of PDI from Humicola insolens, a thermophilic fungus, elucidated by combined use of nuclear magnetic resonance (NMR) and small-angle X-ray scattering (SAXS) methods. Our NMR data showed that the substrates bound to a hydrophobic surface spanning these two domains, which became more exposed to the solvent upon oxidation of the active site of the a' domain. The hydrogen-deuterium exchange and relaxation data indicated that the redox state of the a' domain influences the dynamic properties of the b' domain. Moreover, the SAXS profiles revealed that oxidation of the a' active site causes segregation of the two domains. On the basis of these data, we propose a mechanistic model of PDI action; the a' domain transfers its own disulfide bond into the unfolded protein accommodated on the hydrophobic surface of the substrate-binding region, which consequently changes into a "closed" form releasing the oxidized substrate.
Redox-dependent domain rearrangement of protein disulfide isomerase coupled with exposure of its substrate-binding hydrophobic surface.,Serve O, Kamiya Y, Maeno A, Nakano M, Murakami C, Sasakawa H, Yamaguchi Y, Harada T, Kurimoto E, Yagi-Utsumi M, Iguchi T, Inaba K, Kikuchi J, Asami O, Kajino T, Oka T, Nakasako M, Kato K J Mol Biol. 2010 Feb 19;396(2):361-74. Epub 2009 Nov 26. PMID:19944705[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Serve O, Kamiya Y, Maeno A, Nakano M, Murakami C, Sasakawa H, Yamaguchi Y, Harada T, Kurimoto E, Yagi-Utsumi M, Iguchi T, Inaba K, Kikuchi J, Asami O, Kajino T, Oka T, Nakasako M, Kato K. Redox-dependent domain rearrangement of protein disulfide isomerase coupled with exposure of its substrate-binding hydrophobic surface. J Mol Biol. 2010 Feb 19;396(2):361-74. Epub 2009 Nov 26. PMID:19944705 doi:10.1016/j.jmb.2009.11.049
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