4v8s

From Proteopedia

(Difference between revisions)

Current revision

Archaeal RNAP-DNA binary complex at 4.32Ang

Structural highlights

4v8s is a 20 chain structure with sequence from Saccharolobus shibatae B12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 4.323Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RPO1C_SACSH DNA-dependent RNA polymerase (RNAP) catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Forms part of the jaw domain.[HAMAP-Rule:MF_00411]^[1] ^[2] ^[3]

Publication Abstract from PubMed

Multi-subunit RNA polymerases (RNAPs) in all three domains of life share a common ancestry. The composition of the archaeal RNAP (aRNAP) is not identical between phyla and species, with subunits Rpo8 and Rpo13 found in restricted subsets of archaea. While Rpo8 has an ortholog, Rpb8, in the nuclear eukaryal RNAPs, Rpo13 lacks clear eukaryal orthologs. Here, we report crystal structures of the DNA-bound and free form of the aRNAP from Sulfolobus shibatae. Together with biochemical and biophysical analyses, these data show that Rpo13 C-terminus binds non-specifically to double-stranded DNA. These interactions map on our RNAP-DNA binary complex on the downstream DNA at the far end of the DNA entry channel. Our findings thus support Rpo13 as a RNAP-DNA stabilization factor, a role reminiscent of eukaryotic general transcriptional factors. The data further yield insight into the mechanisms and evolution of RNAP-DNA interaction.

Structural and functional analyses of the interaction of archaeal RNA polymerase with DNA.,Wojtas MN, Mogni M, Millet O, Bell SD, Abrescia NG Nucleic Acids Res. 2012 Jul 30. PMID:22848102^[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
↑ 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

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4v8s"

@@ Line 3: / Line 3: @@
 <StructureSection load='4v8s' size='340' side='right'caption='[[4v8s]], [[Resolution|resolution]] 4.32&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4v8s]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_shibatae_B12 Saccharolobus shibatae B12] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4b1o 4b1o] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4b1p 4b1p]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V8S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4V8S FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4v8s]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_shibatae_B12 Saccharolobus shibatae B12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V8S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4V8S 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]] 4.323&#8491;</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=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=4v8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v8s OCA], [https://pdbe.org/4v8s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4v8s RCSB], [https://www.ebi.ac.uk/pdbsum/4v8s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4v8s ProSAT]</span></td></tr>
 </table>
 == Function ==
-[https://www.uniprot.org/uniprot/RPO6_SACSH RPO6_SACSH] DNA-dependent RNA polymerase (RNAP) catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_00192]
+[https://www.uniprot.org/uniprot/RPO1C_SACSH RPO1C_SACSH] DNA-dependent RNA polymerase (RNAP) catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Forms part of the jaw domain.[HAMAP-Rule:MF_00411]<ref>PMID:19419240</ref> <ref>PMID:21265742</ref> <ref>PMID:22848102</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 28: / Line 28: @@
 [[Category: Large Structures]]
 [[Category: Saccharolobus shibatae B12]]
-[[Category: Synthetic construct]]
 [[Category: Abrescia NGA]]
 [[Category: Bell SD]]

4v8s

From Proteopedia

Current revision

Archaeal RNAP-DNA binary complex at 4.32Ang

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox