1s0v

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(New page: 200px<br /><applet load="1s0v" size="450" color="white" frame="true" align="right" spinBox="true" caption="1s0v, resolution 3.2&Aring;" /> '''Structural basis for ...)
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[[Image:1s0v.gif|left|200px]]<br /><applet load="1s0v" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1s0v, resolution 3.2&Aring;" />
 
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'''Structural basis for substrate selection by T7 RNA polymerase'''<br />
 
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==Overview==
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==Structural basis for substrate selection by T7 RNA polymerase==
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The mechanism by which nucleotide polymerases select the correct substrate, is of fundamental importance to the fidelity of DNA replication and, transcription. During the nucleotide addition cycle, pol I DNA polymerases, undergo the transition from a catalytically inactive "open" to an active, "closed" conformation. All known determinants of substrate selection are, associated with the "closed" state. To elucidate if this mechanism is, conserved in homologous single subunit RNA polymerases (RNAPs), we have, determined the structure of T7 RNAP elongation complex with the incoming, substrate analog. Surprisingly, the substrate specifically binds to RNAP, in the "open" conformation, where it is base paired with the acceptor, template base, while Tyr639 provides discrimination of ribose versus, deoxyribose substrates. The structure therefore suggests a novel, mechanism, in which the substrate selection occurs prior to the, isomerization to the catalytically active conformation. Modeling of, multisubunit RNAPs suggests that this mechanism might be universal for all, RNAPs.
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<StructureSection load='1s0v' size='340' side='right'caption='[[1s0v]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1s0v]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_T7 Escherichia phage T7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S0V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S0V FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.2&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1s0v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s0v OCA], [https://pdbe.org/1s0v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s0v RCSB], [https://www.ebi.ac.uk/pdbsum/1s0v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s0v ProSAT], [https://www.topsan.org/Proteins/RSGI/1s0v TOPSAN]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RPOL_BPT7 RPOL_BPT7] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Responsible for the transcription of the late genes of T7. It is rifampicin-resistant. It recognizes a specific promoter sequence, unwinds the double-stranded RNA to expose the coding strand for templating, initiates transcription preferentially with a purine.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/s0/1s0v_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=1s0v ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The mechanism by which nucleotide polymerases select the correct substrate is of fundamental importance to the fidelity of DNA replication and transcription. During the nucleotide addition cycle, pol I DNA polymerases undergo the transition from a catalytically inactive "open" to an active "closed" conformation. All known determinants of substrate selection are associated with the "closed" state. To elucidate if this mechanism is conserved in homologous single subunit RNA polymerases (RNAPs), we have determined the structure of T7 RNAP elongation complex with the incoming substrate analog. Surprisingly, the substrate specifically binds to RNAP in the "open" conformation, where it is base paired with the acceptor template base, while Tyr639 provides discrimination of ribose versus deoxyribose substrates. The structure therefore suggests a novel mechanism, in which the substrate selection occurs prior to the isomerization to the catalytically active conformation. Modeling of multisubunit RNAPs suggests that this mechanism might be universal for all RNAPs.
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==About this Structure==
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Structural basis for substrate selection by t7 RNA polymerase.,Temiakov D, Patlan V, Anikin M, McAllister WT, Yokoyama S, Vassylyev DG Cell. 2004 Feb 6;116(3):381-91. PMID:15016373<ref>PMID:15016373</ref>
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1S0V is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t7 Bacteriophage t7] with MG and APC as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1S0V OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Structural basis for substrate selection by t7 RNA polymerase., Temiakov D, Patlan V, Anikin M, McAllister WT, Yokoyama S, Vassylyev DG, Cell. 2004 Feb 6;116(3):381-91. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15016373 15016373]
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</div>
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[[Category: Bacteriophage t7]]
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<div class="pdbe-citations 1s0v" style="background-color:#fffaf0;"></div>
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[[Category: DNA-directed RNA polymerase]]
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[[Category: Single protein]]
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[[Category: Anikin, M.]]
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[[Category: McAllister, W.T.]]
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[[Category: Patlan, V.]]
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[[Category: RSGI, RIKEN.Structural.Genomics/Proteomics.Initiative.]]
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[[Category: Temiakov, D.]]
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[[Category: Vassylyev, D.G.]]
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[[Category: Yokoyama, S.]]
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[[Category: APC]]
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[[Category: MG]]
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[[Category: dna]]
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[[Category: riken structural genomics/proteomics initiative]]
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[[Category: rna]]
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[[Category: rsgi]]
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[[Category: structural genomics]]
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[[Category: t7 rna polymerase]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 02:01:20 2007''
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==See Also==
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*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Escherichia phage T7]]
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[[Category: Large Structures]]
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[[Category: Anikin M]]
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[[Category: McAllister WT]]
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[[Category: Patlan V]]
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[[Category: Temiakov D]]
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[[Category: Vassylyev DG]]
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[[Category: Yokoyama S]]

Current revision

Structural basis for substrate selection by T7 RNA polymerase

PDB ID 1s0v

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