2pi5

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[[Image:2pi5.gif|left|200px]]
 
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{{Structure
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==T7 RNA polymerase complexed with a phi10 promoter==
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|PDB= 2pi5 |SIZE=350|CAPTION= <scene name='initialview01'>2pi5</scene>, resolution 2.90&Aring;
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<StructureSection load='2pi5' size='340' side='right'caption='[[2pi5]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>
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<table><tr><td colspan='2'>[[2pi5]] is a 3 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=2PI5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PI5 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]] 2.9&#8491;</td></tr>
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|GENE=
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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=2pi5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pi5 OCA], [https://pdbe.org/2pi5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pi5 RCSB], [https://www.ebi.ac.uk/pdbsum/2pi5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pi5 ProSAT]</span></td></tr>
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|DOMAIN=
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</table>
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|RELATEDENTRY=[[2pi4|2PI4]]
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== Function ==
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2pi5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pi5 OCA], [http://www.ebi.ac.uk/pdbsum/2pi5 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2pi5 RCSB]</span>
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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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}}
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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/pi/2pi5_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=2pi5 ConSurf].
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<div style="clear:both"></div>
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'''T7 RNA polymerase complexed with a phi10 promoter'''
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==See Also==
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*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
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__TOC__
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==Overview==
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</StructureSection>
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DNA-directed RNA polymerases are capable of initiating synthesis of RNA without primers, the first catalytic stage of initiation is referred to as de novo RNA synthesis. De novo synthesis is a unique phase in the transcription cycle where the RNA polymerase binds two nucleotides rather than a nascent RNA polymer and a single nucleotide. For bacteriophage T7 RNA polymerase, transcription begins with a marked preference for GTP at the +1 and +2 positions. We determined the crystal structures of T7 RNA polymerase complexes captured during the de novo RNA synthesis. The DNA substrates in the structures in the complexes contain a common Phi 10 duplex promoter followed by a unique five base single-stranded extension of template DNA whose sequences varied at positions +1 and +2, thereby allowing for different pairs of initiating nucleotides GTP, ATP, CTP or UTP to bind. The structures show that the initiating nucleotides bind RNA polymerase in locations distinct from those described previously for elongation complexes. Selection bias in favor of GTP as an initiating nucleotide is accomplished by shape complementarity, extensive protein side-chain and strong base-stacking interactions for the guanine moiety in the enzyme active site. Consequently, an initiating GTP provides the largest stabilization force for the open promoter conformation.
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[[Category: Escherichia phage T7]]
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[[Category: Large Structures]]
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==About this Structure==
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[[Category: Kennedy WP]]
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2PI5 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t7 Enterobacteria phage t7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PI5 OCA].
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[[Category: Momand JR]]
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[[Category: Yin YW]]
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==Reference==
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Mechanism for de novo RNA synthesis and initiating nucleotide specificity by t7 RNA polymerase., Kennedy WP, Momand JR, Yin YW, J Mol Biol. 2007 Jul 6;370(2):256-68. Epub 2007 Mar 21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17512007 17512007]
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[[Category: DNA-directed RNA polymerase]]
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[[Category: Enterobacteria phage t7]]
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[[Category: Single protein]]
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[[Category: Kennedy, W P.]]
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[[Category: Momand, J R.]]
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[[Category: Yin, Y W.]]
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[[Category: initiating nucleoite]]
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[[Category: t7 rna polymerase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:36:10 2008''
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Current revision

T7 RNA polymerase complexed with a phi10 promoter

PDB ID 2pi5

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