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| | <StructureSection load='6jcy' size='340' side='right'caption='[[6jcy]], [[Resolution|resolution]] 3.11Å' scene=''> | | <StructureSection load='6jcy' size='340' side='right'caption='[[6jcy]], [[Resolution|resolution]] 3.11Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6jcy]] is a 9 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JCY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JCY FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6jcy]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv] 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=6JCY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JCY FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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">X-ray diffraction, [[Resolution|Resolution]] 3.106Å</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=6jcy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jcy OCA], [http://pdbe.org/6jcy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jcy RCSB], [http://www.ebi.ac.uk/pdbsum/6jcy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jcy 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=6jcy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jcy OCA], [https://pdbe.org/6jcy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jcy RCSB], [https://www.ebi.ac.uk/pdbsum/6jcy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jcy ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RPOC_MYCTU RPOC_MYCTU]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01322]<ref>PMID:22570422</ref> [[http://www.uniprot.org/uniprot/RPOB_MYCTU RPOB_MYCTU]] 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_MYCTU RPOA_MYCTU]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_00059]<ref>PMID:22570422</ref> [[http://www.uniprot.org/uniprot/RPOZ_MYCTU RPOZ_MYCTU]] 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.<ref>PMID:22570422</ref> [[http://www.uniprot.org/uniprot/SIGH_MYCTU SIGH_MYCTU]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. Extracytoplasmic function (ECF) sigma factors are held in an inactive form by a cognate anti-sigma factor (RshA) until released. This sigma factor is involved in heat shock and oxidative stress responses; it positively regulates the expression of itself, sigE, sigB and a number of transcriptional regulators as well as other effectors of heat and oxidative stress, leading to direct and indirect control of up to 25% of the bacterial genome. Modulates expression of host genes for intercrine beta (chemokine CC) and apoptosis, altering the host immune response.<ref>PMID:11567012</ref> <ref>PMID:12123450</ref> <ref>PMID:14617153</ref> <ref>PMID:16298337</ref> | + | [https://www.uniprot.org/uniprot/RPOA_MYCTU RPOA_MYCTU] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_00059]<ref>PMID:22570422</ref> |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | Bacterial RNA polymerase (RNAP) forms distinct holoenzymes with extra-cytoplasmic function (ECF) sigma factors to initiate specific gene expression programs. In this study, we report a cryo-EM structure at 4.0 A of Escherichia coli transcription initiation complex comprising sigmaE-the most-studied bacterial ECF sigma factor (Ec sigmaE-RPo), and a crystal structure at 3.1 A of Mycobacterium tuberculosis transcription initiation complex with a chimeric sigmaH/E (Mtb sigmaH/E-RPo). The structure of Ec sigmaE-RPo reveals key interactions essential for assembly of E. coli sigmaE-RNAP holoenzyme and for promoter recognition and unwinding by E. coli sigmaE. Moreover, both structures show that the non-conserved linkers (sigma2/sigma4 linker) of the two ECF sigma factors are inserted into the active-center cleft and exit through the RNA-exit channel. We performed secondary-structure prediction of 27,670 ECF sigma factors and find that their non-conserved linkers probably reach into and exit from RNAP active-center cleft in a similar manner. Further biochemical results suggest that such sigma2/sigma4 linker plays an important role in RPo formation, abortive production and promoter escape during ECF sigma factors-mediated transcription initiation. |
| | + | |
| | + | Structures and mechanism of transcription initiation by bacterial ECF factors.,Fang C, Li L, Shen L, Shi J, Wang S, Feng Y, Zhang Y Nucleic Acids Res. 2019 May 27. pii: 5498757. doi: 10.1093/nar/gkz470. PMID:31131408<ref>PMID:31131408</ref> |
| | + | |
| | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | + | </div> |
| | + | <div class="pdbe-citations 6jcy" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[RNA polymerase 3D structures|RNA polymerase 3D structures]] |
| | + | *[[Sigma factor 3D structures|Sigma factor 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: DNA-directed RNA polymerase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Li, L]]
| + | [[Category: Mycobacterium tuberculosis H37Rv]] |
| - | [[Category: Zhang, Y]]
| + | [[Category: Synthetic construct]] |
| - | [[Category: Mycobacterium tuberculosis]] | + | [[Category: Li L]] |
| - | [[Category: Open complex]] | + | [[Category: Zhang Y]] |
| - | [[Category: Rna polymerase]] | + | |
| - | [[Category: Sigma h/e]] | + | |
| - | [[Category: Transcription]]
| + | |
| Structural highlights
Function
RPOA_MYCTU DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_00059][1]
Publication Abstract from PubMed
Bacterial RNA polymerase (RNAP) forms distinct holoenzymes with extra-cytoplasmic function (ECF) sigma factors to initiate specific gene expression programs. In this study, we report a cryo-EM structure at 4.0 A of Escherichia coli transcription initiation complex comprising sigmaE-the most-studied bacterial ECF sigma factor (Ec sigmaE-RPo), and a crystal structure at 3.1 A of Mycobacterium tuberculosis transcription initiation complex with a chimeric sigmaH/E (Mtb sigmaH/E-RPo). The structure of Ec sigmaE-RPo reveals key interactions essential for assembly of E. coli sigmaE-RNAP holoenzyme and for promoter recognition and unwinding by E. coli sigmaE. Moreover, both structures show that the non-conserved linkers (sigma2/sigma4 linker) of the two ECF sigma factors are inserted into the active-center cleft and exit through the RNA-exit channel. We performed secondary-structure prediction of 27,670 ECF sigma factors and find that their non-conserved linkers probably reach into and exit from RNAP active-center cleft in a similar manner. Further biochemical results suggest that such sigma2/sigma4 linker plays an important role in RPo formation, abortive production and promoter escape during ECF sigma factors-mediated transcription initiation.
Structures and mechanism of transcription initiation by bacterial ECF factors.,Fang C, Li L, Shen L, Shi J, Wang S, Feng Y, Zhang Y Nucleic Acids Res. 2019 May 27. pii: 5498757. doi: 10.1093/nar/gkz470. PMID:31131408[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Hu Y, Morichaud Z, Chen S, Leonetti JP, Brodolin K. Mycobacterium tuberculosis RbpA protein is a new type of transcriptional activator that stabilizes the sigma A-containing RNA polymerase holoenzyme. Nucleic Acids Res. 2012 Aug;40(14):6547-57. doi: 10.1093/nar/gks346. Epub 2012, May 8. PMID:22570422 doi:http://dx.doi.org/10.1093/nar/gks346
- ↑ Fang C, Li L, Shen L, Shi J, Wang S, Feng Y, Zhang Y. Structures and mechanism of transcription initiation by bacterial ECF factors. Nucleic Acids Res. 2019 May 27. pii: 5498757. doi: 10.1093/nar/gkz470. PMID:31131408 doi:http://dx.doi.org/10.1093/nar/gkz470
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