2waq

From Proteopedia

(Difference between revisions)

Current revision

The complete structure of the archaeal 13-subunit DNA-directed RNA Polymerase

Structural highlights

2waq is a 10 chain structure with sequence from Saccharolobus shibatae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.35Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RPO2_SACSH DNA-dependent RNA polymerase (RNAP) catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates (Probable). This subunit is involved in DNA promoter recognition (PubMed:22848102).^[1] ^[2] ^[3] ^[4]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The archaeal RNA polymerase (RNAP) shares structural similarities with eukaryotic RNAP II but requires a reduced subset of general transcription factors for promoter-dependent initiation. To deepen our knowledge of cellular transcription, we have determined the structure of the 13-subunit DNA-directed RNAP from Sulfolobus shibatae at 3.35 A resolution. The structure contains the full complement of subunits, including RpoG/Rpb8 and the equivalent of the clamp-head and jaw domains of the eukaryotic Rpb1. Furthermore, we have identified subunit Rpo13, an RNAP component in the order Sulfolobales, which contains a helix-turn-helix motif that interacts with the RpoH/Rpb5 and RpoA'/Rpb1 subunits. Its location and topology suggest a role in the formation of the transcription bubble.

Evolution of Complex RNA Polymerases: The Complete Archaeal RNA Polymerase Structure.,Korkhin Y, Unligil UM, Littlefield O, Nelson PJ, Stuart DI, Sigler PB, Bell SD, Abrescia NG PLoS Biol. 2009 May 5;7(5):e102. PMID:19419240^[5]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Wojtas MN, Mogni M, Millet O, Bell SD, Abrescia NG. Structural and functional analyses of the interaction of archaeal RNA polymerase with DNA. Nucleic Acids Res. 2012 Jul 30. PMID:22848102 doi:10.1093/nar/gks692
↑ Korkhin Y, Unligil UM, Littlefield O, Nelson PJ, Stuart DI, Sigler PB, Bell SD, Abrescia NG. Evolution of Complex RNA Polymerases: The Complete Archaeal RNA Polymerase Structure. PLoS Biol. 2009 May 5;7(5):e102. PMID:19419240 doi:10.1371/journal.pbio.1000102
↑ Wojtas M, Peralta B, Ondiviela M, Mogni M, Bell SD, Abrescia NG. Archaeal RNA polymerase: the influence of the protruding stalk in crystal packing and preliminary biophysical analysis of the Rpo13 subunit. Biochem Soc Trans. 2011 Jan 19;39(1):25-30. PMID:21265742 doi:10.1042/BST0390025
↑ Wojtas MN, Mogni M, Millet O, Bell SD, Abrescia NG. Structural and functional analyses of the interaction of archaeal RNA polymerase with DNA. Nucleic Acids Res. 2012 Jul 30. PMID:22848102 doi:10.1093/nar/gks692
↑ Korkhin Y, Unligil UM, Littlefield O, Nelson PJ, Stuart DI, Sigler PB, Bell SD, Abrescia NG. Evolution of Complex RNA Polymerases: The Complete Archaeal RNA Polymerase Structure. PLoS Biol. 2009 May 5;7(5):e102. PMID:19419240 doi:10.1371/journal.pbio.1000102

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2waq"

@@ Line 1: / Line 1: @@
-==THE COMPLETE STRUCTURE OF THE ARCHAEAL 13-SUBUNIT DNA-DIRECTED RNA POLYMERASE==
-<StructureSection load='2waq' size='340' side='right' caption='[[2waq]], [[Resolution|resolution]] 3.35&Aring;' scene=''>
+==The complete structure of the archaeal 13-subunit DNA-directed RNA Polymerase==
+<StructureSection load='2waq' size='340' side='right'caption='[[2waq]], [[Resolution|resolution]] 3.35&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2waq]] is a 13 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_shibatae Sulfolobus shibatae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WAQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2WAQ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2waq]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_shibatae Saccharolobus shibatae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WAQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WAQ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.35&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2wb1|2wb1]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2waq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2waq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2waq RCSB], [http://www.ebi.ac.uk/pdbsum/2waq PDBsum]</span></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=2waq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2waq OCA], [https://pdbe.org/2waq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2waq RCSB], [https://www.ebi.ac.uk/pdbsum/2waq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2waq ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/RPO2_SACSH RPO2_SACSH] DNA-dependent RNA polymerase (RNAP) catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates (Probable). This subunit is involved in DNA promoter recognition (PubMed:22848102).<ref>PMID:22848102</ref> <ref>PMID:19419240</ref> <ref>PMID:21265742</ref> <ref>PMID:22848102</ref>
 == 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/wa/2waq_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wa/2waq_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2waq ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 25: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2waq" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[RNA polymerase|RNA polymerase]]
+*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Sulfolobus shibatae]]
+[[Category: Large Structures]]
-[[Category: Abrescia, N G.A]]
+[[Category: Saccharolobus shibatae]]
-[[Category: Bell, S D]]
+[[Category: Abrescia NGA]]
-[[Category: Korkhin, Y]]
+[[Category: Bell SD]]
-[[Category: Littlefield, O]]
+[[Category: Korkhin Y]]
-[[Category: Nelson, P J]]
+[[Category: Littlefield O]]
-[[Category: Sigler, P B]]
+[[Category: Nelson PJ]]
-[[Category: Stuart, D I]]
+[[Category: Sigler PB]]
-[[Category: Unligil, U M]]
+[[Category: Stuart DI]]
-[[Category: Multi-subunit]]
+[[Category: Unligil UM]]
-[[Category: Rna polymerase]]
-[[Category: Transcription]]

2waq

From Proteopedia

Current revision

The complete structure of the archaeal 13-subunit DNA-directed RNA Polymerase

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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