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| | ==Crystal Structure of BdbD from Bacillus subtilis (oxidised)== | | ==Crystal Structure of BdbD from Bacillus subtilis (oxidised)== |
| - | <StructureSection load='3eu4' size='340' side='right' caption='[[3eu4]], [[Resolution|resolution]] 2.30Å' scene=''> | + | <StructureSection load='3eu4' size='340' side='right'caption='[[3eu4]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3eu4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EU4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EU4 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3eu4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EU4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EU4 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 2.3Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3eu3|3eu3]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">bdbD, BSU33480, yvgV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</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=3eu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eu4 OCA], [https://pdbe.org/3eu4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3eu4 RCSB], [https://www.ebi.ac.uk/pdbsum/3eu4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3eu4 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=3eu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eu4 OCA], [http://pdbe.org/3eu4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3eu4 RCSB], [http://www.ebi.ac.uk/pdbsum/3eu4 PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/BDBD_BACSU BDBD_BACSU]] Required for the stabilization, possibly via formation of a disulfide bond, of the obligatory competence protein ComGC. May be required for the stability of secreted proteins with disulfide bonds. Not required for sporulation.<ref>PMID:11744713</ref> | + | [https://www.uniprot.org/uniprot/BDBD_BACSU BDBD_BACSU] Required for the stabilization, possibly via formation of a disulfide bond, of the obligatory competence protein ComGC. May be required for the stability of secreted proteins with disulfide bonds. Not required for sporulation.<ref>PMID:11744713</ref> |
| | == 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/eu/3eu4_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/eu/3eu4_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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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus globigii migula 1900]] | + | [[Category: Bacillus subtilis]] |
| - | [[Category: Brun, N Le]] | + | [[Category: Large Structures]] |
| - | [[Category: Crow, A]] | + | [[Category: Crow A]] |
| - | [[Category: Hederstedt, L]] | + | [[Category: Hederstedt L]] |
| - | [[Category: Moller, M C]] | + | [[Category: Le Brun N]] |
| - | [[Category: Bdbdb]] | + | [[Category: Moller MC]] |
| - | [[Category: Competence]]
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| - | [[Category: Disulfide bridge]]
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| - | [[Category: Oxidised]]
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| - | [[Category: Oxidoreductase]]
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| - | [[Category: Partially broken disulfide]]
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| - | [[Category: Redox-active center]]
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| Structural highlights
Function
BDBD_BACSU Required for the stabilization, possibly via formation of a disulfide bond, of the obligatory competence protein ComGC. May be required for the stability of secreted proteins with disulfide bonds. Not required for sporulation.[1]
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
BdbD is a thiol:disulfide oxidoreductase (TDOR) from Bacillus subtilis that functions to introduce disulfide bonds in substrate proteins/peptides on the outside of the cytoplasmic membrane and, as such, plays a key role in disulfide bond management. Here we demonstrate that the protein is membrane-associated in B. subtilis and present the crystal structure of the soluble part of the protein lacking its membrane anchor. This reveals that BdbD is similar in structure to Escherichia coli DsbA, with a thioredoxin-like domain with an inserted helical domain. A major difference, however, is the presence in BdbD of a metal site, fully occupied by Ca(2+), at an inter-domain position some 14 A away from the CXXC active site. The midpoint reduction potential of soluble BdbD was determined as -75 mV versus normal hydrogen electrode, and the active site N-terminal cysteine thiol was shown to have a low pK(a), consistent with BdbD being an oxidizing TDOR. Equilibrium unfolding studies revealed that the oxidizing power of the protein is based on the instability introduced by the disulfide bond in the oxidized form. The crystal structure of Ca(2+)-depleted BdbD showed that the protein remained folded, with only minor conformational changes. However, the reduced form of Ca(2+)-depleted BdbD was significantly less stable than reduced Ca(2+)-containing protein, and the midpoint reduction potential was shifted by approximately -20 mV, suggesting that Ca(2+) functions to boost the oxidizing power of the protein. Finally, we demonstrate that electron exchange does not occur between BdbD and B. subtilis ResA, a low potential extra-cytoplasmic TDOR.
Crystal structure and biophysical properties of Bacillus subtilis BdbD. An oxidizing thiol:disulfide oxidoreductase containing a novel metal site.,Crow A, Lewin A, Hecht O, Carlsson Moller M, Moore GR, Hederstedt L, Le Brun NE J Biol Chem. 2009 Aug 28;284(35):23719-33. Epub 2009 Jun 17. PMID:19535335[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Meima R, Eschevins C, Fillinger S, Bolhuis A, Hamoen LW, Dorenbos R, Quax WJ, van Dijl JM, Provvedi R, Chen I, Dubnau D, Bron S. The bdbDC operon of Bacillus subtilis encodes thiol-disulfide oxidoreductases required for competence development. J Biol Chem. 2002 Mar 1;277(9):6994-7001. Epub 2001 Dec 13. PMID:11744713 doi:http://dx.doi.org/10.1074/jbc.M111380200
- ↑ Crow A, Lewin A, Hecht O, Carlsson Moller M, Moore GR, Hederstedt L, Le Brun NE. Crystal structure and biophysical properties of Bacillus subtilis BdbD. An oxidizing thiol:disulfide oxidoreductase containing a novel metal site. J Biol Chem. 2009 Aug 28;284(35):23719-33. Epub 2009 Jun 17. PMID:19535335 doi:10.1074/jbc.M109.005785
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