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| | <StructureSection load='5jji' size='340' side='right'caption='[[5jji]], [[Resolution|resolution]] 2.60Å' scene=''> | | <StructureSection load='5jji' size='340' side='right'caption='[[5jji]], [[Resolution|resolution]] 2.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5jji]] is a 7 chain structure with sequence from [http://en.wikipedia.org/wiki/Eco57 Eco57]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JJI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JJI FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5jji]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_O157:H7 Escherichia coli O157:H7] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JJI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JJI FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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]] 2.601Å</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=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5jjk|5jjk]], [[5jjl|5jjl]]</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=5jji FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jji OCA], [https://pdbe.org/5jji PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jji RCSB], [https://www.ebi.ac.uk/pdbsum/5jji PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jji ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rho, Z5293, ECs4716 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83334 ECO57])</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=5jji FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jji OCA], [http://pdbe.org/5jji PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jji RCSB], [http://www.ebi.ac.uk/pdbsum/5jji PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jji ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RHO_ECO57 RHO_ECO57]] Facilitates transcription termination by a mechanism that involves Rho binding to the nascent RNA, activation of Rho's RNA-dependent ATPase activity, and release of the mRNA from the DNA template. | + | [https://www.uniprot.org/uniprot/RHO_ECOLI RHO_ECOLI] Facilitates transcription termination by a mechanism that involves rho binding to the nascent RNA, activation of rho's RNA-dependent ATPase activity, and release of the mRNA from the DNA template. RNA-dependent NTPAse which utilizes all four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01884] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Eco57]] | + | [[Category: Escherichia coli O157:H7]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Berger, J M]] | + | [[Category: Synthetic construct]] |
| - | [[Category: Lawson, M R]] | + | [[Category: Berger JM]] |
| - | [[Category: Qu, S]] | + | [[Category: Lawson MR]] |
| - | [[Category: Thomsen, N D]] | + | [[Category: Qu S]] |
| - | [[Category: Witkowsky, L B]] | + | [[Category: Thomsen ND]] |
| - | [[Category: Protein-rna complex]] | + | [[Category: Witkowsky LB]] |
| - | [[Category: Transcription-rna complex]]
| + | |
| Structural highlights
5jji is a 7 chain structure with sequence from Escherichia coli O157:H7 and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.601Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
RHO_ECOLI Facilitates transcription termination by a mechanism that involves rho binding to the nascent RNA, activation of rho's RNA-dependent ATPase activity, and release of the mRNA from the DNA template. RNA-dependent NTPAse which utilizes all four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01884]
Publication Abstract from PubMed
Ring-shaped hexameric helicases and translocases support essential DNA-, RNA-, and protein-dependent transactions in all cells and many viruses. How such systems coordinate ATPase activity between multiple subunits to power conformational changes that drive the engagement and movement of client substrates is a fundamental question. Using the Escherichia coli Rho transcription termination factor as a model system, we have used solution and crystallographic structural methods to delineate the range of conformational changes that accompany distinct substrate and nucleotide cofactor binding events. Small-angle X-ray scattering data show that Rho preferentially adopts an open-ring state in solution and that RNA and ATP are both required to cooperatively promote ring closure. Multiple closed-ring structures with different RNA substrates and nucleotide occupancies capture distinct catalytic intermediates accessed during translocation. Our data reveal how RNA-induced ring closure templates a sequential ATP-hydrolysis mechanism, provide a molecular rationale for how the Rho ATPase domains distinguishes between distinct RNA sequences, and establish structural snapshots of substepping events in a hexameric helicase/translocase.
Molecular mechanisms of substrate-controlled ring dynamics and substepping in a nucleic acid-dependent hexameric motor.,Thomsen ND, Lawson MR, Witkowsky LB, Qu S, Berger JM Proc Natl Acad Sci U S A. 2016 Nov 29;113(48):E7691-E7700. Epub 2016 Nov 16. PMID:27856760[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Thomsen ND, Lawson MR, Witkowsky LB, Qu S, Berger JM. Molecular mechanisms of substrate-controlled ring dynamics and substepping in a nucleic acid-dependent hexameric motor. Proc Natl Acad Sci U S A. 2016 Nov 29;113(48):E7691-E7700. Epub 2016 Nov 16. PMID:27856760 doi:http://dx.doi.org/10.1073/pnas.1616745113
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