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==Structure of Mycobacterium smegmatis transcription initiation complex with a full transcription bubble==
==Structure of Mycobacterium smegmatis transcription initiation complex with a full transcription bubble==
<StructureSection load='5vi5' size='340' side='right' caption='[[5vi5]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
<StructureSection load='5vi5' size='340' side='right'caption='[[5vi5]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5vi5]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycs2 Mycs2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VI5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VI5 FirstGlance]. <br>
<table><tr><td colspan='2'>[[5vi5]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis_MC2_155 Mycolicibacterium smegmatis MC2 155] 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=5VI5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VI5 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 3.196&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rpoD, sigA, MSMEG_2758, MSMEI_2690 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246196 MYCS2]), rbpA, MSMEG_3858, MSMEI_3768 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246196 MYCS2])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5vi5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vi5 OCA], [https://pdbe.org/5vi5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vi5 RCSB], [https://www.ebi.ac.uk/pdbsum/5vi5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vi5 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=5vi5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vi5 OCA], [http://pdbe.org/5vi5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vi5 RCSB], [http://www.ebi.ac.uk/pdbsum/5vi5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vi5 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/RPOC_MYCS2 RPOC_MYCS2]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01322]<ref>PMID:19926651</ref>  [[http://www.uniprot.org/uniprot/RPOZ_MYCS2 RPOZ_MYCS2]] 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]<ref>PMID:19926651</ref>  [[http://www.uniprot.org/uniprot/RBPA_MYCS2 RBPA_MYCS2]] Binds to RNA polymerase (RNAP), probably stimulating transcriptions from principal, but not alternative sigma factor promoters (By similarity). Partially restores transcription in the presence of rifampicin (Rif) in vitro; overexpression leads to an increase in the Rif tolerance in vivo, with smaller colonies. Seems to act by removing Rif from its binding site and preventing its further binding. No longer stimulates transcription in Rif-resistant RNA polymerase (with mutations in rpoB).<ref>PMID:19926651</ref> <ref>PMID:21415119</ref>  [[http://www.uniprot.org/uniprot/A0QW02_MYCS2 A0QW02_MYCS2]] 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] [[http://www.uniprot.org/uniprot/RPOA_MYCS2 RPOA_MYCS2]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_00059]<ref>PMID:19926651</ref> [[http://www.uniprot.org/uniprot/RPOB_MYCS2 RPOB_MYCS2]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. This subunit often mutates to generate rifampicin (Rif) resistance. Interaction with RbpA partially restores Rif-inhibited transcription; once the subunit is Rif-resistant however RbpA no longer stimulates transcription.[HAMAP-Rule:MF_01321]<ref>PMID:19926651</ref> 
[https://www.uniprot.org/uniprot/RPOA_MYCS2 RPOA_MYCS2] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_00059]<ref>PMID:19926651</ref>  
<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 5vi5" style="background-color:#fffaf0;"></div>
<div class="pdbe-citations 5vi5" style="background-color:#fffaf0;"></div>
==See Also==
*[[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: Mycs2]]
[[Category: Mycolicibacterium smegmatis MC2 155]]
[[Category: Campbell, E A]]
[[Category: Synthetic construct]]
[[Category: Darst, S A]]
[[Category: Campbell EA]]
[[Category: Lilic, M]]
[[Category: Darst SA]]
[[Category: Dna-dependent rna polymerase]]
[[Category: Lilic M]]
[[Category: Nucleotidyl transferase]]
[[Category: Transcription]]
[[Category: Transcriptioni initiation complex]]

Latest revision as of 16:49, 4 October 2023

Structure of Mycobacterium smegmatis transcription initiation complex with a full transcription bubbleStructure of Mycobacterium smegmatis transcription initiation complex with a full transcription bubble

Structural highlights

5vi5 is a 10 chain structure with sequence from Mycolicibacterium smegmatis MC2 155 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 3.196Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RPOA_MYCS2 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

The mycobacteria RNA polymerase (RNAP) is a target for antimicrobials against tuberculosis, motivating structure/function studies. Here we report a 3.2 A-resolution crystal structure of a Mycobacterium smegmatis (Msm) open promoter complex (RPo), along with structural analysis of the Msm RPo and a previously reported 2.76 A-resolution crystal structure of an Msm transcription initiation complex with a promoter DNA fragment. We observe the interaction of the Msm RNAP alpha-subunit C-terminal domain (alphaCTD) with DNA, and we provide evidence that the alphaCTD may play a role in Mtb transcription regulation. Our results reveal the structure of an Actinobacteria-unique insert of the RNAP beta' subunit. Finally, our analysis reveals the disposition of the N-terminal segment of Msm sigmaA, which may comprise an intrinsically disordered protein domain unique to mycobacteria. The clade-specific features of the mycobacteria RNAP provide clues to the profound instability of mycobacteria RPo compared with E. coli.

Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures.,Hubin EA, Lilic M, Darst SA, Campbell EA Nat Commun. 2017 Jul 13;8:16072. doi: 10.1038/ncomms16072. PMID:28703128[2]

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

See Also

References

  1. ↑ Dey A, Verma AK, Chatterji D. Role of an RNA polymerase interacting protein, MsRbpA, from Mycobacterium smegmatis in phenotypic tolerance to rifampicin. Microbiology. 2010 Mar;156(Pt 3):873-83. doi: 10.1099/mic.0.033670-0. Epub 2009, Nov 19. PMID:19926651 doi:http://dx.doi.org/10.1099/mic.0.033670-0
  2. ↑ Hubin EA, Lilic M, Darst SA, Campbell EA. Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures. Nat Commun. 2017 Jul 13;8:16072. doi: 10.1038/ncomms16072. PMID:28703128 doi:http://dx.doi.org/10.1038/ncomms16072

5vi5, resolution 3.20Å

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