2pi5

<StructureSection load='2pi5' size='340' side='right' caption='[[2pi5]], [[Resolution|resolution]] 2.90&Aring;' scene=''>

<table><tr><td colspan='2'>[[2pi5]] is a 3 chain structure with 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]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PI5 FirstGlance]. <br>

</td></tr><tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2pi4|2pi4]]</td></tr>

<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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></td></tr>

<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><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.rcsb.org/pdb/explore.do?structureId=2pi5 RCSB], [http://www.ebi.ac.uk/pdbsum/2pi5 PDBsum]</span></td></tr>

<table>

<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pi/2pi5_consurf.spt"</scriptWhenChecked>

</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/chain_selection.php?pdb_ID=2ata ConSurf].

<div style="background-color:#fffaf0;">

== Publication Abstract from PubMed ==

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.

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:17512007<ref>PMID:17512007</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>

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*[[RNA polymerase|RNA polymerase]]

[[Category: DNA-directed RNA polymerase]]

[[Category: Enterobacteria phage t7]]

[[Category: Kennedy, W P.]]

[[Category: Momand, J R.]]

[[Category: Yin, Y W.]]

[[Category: Transferase-dna complex]]