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| | ==crystal structure of the C-terminal domain of the electron transfer catalyst DsbD (oxidized form)== | | ==crystal structure of the C-terminal domain of the electron transfer catalyst DsbD (oxidized form)== |
| - | <StructureSection load='2fwe' size='340' side='right' caption='[[2fwe]], [[Resolution|resolution]] 1.65Å' scene=''> | + | <StructureSection load='2fwe' size='340' side='right'caption='[[2fwe]], [[Resolution|resolution]] 1.65Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2fwe]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FWE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FWE FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2fwe]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FWE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FWE FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.65Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2fwf|2fwf]], [[2fwg|2fwg]], [[2fwh|2fwh]], [[1vrs|1vrs]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DSBD, DIPZ, CYCZ, CUTA2, B4136 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=2fwe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fwe OCA], [https://pdbe.org/2fwe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fwe RCSB], [https://www.ebi.ac.uk/pdbsum/2fwe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fwe ProSAT]</span></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_reductase Protein-disulfide reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.1.8 1.8.1.8] </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=2fwe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fwe OCA], [http://pdbe.org/2fwe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2fwe RCSB], [http://www.ebi.ac.uk/pdbsum/2fwe PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DSBD_ECOLI DSBD_ECOLI]] Required to facilitate the formation of correct disulfide bonds in some periplasmic proteins and for the assembly of the periplasmic c-type cytochromes. Acts by transferring electrons from cytoplasmic thioredoxin to the periplasm, thereby maintaining the active site of DsbC, DsbE and DsbG in a reduced state. This transfer involves a cascade of disulfide bond formation and reduction steps.[HAMAP-Rule:MF_00399] | + | [https://www.uniprot.org/uniprot/DSBD_ECOLI DSBD_ECOLI] Required to facilitate the formation of correct disulfide bonds in some periplasmic proteins and for the assembly of the periplasmic c-type cytochromes. Acts by transferring electrons from cytoplasmic thioredoxin to the periplasm, thereby maintaining the active site of DsbC, DsbE and DsbG in a reduced state. This transfer involves a cascade of disulfide bond formation and reduction steps.[HAMAP-Rule:MF_00399] |
| | == 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/fw/2fwe_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fw/2fwe_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> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | ==See Also== | | ==See Also== |
| - | *[[Thiol:disulfide interchange protein|Thiol:disulfide interchange protein]] | + | *[[Thiol:disulfide interchange protein 3D structures|Thiol:disulfide interchange protein 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| - | [[Category: Protein-disulfide reductase]] | + | [[Category: Large Structures]] |
| - | [[Category: Boeckmann, R A]] | + | [[Category: Boeckmann RA]] |
| - | [[Category: Capitani, G]] | + | [[Category: Capitani G]] |
| - | [[Category: Glockshuber, R]] | + | [[Category: Glockshuber R]] |
| - | [[Category: Grauschopf, U]] | + | [[Category: Grauschopf U]] |
| - | [[Category: Gruetter, M G]] | + | [[Category: Gruetter MG]] |
| - | [[Category: Rozhkova, A]] | + | [[Category: Rozhkova A]] |
| - | [[Category: Stirnimann, C U]] | + | [[Category: Stirnimann CU]] |
| - | [[Category: C-terminal domain]]
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| - | [[Category: Dsbd]]
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| - | [[Category: Oxidized form]]
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| - | [[Category: Oxidoreductase]]
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| - | [[Category: Thioredoxin-like]]
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| Structural highlights
Function
DSBD_ECOLI Required to facilitate the formation of correct disulfide bonds in some periplasmic proteins and for the assembly of the periplasmic c-type cytochromes. Acts by transferring electrons from cytoplasmic thioredoxin to the periplasm, thereby maintaining the active site of DsbC, DsbE and DsbG in a reduced state. This transfer involves a cascade of disulfide bond formation and reduction steps.[HAMAP-Rule:MF_00399]
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
Escherichia coli DsbD transports electrons from cytoplasmic thioredoxin to periplasmic target proteins. DsbD is composed of an N-terminal (nDsbD) and a C-terminal (cDsbD) periplasmic domain, connected by a central transmembrane domain. Each domain possesses two cysteine residues essential for electron transport. The transport proceeds via disulfide exchange reactions from cytoplasmic thioredoxin to the central transmembrane domain and via cDsbD to nDsbD, which then reduces the periplasmic target proteins. We determined four high-resolution structures of cDsbD: oxidized (1.65 A resolution), chemically reduced (1.3 A), photo-reduced (1.1 A) and chemically reduced at pH increased from 4.6 to 7. The latter structure was refined at 0.99 A resolution, the highest achieved so far for a thioredoxin superfamily member. The data reveal unprecedented structural details of cDsbD, demonstrating that the domain is very rigid and undergoes hardly any conformational change upon disulfide reduction or interaction with nDsbD. In full agreement with the crystallographic results, guanidinium chloride-induced unfolding and refolding experiments indicate that oxidized and reduced cDsbD are equally stable. We confirmed the structural rigidity of cDsbD by molecular dynamics simulations. A remarkable feature of cDsbD is the pKa of 9.3 for the active site Cys461: this value, determined using two different experimental methods, surprisingly was around 2.5 units higher than expected on the basis of the redox potential. Additionally, taking advantage of the very high quality of the cDsbD structures, we carried out pKa calculations, which gave results in agreement with the experimental findings. In conclusion, our wide-scope analysis of cDsbD, encompassing atomic-resolution crystallography, computational chemistry and biophysical measurements, highlighted two so far unrecognized key aspects of this domain: its unusual redox properties and extreme rigidity. Both are likely to be correlated to the role of cDsbD as a covalently linked electron shuttle between the membrane domain and the N-terminal periplasmic domain of DsbD.
High-resolution structures of Escherichia coli cDsbD in different redox states: A combined crystallographic, biochemical and computational study.,Stirnimann CU, Rozhkova A, Grauschopf U, Bockmann RA, Glockshuber R, Capitani G, Grutter MG J Mol Biol. 2006 May 5;358(3):829-45. Epub 2006 Feb 28. PMID:16545842[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Stirnimann CU, Rozhkova A, Grauschopf U, Bockmann RA, Glockshuber R, Capitani G, Grutter MG. High-resolution structures of Escherichia coli cDsbD in different redox states: A combined crystallographic, biochemical and computational study. J Mol Biol. 2006 May 5;358(3):829-45. Epub 2006 Feb 28. PMID:16545842 doi:10.1016/j.jmb.2006.02.030
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