1ynn: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1ynn]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YNN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YNN FirstGlance]. <br>
<table><tr><td colspan='2'>[[1ynn]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YNN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YNN FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=RFP:RIFAMPICIN'>RFP</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]] 3.3&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ynj|1ynj]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=RFP:RIFAMPICIN'>RFP</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'>[https://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [https://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=1ynn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ynn OCA], [https://pdbe.org/1ynn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ynn RCSB], [https://www.ebi.ac.uk/pdbsum/1ynn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ynn 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=1ynn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ynn OCA], [https://pdbe.org/1ynn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ynn RCSB], [https://www.ebi.ac.uk/pdbsum/1ynn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ynn ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/RPOZ_THEAQ RPOZ_THEAQ]] 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:11158566</ref> 
[https://www.uniprot.org/uniprot/RPOA_THEAQ RPOA_THEAQ]  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ynn ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ynn ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
A combined structural, functional, and genetic approach was used to investigate inhibition of bacterial RNA polymerase (RNAP) by sorangicin (Sor), a macrolide polyether antibiotic. Sor lacks chemical and structural similarity to the ansamycin rifampicin (Rif), an RNAP inhibitor widely used to treat tuberculosis. Nevertheless, structural analysis revealed Sor binds in the same RNAP beta subunit pocket as Rif, with almost complete overlap of RNAP binding determinants, and functional analysis revealed that both antibiotics inhibit transcription by directly blocking the path of the elongating transcript at a length of 2-3 nucleotides. Genetic analysis indicates that Rif binding is extremely sensitive to mutations expected to change the shape of the antibiotic binding pocket, while Sor is not. We suggest that conformational flexibility of Sor, in contrast to the rigid conformation of Rif, allows Sor to adapt to changes in the binding pocket. This has important implications for drug design against rapidly mutating targets.
Structural, functional, and genetic analysis of sorangicin inhibition of bacterial RNA polymerase.,Campbell EA, Pavlova O, Zenkin N, Leon F, Irschik H, Jansen R, Severinov K, Darst SA EMBO J. 2005 Feb 23;24(4):674-82. Epub 2005 Feb 3. PMID:15692574<ref>PMID:15692574</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1ynn" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: DNA-directed RNA polymerase]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Thermus aquaticus]]
[[Category: Thermus aquaticus]]
[[Category: Campbell, E A]]
[[Category: Campbell EA]]
[[Category: Darst, S A]]
[[Category: Darst SA]]
[[Category: Irschik, H]]
[[Category: Irschik H]]
[[Category: Jansen, R]]
[[Category: Jansen R]]
[[Category: Leon, F]]
[[Category: Leon F]]
[[Category: Pavlova, O]]
[[Category: Pavlova O]]
[[Category: Severinov, K]]
[[Category: Severinov K]]
[[Category: Zenkin, N]]
[[Category: Zenkin N]]
[[Category: Rifampicin]]
[[Category: Rna polymerase]]
[[Category: Transferase]]

Latest revision as of 11:58, 14 February 2024

Taq RNA polymerase-rifampicin complexTaq RNA polymerase-rifampicin complex

Structural highlights

1ynn is a 6 chain structure with sequence from Thermus aquaticus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3.3Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RPOA_THEAQ

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1ynn, resolution 3.30Å

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
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