1smy

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[[Image:1smy.gif|left|200px]]
 
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{{Structure
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==Structural basis for transcription regulation by alarmone ppGpp==
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|PDB= 1smy |SIZE=350|CAPTION= <scene name='initialview01'>1smy</scene>, resolution 2.70&Aring;
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<StructureSection load='1smy' size='340' side='right'caption='[[1smy]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=G4P:GUANOSINE-5&#39;,3&#39;-TETRAPHOSPHATE'>G4P</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
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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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|ACTIVITY= <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>
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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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|GENE=
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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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|DOMAIN=
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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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|RELATEDENTRY=[[1iw7|1IW7]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1smy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1smy OCA], [http://www.ebi.ac.uk/pdbsum/1smy PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1smy RCSB]</span>
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== Function ==
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}}
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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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==Overview==
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==See Also==
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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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*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
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*[[Sigma factor 3D structures|Sigma factor 3D structures]]
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==About this Structure==
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== References ==
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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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<references/>
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__TOC__
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==Reference==
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</StructureSection>
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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: Large Structures]]
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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 Sun Mar 30 23:44:17 2008''
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Current revision

Structural basis for transcription regulation by alarmone ppGpp

PDB ID 1smy

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