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| | ==Caulobacter crescentus GcrA sigma-interacting domain (SID) in complex with domain 2 of sigma 70== | | ==Caulobacter crescentus GcrA sigma-interacting domain (SID) in complex with domain 2 of sigma 70== |
| - | <StructureSection load='5yix' size='340' side='right' caption='[[5yix]], [[Resolution|resolution]] 2.30Å' scene=''> | + | <StructureSection load='5yix' size='340' side='right'caption='[[5yix]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5yix]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Cauvn Cauvn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YIX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YIX FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5yix]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Caulobacter_vibrioides_NA1000 Caulobacter vibrioides NA1000]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YIX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YIX FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BU3:(R,R)-2,3-BUTANEDIOL'>BU3</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.302Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rpoD, CCNA_03142 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=565050 CAUVN]), gcrA, CCNA_02328 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=565050 CAUVN])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BU3:(R,R)-2,3-BUTANEDIOL'>BU3</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=5yix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yix OCA], [http://pdbe.org/5yix PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yix RCSB], [http://www.ebi.ac.uk/pdbsum/5yix PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yix ProSAT]</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=5yix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yix OCA], [https://pdbe.org/5yix PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yix RCSB], [https://www.ebi.ac.uk/pdbsum/5yix PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yix ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/A0A0H3CAV3_CAUCN A0A0H3CAV3_CAUCN]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is the primary sigma factor during exponential growth.[SAAS:SAAS00535554] | + | [https://www.uniprot.org/uniprot/A0A0H3CAV3_CAUVN A0A0H3CAV3_CAUVN] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is the primary sigma factor during exponential growth.[HAMAP-Rule:MF_00963] |
| - | <div style="background-color:#fffaf0;">
| + | |
| - | == Publication Abstract from PubMed ==
| + | |
| - | Canonical bacterial transcription activators bind to non-transcribed promoter elements to increase transcription of their target genes. Here we report crystal structures of binary complexes comprising domains of Caulobacter crescentus GcrA, a noncanonical bacterial transcription factor, that support a novel mechanism for transcription activation through the preferential binding of methylated cis-regulatory elements and the promotion of open complex formation through an interaction with region 2 of the principal sigma factor, sigma70. We present crystal structures of the C-terminal, sigma factor-interacting domain (GcrA-SID) in complex with domain 2 of sigma70 (sigma702), and the N-terminal, DNA-binding domain (GcrA-DBD) in complex with methylated double-stranded DNA (dsDNA). The structures reveal interactions essential for transcription activation and DNA recognition by GcrA. These structures, along with mutational analyses, support a mechanism of transcription activation in which GcrA associates with RNA polymerase (RNAP) prior to promoter binding through GcrA-SID, arming RNAP with a flexible GcrA-DBD. The RNAP-GcrA complex then binds and activates target promoters harboring a methylated GcrA binding site either upstream or downstream of the transcription start site.
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| - | Structural insights into the unique mechanism of transcription activation by Caulobacter crescentus GcrA.,Wu X, Haakonsen DL, Sanderlin AG, Liu YJ, Shen L, Zhuang N, Laub MT, Zhang Y Nucleic Acids Res. 2018 Mar 5. pii: 4920855. doi: 10.1093/nar/gky161. PMID:29514271<ref>PMID:29514271</ref>
| + | ==See Also== |
| - | | + | *[[Sigma factor 3D structures|Sigma factor 3D structures]] |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | |
| - | </div>
| + | |
| - | <div class="pdbe-citations 5yix" style="background-color:#fffaf0;"></div>
| + | |
| - | == References == | + | |
| - | <references/>
| + | |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Cauvn]]
| + | [[Category: Caulobacter vibrioides NA1000]] |
| - | [[Category: Wu, X]]
| + | [[Category: Large Structures]] |
| - | [[Category: Zhang, Y]]
| + | [[Category: Wu X]] |
| - | [[Category: Caulobacter crescentus]] | + | [[Category: Zhang Y]] |
| - | [[Category: Dna binding protein]] | + | |
| - | [[Category: Gcra]] | + | |
| - | [[Category: Sigma-interacting domain]] | + | |
| - | [[Category: Transcription factor]]
| + | |
