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| | ==Crystal Structure of the Apo Form of RapI== | | ==Crystal Structure of the Apo Form of RapI== |
| - | <StructureSection load='4i1a' size='340' side='right' caption='[[4i1a]], [[Resolution|resolution]] 2.44Å' scene=''> | + | <StructureSection load='4i1a' size='340' side='right'caption='[[4i1a]], [[Resolution|resolution]] 2.44Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4i1a]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I1A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4I1A FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4i1a]] 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]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I1A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4I1A FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 2.443Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4gyo|4gyo]], [[3q15|3q15]], [[3ulq|3ulq]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BSU05010, rapI, yddL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</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=4i1a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i1a OCA], [https://pdbe.org/4i1a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4i1a RCSB], [https://www.ebi.ac.uk/pdbsum/4i1a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4i1a 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=4i1a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i1a OCA], [http://pdbe.org/4i1a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4i1a RCSB], [http://www.ebi.ac.uk/pdbsum/4i1a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4i1a ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [https://www.uniprot.org/uniprot/RAPI_BACSU RAPI_BACSU] |
| - | The large family of Gram-positive quorum-sensing receptors known as the RNPP proteins consists of receptors homologous to the Rap, NprR, PlcR, and PrgX proteins that are regulated by imported oligopeptide autoinducers. Rap proteins are phosphatases and transcriptional anti-activators, and NprR, PlcR, and PrgX proteins are DNA binding transcription factors. Despite their obvious importance, the mechanistic basis of oligopeptide receptor regulation is largely unknown. Here, we report the X-ray crystal structure of the Bacillus subtilis quorum-sensing receptor RapJ in complex with the centrally important oligopeptide autoinducer competence and sporulation factor (CSF, also termed PhrC), a member of the Phr family of quorum-sensing signals. Furthermore, we present the crystal structure of RapI. Comparison of the RapJ-PhrC, RapI, RapH-Spo0F, and RapF-ComAC crystal structures reveals the mechanistic basis of Phr activity. More specifically, when complexed with target proteins, Rap proteins consist of a C-terminal tetratricopeptide repeat (TPR) domain connected by a flexible helix-containing linker to an N-terminal 3-helix bundle. In the absence of a target protein or regulatory peptide, the Rap protein 3-helix bundle adopts different conformations. However, in the peptide-bound conformation, the Rap protein N-terminal 3-helix bundle and linker undergo a radical conformational change, form TPR-like folds, and merge with the existing C-terminal TPR domain. To our knowledge, this is the first example of conformational change-induced repeat domain expansion. Furthermore, upon Phr binding, the entire Rap protein is compressed along the TPR superhelical axis, generating new intramolecular contacts that lock the Rap protein in an inactive state. The fact that Rap proteins are conformationally flexible is surprising considering that it is accepted dogma that TPR proteins do not undergo large conformational changes. Repeat proteins are widely used as scaffolds for the development of designed affinity reagents, and we propose that Rap proteins could be used as scaffolds for engineering novel ligand-switchable affinity reagents.
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| - | Conformational change-induced repeat domain expansion regulates rap phosphatase quorum-sensing signal receptors.,Parashar V, Jeffrey PD, Neiditch MB PLoS Biol. 2013 Mar;11(3):e1001512. doi: 10.1371/journal.pbio.1001512. Epub 2013 , Mar 19. PMID:23526881<ref>PMID:23526881</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| - | <div class="pdbe-citations 4i1a" style="background-color:#fffaf0;"></div>
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| - | == References ==
| + | |
| - | <references/>
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacsu]] | + | [[Category: Bacillus subtilis subsp. subtilis str. 168]] |
| - | [[Category: Jeffrey, P D]] | + | [[Category: Large Structures]] |
| - | [[Category: Neiditch, M B]] | + | [[Category: Jeffrey PD]] |
| - | [[Category: Parashar, V]] | + | [[Category: Neiditch MB]] |
| - | [[Category: Hydrolase]] | + | [[Category: Parashar V]] |
| - | [[Category: Phosphatase]]
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| - | [[Category: Spo0f]]
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| - | [[Category: Tetratricopeptide repeat]]
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