2wb1: Difference between revisions

Latest revision as of 09:34, 6 November 2024

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

Structural highlights

2wb1 is a 20 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 3.52Å
Ligands:	MG, ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RPO1N_SACSH DNA-dependent RNA polymerase (RNAP) catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Forms the clamp head domain.[HAMAP-Rule:MF_00863]^[1] ^[2] ^[3]

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^[4]

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

References

↑ 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

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] 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

[2] 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

[3] 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

[4] 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

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[2]

[3]

[4]

@@ Line 1: / Line 1: @@
 ==The complete structure of the archaeal 13-subunit DNA-directed RNA Polymerase==
-<StructureSection load='2wb1' size='340' side='right' caption='[[2wb1]], [[Resolution|resolution]] 3.52&Aring;' scene=''>
+<StructureSection load='2wb1' size='340' side='right'caption='[[2wb1]], [[Resolution|resolution]] 3.52&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2wb1]] is a 26 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=2WB1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2WB1 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2wb1]] is a 20 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=2WB1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WB1 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]] 3.52&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2waq|2waq]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=2wb1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wb1 OCA], [http://pdbe.org/2wb1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2wb1 RCSB], [http://www.ebi.ac.uk/pdbsum/2wb1 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=2wb1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wb1 OCA], [https://pdbe.org/2wb1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2wb1 RCSB], [https://www.ebi.ac.uk/pdbsum/2wb1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2wb1 ProSAT]</span></td></tr>
 </table>
-{{Large structure}}
+== Function ==
+[https://www.uniprot.org/uniprot/RPO1N_SACSH RPO1N_SACSH] DNA-dependent RNA polymerase (RNAP) catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Forms the clamp head domain.[HAMAP-Rule:MF_00863]<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/wb/2wb1_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wb/2wb1_consurf.spt"</scriptWhenChecked>
-     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
@@ Line 29: / Line 31: @@
 ==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 enzyme]]
+[[Category: Unligil UM]]
-[[Category: Rna-polymerase]]
-[[Category: Transcription]]

2wb1: Difference between revisions

Latest revision as of 09:34, 6 November 2024

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?)

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