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<StructureSection load='5zx2' size='340' side='right'caption='[[5zx2]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
<StructureSection load='5zx2' size='340' side='right'caption='[[5zx2]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5zx2]] is a 9 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZX2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZX2 FirstGlance]. <br>
<table><tr><td colspan='2'>[[5zx2]] 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=5ZX2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZX2 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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]] 2.8&#8491;</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=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=5zx2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zx2 OCA], [http://pdbe.org/5zx2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zx2 RCSB], [http://www.ebi.ac.uk/pdbsum/5zx2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zx2 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=5zx2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zx2 OCA], [https://pdbe.org/5zx2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zx2 RCSB], [https://www.ebi.ac.uk/pdbsum/5zx2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zx2 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 employs extra-cytoplasmic function (ECF) sigma factors to regulate context-specific gene expression programs. Despite being the most abundant and divergent sigma factor class, the structural basis of ECF sigma factor-mediated transcription initiation remains unknown. Here, we determine a crystal structure of Mycobacterium tuberculosis (Mtb) RNAP holoenzyme comprising an RNAP core enzyme and the ECF sigma factor sigma(H) (sigma(H)-RNAP) at 2.7 A, and solve another crystal structure of a transcription initiation complex of Mtb sigma(H)-RNAP (sigma(H)-RPo) comprising promoter DNA and an RNA primer at 2.8 A. The two structures together reveal the interactions between sigma(H) and RNAP that are essential for sigma(H)-RNAP holoenzyme assembly as well as the interactions between sigma(H)-RNAP and promoter DNA responsible for stringent promoter recognition and for promoter unwinding. Our study establishes that ECF sigma factors and primary sigma factors employ distinct mechanisms for promoter recognition and for promoter unwinding.
 
Structural basis for transcription initiation by bacterial ECF sigma factors.,Li L, Fang C, Zhuang N, Wang T, Zhang Y Nat Commun. 2019 Mar 11;10(1):1153. doi: 10.1038/s41467-019-09096-y. PMID:30858373<ref>PMID:30858373</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5zx2" 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: Rna polymerase]]
[[Category: Zhang Y]]
[[Category: Sigma h]]
[[Category: Transcription initiation]]
[[Category: Transcription-dna-rna complex]]

Latest revision as of 12:09, 22 November 2023

Mycobacterium tuberculosis RNA polymerase transcription initiation complex with ECF sigma factor sigma H and 7nt RNAMycobacterium tuberculosis RNA polymerase transcription initiation complex with ECF sigma factor sigma H and 7nt RNA

Structural highlights

5zx2 is a 9 chain structure with sequence from Mycobacterium tuberculosis H37Rv 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 2.8Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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 employs extra-cytoplasmic function (ECF) sigma factors to regulate context-specific gene expression programs. Despite being the most abundant and divergent sigma factor class, the structural basis of ECF sigma factor-mediated transcription initiation remains unknown. Here, we determine a crystal structure of Mycobacterium tuberculosis (Mtb) RNAP holoenzyme comprising an RNAP core enzyme and the ECF sigma factor sigma(H) (sigma(H)-RNAP) at 2.7 A, and solve another crystal structure of a transcription initiation complex of Mtb sigma(H)-RNAP (sigma(H)-RPo) comprising promoter DNA and an RNA primer at 2.8 A. The two structures together reveal the interactions between sigma(H) and RNAP that are essential for sigma(H)-RNAP holoenzyme assembly as well as the interactions between sigma(H)-RNAP and promoter DNA responsible for stringent promoter recognition and for promoter unwinding. Our study establishes that ECF sigma factors and primary sigma factors employ distinct mechanisms for promoter recognition and for promoter unwinding.

Structural basis for transcription initiation by bacterial ECF sigma factors.,Li L, Fang C, Zhuang N, Wang T, Zhang Y Nat Commun. 2019 Mar 11;10(1):1153. doi: 10.1038/s41467-019-09096-y. PMID:30858373[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ 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
  2. ↑ Li L, Fang C, Zhuang N, Wang T, Zhang Y. Structural basis for transcription initiation by bacterial ECF sigma factors. Nat Commun. 2019 Mar 11;10(1):1153. doi: 10.1038/s41467-019-09096-y. PMID:30858373 doi:http://dx.doi.org/10.1038/s41467-019-09096-y

5zx2, resolution 2.80Å

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