1smy

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{{Seed}}
 
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[[Image:1smy.png|left|200px]]
 
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==Structural basis for transcription regulation by alarmone ppGpp==
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The line below this paragraph, containing "STRUCTURE_1smy", creates the "Structure Box" on the page.
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<StructureSection load='1smy' size='340' side='right'caption='[[1smy]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1smy]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SMY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SMY FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 2.7&#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=G4P:GUANOSINE-5,3-TETRAPHOSPHATE'>G4P</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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{{STRUCTURE_1smy| PDB=1smy | SCENE= }}
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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=1smy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1smy OCA], [https://pdbe.org/1smy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1smy RCSB], [https://www.ebi.ac.uk/pdbsum/1smy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1smy ProSAT], [https://www.topsan.org/Proteins/RSGI/1smy TOPSAN]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RPOA_THETH RPOA_THETH] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.
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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/sm/1smy_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=1smy 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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Guanosine-tetraphosphate (ppGpp) is a major regulator of stringent control, an adaptive response of bacteria to amino acid starvation. The 2.7 A resolution structure of the Thermus thermophilus RNA polymerase (RNAP) holoenzyme in complex with ppGpp reveals that ppGpp binds to the same site near the active center in both independent RNAP molecules in the crystal but in strikingly distinct orientations. Binding is symmetrical with respect to the two diphosphates of ppGpp and is relaxed with respect to the orientation of the nucleotide base. Different modes of ppGpp binding are coupled with asymmetry of the active site configurations. The results suggest that base pairing of ppGpp with cytosines in the nontemplate DNA strand might be an essential component of transcription control by ppGpp. We present experimental evidence highlighting the importance of base-specific contacts between ppGpp and specific cytosine residues during both transcription initiation and elongation.
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===Structural basis for transcription regulation by alarmone ppGpp===
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Structural basis for transcription regulation by alarmone ppGpp.,Artsimovitch I, Patlan V, Sekine S, Vassylyeva MN, Hosaka T, Ochi K, Yokoyama S, Vassylyev DG Cell. 2004 Apr 30;117(3):299-310. PMID:15109491<ref>PMID:15109491</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 1smy" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_15109491}}, adds the Publication Abstract to the page
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*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 15109491 is the PubMed ID number.
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*[[Sigma factor 3D structures|Sigma factor 3D structures]]
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== References ==
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{{ABSTRACT_PUBMED_15109491}}
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<references/>
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__TOC__
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==About this Structure==
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</StructureSection>
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1SMY is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SMY OCA].
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[[Category: Large Structures]]
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==Reference==
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Structural basis for transcription regulation by alarmone ppGpp., Artsimovitch I, Patlan V, Sekine S, Vassylyeva MN, Hosaka T, Ochi K, Yokoyama S, Vassylyev DG, Cell. 2004 Apr 30;117(3):299-310. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15109491 15109491]
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[[Category: DNA-directed RNA polymerase]]
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[[Category: Protein complex]]
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[[Category: Thermus thermophilus]]
[[Category: Thermus thermophilus]]
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[[Category: Artsimovitch, I.]]
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[[Category: Artsimovitch I]]
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[[Category: Hosaka, T.]]
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[[Category: Hosaka T]]
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[[Category: Ochi, K.]]
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[[Category: Ochi K]]
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[[Category: Patlan, V.]]
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[[Category: Patlan V]]
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[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
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[[Category: Sekine S]]
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[[Category: Sekine, S.]]
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[[Category: Vassylyev DG]]
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[[Category: Vassylyev, D G.]]
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[[Category: Vassylyeva MN]]
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[[Category: Vassylyeva, M N.]]
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[[Category: Yokoyama S]]
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[[Category: Yokoyama, S.]]
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[[Category: Guanosine-tetraphosphate]]
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[[Category: Ppgpp]]
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[[Category: Riken structural genomics/proteomics initiative]]
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[[Category: Rna polymerase holoenzyme]]
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[[Category: Rsgi]]
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[[Category: Structural genomic]]
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[[Category: Transcription regulation]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 10:20:31 2008''
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Current revision

Structural basis for transcription regulation by alarmone ppGpp

PDB ID 1smy

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