2pi5

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:09, 21 February 2024) (edit) (undo)
 
(16 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2pi5.gif|left|200px]]<br /><applet load="2pi5" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="2pi5, resolution 2.90&Aring;" />
 
-
'''T7 RNA polymerase complexed with a phi10 promoter'''<br />
 
-
==Overview==
+
==T7 RNA polymerase complexed with a phi10 promoter==
-
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 Phi10, 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.
+
<StructureSection load='2pi5' size='340' side='right'caption='[[2pi5]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
 +
== Structural highlights ==
 +
<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>
 +
</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>
 +
<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>
 +
</table>
 +
== Function ==
 +
[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.
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pi/2pi5_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</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].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
2PI5 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t7 Bacteriophage t7]. 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://oca.weizmann.ac.il/oca-bin/ocashort?id=2PI5 OCA].
+
*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
-
 
+
__TOC__
-
==Reference==
+
</StructureSection>
-
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://ispc.weizmann.ac.il//pmbin/getpm?pmid=17512007 17512007]
+
[[Category: Escherichia phage T7]]
-
[[Category: Bacteriophage t7]]
+
[[Category: Large Structures]]
-
[[Category: DNA-directed RNA polymerase]]
+
[[Category: Kennedy WP]]
-
[[Category: Single protein]]
+
[[Category: Momand JR]]
-
[[Category: Kennedy, W.P.]]
+
[[Category: Yin YW]]
-
[[Category: Momand, J.R.]]
+
-
[[Category: Yin, Y.W.]]
+
-
[[Category: initiating nucleoites]]
+
-
[[Category: t7 rna polymerase]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 14:50:24 2008''
+

Current revision

T7 RNA polymerase complexed with a phi10 promoter

PDB ID 2pi5

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2pi5"
Personal tools