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| | ==The crystal structure of sporulation kinase d sensor domain from Bacillus subtilis subsp.== | | ==The crystal structure of sporulation kinase d sensor domain from Bacillus subtilis subsp.== |
| - | <StructureSection load='4jgo' size='340' side='right' caption='[[4jgo]], [[Resolution|resolution]] 2.28Å' scene=''> | + | <StructureSection load='4jgo' size='340' side='right'caption='[[4jgo]], [[Resolution|resolution]] 2.28Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4jgo]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. This structure supersedes the now removed PDB entries and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3fos 3fos]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JGO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JGO FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4jgo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4dbj 4dbj] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3fos 3fos]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JGO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JGO FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</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]] 2.28Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4jgp|4jgp]], [[4jgq|4jgq]], [[4jgr|4jgr]]</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=4jgo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jgo OCA], [https://pdbe.org/4jgo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jgo RCSB], [https://www.ebi.ac.uk/pdbsum/4jgo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jgo ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BSU13660, kinD, ykvD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 Bacillus subtilis subsp. subtilis str. 168])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histidine_kinase Histidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.13.3 2.7.13.3] </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=4jgo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jgo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4jgo RCSB], [http://www.ebi.ac.uk/pdbsum/4jgo PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/KIND_BACSU KIND_BACSU]] Phosphorylates the sporulation-regulatory protein spo0F and, to a minor extent, is responsible for heterogeneous expression of spo0A during logarithmical growth. Also phosphorylates spo0A under biofilm growth conditions.<ref>PMID:11069677</ref> <ref>PMID:11886552</ref> <ref>PMID:18410285</ref> | + | [https://www.uniprot.org/uniprot/KIND_BACSU KIND_BACSU] Phosphorylates the sporulation-regulatory protein spo0F and, to a minor extent, is responsible for heterogeneous expression of spo0A during logarithmical growth. Also phosphorylates spo0A under biofilm growth conditions.<ref>PMID:11069677</ref> <ref>PMID:11886552</ref> <ref>PMID:18410285</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 4jgo" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Bacillus subtilis subsp. subtilis str. 168]] | | [[Category: Bacillus subtilis subsp. subtilis str. 168]] |
| - | [[Category: Histidine kinase]] | + | [[Category: Large Structures]] |
| - | [[Category: Gu, M]] | + | [[Category: Gu M]] |
| - | [[Category: Joachimiak, A]] | + | [[Category: Joachimiak A]] |
| - | [[Category: Structural genomic]]
| + | [[Category: Schiffer M]] |
| - | [[Category: Schiffer, M]] | + | [[Category: Wu R]] |
| - | [[Category: Wu, R]] | + | |
| - | [[Category: Alpha-beta-alpha structure]]
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| - | [[Category: Extracytoplasmic]]
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| - | [[Category: Mcsg]]
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| - | [[Category: Pas-like fold]]
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| - | [[Category: Psi-biology]]
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| - | [[Category: Transferase]]
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| Structural highlights
Function
KIND_BACSU Phosphorylates the sporulation-regulatory protein spo0F and, to a minor extent, is responsible for heterogeneous expression of spo0A during logarithmical growth. Also phosphorylates spo0A under biofilm growth conditions.[1] [2] [3]
Publication Abstract from PubMed
The Bacillus subtilis KinD signal-transducing histidine kinase is a part of the sporulation phosphorelay known to regulate important developmental decisions such as sporulation and biofilm formation. We have determined crystal structures of the extracytoplasmic sensing domain of KinD, which was copurified and crystallized with a pyruvate ligand. The structure of a ligand-binding site mutant was also determined; it was copurified and crystallized with an acetate ligand. The structure of the KinD extracytoplasmic segment is similar to that of several other sensing domains of signal transduction proteins and is composed of tandem Per-Arnt-Sim (PAS)-like domains. The KinD ligand-binding site is located on the membrane distal PAS-like domain and appears to be highly selective; a single mutation, R131A, abolishes pyruvate binding and the mutant binds acetate instead. Differential scanning fluorimetry, using a variety of monocarboxylic and dicarboxylic acids, identified pyruvate, propionate, and butyrate but not lactate, acetate, or malate as KinD ligands. A recent report found that malate induces biofilm formation in a KinD-dependent manner. It was suggested that malate might induce a metabolic shift and increased secretion of the KinD ligand of unknown identity. The structure and binding assays now suggests that this ligand is pyruvate and/or other small monocarboxylic acids. In summary, this study gives a first insight into the identity of a molecular ligand for one of the five phosphorelay kinases of B. subtilis.
Insight into the sporulation phosphorelay: Crystal structure of the sensor domain of Bacillus subtilis histidine kinase, KinD.,Wu R, Gu M, Wilton R, Babnigg G, Kim Y, Pokkuluri PR, Szurmant H, Joachimiak A, Schiffer M Protein Sci. 2013 May;22(5):564-76. doi: 10.1002/pro.2237. Epub 2013 Mar 18. PMID:23436677[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Jiang M, Shao W, Perego M, Hoch JA. Multiple histidine kinases regulate entry into stationary phase and sporulation in Bacillus subtilis. Mol Microbiol. 2000 Nov;38(3):535-42. PMID:11069677
- ↑ Hamon MA, Lazazzera BA. The sporulation transcription factor Spo0A is required for biofilm development in Bacillus subtilis. Mol Microbiol. 2001 Dec;42(5):1199-209. PMID:11886552
- ↑ Castilla-Llorente V, Salas M, Meijer WJ. kinC/D-mediated heterogeneous expression of spo0A during logarithmical growth in Bacillus subtilis is responsible for partial suppression of phi 29 development. Mol Microbiol. 2008 Jun;68(6):1406-17. doi: 10.1111/j.1365-2958.2008.06234.x., Epub 2008 Apr 8. PMID:18410285 doi:10.1111/j.1365-2958.2008.06234.x
- ↑ Wu R, Gu M, Wilton R, Babnigg G, Kim Y, Pokkuluri PR, Szurmant H, Joachimiak A, Schiffer M. Insight into the sporulation phosphorelay: Crystal structure of the sensor domain of Bacillus subtilis histidine kinase, KinD. Protein Sci. 2013 May;22(5):564-76. doi: 10.1002/pro.2237. Epub 2013 Mar 18. PMID:23436677 doi:10.1002/pro.2237
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