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| | ==Cryo-EM structure of E. coli RNA polymerase elongation complex bound to CTP substrate== | | ==Cryo-EM structure of E. coli RNA polymerase elongation complex bound to CTP substrate== |
| - | <StructureSection load='6rh3' size='340' side='right'caption='[[6rh3]], [[Resolution|resolution]] 3.60Å' scene=''> | + | <SX load='6rh3' size='340' side='right' viewer='molstar' caption='[[6rh3]], [[Resolution|resolution]] 3.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6rh3]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RH3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RH3 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6rh3]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RH3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6RH3 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CTP:CYTIDINE-5-TRIPHOSPHATE'>CTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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">Electron Microscopy, [[Resolution|Resolution]] 3.6Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KAK:'>KAK</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CTP:CYTIDINE-5-TRIPHOSPHATE'>CTP</scene>, <scene name='pdbligand=KAK:3-deoxy-guanosine-5-monophosphate'>KAK</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </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=6rh3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rh3 OCA], [https://pdbe.org/6rh3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6rh3 RCSB], [https://www.ebi.ac.uk/pdbsum/6rh3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6rh3 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=6rh3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rh3 OCA], [http://pdbe.org/6rh3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rh3 RCSB], [http://www.ebi.ac.uk/pdbsum/6rh3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rh3 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/L4IY67_ECOLX L4IY67_ECOLX]] Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits.[HAMAP-Rule:MF_00366][SAAS:SAAS00387808] [[http://www.uniprot.org/uniprot/RPOB_ECOLI RPOB_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01321] [[http://www.uniprot.org/uniprot/RPOA_ECOLI RPOA_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. This subunit plays an important role in subunit assembly since its dimerization is the first step in the sequential assembly of subunits to form the holoenzyme.[HAMAP-Rule:MF_00059] [[http://www.uniprot.org/uniprot/RPOC_ECOLI RPOC_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01322] | + | [https://www.uniprot.org/uniprot/RPOA_ECOLI RPOA_ECOLI] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. This subunit plays an important role in subunit assembly since its dimerization is the first step in the sequential assembly of subunits to form the holoenzyme.[HAMAP-Rule:MF_00059] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 6rh3" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6rh3" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[RNA polymerase 3D structures|RNA polymerase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| - | </StructureSection> | + | </SX> |
| - | [[Category: DNA-directed RNA polymerase]] | + | [[Category: Escherichia coli K-12]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Abdelkareem, M]] | + | [[Category: Abdelkareem M]] |
| - | [[Category: Crucifix, C]] | + | [[Category: Crucifix C]] |
| - | [[Category: Guo, X]] | + | [[Category: Guo X]] |
| - | [[Category: Ortiz, J]] | + | [[Category: Ortiz J]] |
| - | [[Category: Papai, G]] | + | [[Category: Papai G]] |
| - | [[Category: Saint-Andre, C]] | + | [[Category: Saint-Andre C]] |
| - | [[Category: Takacs, M]] | + | [[Category: Takacs M]] |
| - | [[Category: Weixlbaumer, A]] | + | [[Category: Weixlbaumer A]] |
| - | [[Category: Ctp]]
| + | |
| - | [[Category: E. coli rna polymerase]]
| + | |
| - | [[Category: Elongation complex]]
| + | |
| - | [[Category: Greb]]
| + | |
| - | [[Category: Transcription]]
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| Structural highlights
Function
RPOA_ECOLI DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. This subunit plays an important role in subunit assembly since its dimerization is the first step in the sequential assembly of subunits to form the holoenzyme.[HAMAP-Rule:MF_00059]
Publication Abstract from PubMed
Regulatory sequences or erroneous incorporations during DNA transcription cause RNA polymerase backtracking and inactivation in all kingdoms of life. Reactivation requires RNA transcript cleavage. Essential transcription factors (GreA and GreB, or TFIIS) accelerate this reaction. We report four cryo-EM reconstructions of Escherichia coli RNA polymerase representing the entire reaction pathway: (1) a backtracked complex; a backtracked complex with GreB (2) before and (3) after RNA cleavage; and (4) a reactivated, substrate-bound complex with GreB before RNA extension. Compared with eukaryotes, the backtracked RNA adopts a different conformation. RNA polymerase conformational changes cause distinct GreB states: a fully engaged GreB before cleavage; a disengaged GreB after cleavage; and a dislodged, loosely bound GreB removed from the active site to allow RNA extension. These reconstructions provide insight into the catalytic mechanism and dynamics of RNA cleavage and extension and suggest how GreB targets backtracked complexes without interfering with canonical transcription.
Structural Basis of Transcription: RNA Polymerase Backtracking and Its Reactivation.,Abdelkareem M, Saint-Andre C, Takacs M, Papai G, Crucifix C, Guo X, Ortiz J, Weixlbaumer A Mol Cell. 2019 May 8. pii: S1097-2765(19)30321-1. doi:, 10.1016/j.molcel.2019.04.029. PMID:31103420[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Abdelkareem M, Saint-Andre C, Takacs M, Papai G, Crucifix C, Guo X, Ortiz J, Weixlbaumer A. Structural Basis of Transcription: RNA Polymerase Backtracking and Its Reactivation. Mol Cell. 2019 May 8. pii: S1097-2765(19)30321-1. doi:, 10.1016/j.molcel.2019.04.029. PMID:31103420 doi:http://dx.doi.org/10.1016/j.molcel.2019.04.029
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