This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

4v8s

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 16:13, 1 September 2015

Archaeal RNAP-DNA binary complex at 4.32Ang

Structural highlights

4v8s is a 30 chain structure with sequence from Sulfolobus shibatae b12. This structure supersedes and combines the now removed PDB entries 4b1o and 4b1p. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Related:	2y0s, 4ayb
Activity:	DNA-directed RNA polymerase, with EC number 2.7.7.6
Resources:	FirstGlance, OCA, RCSB, PDBsum

Warning: this is a large structure, and loading might take a long time or not happen at all.

Function

[B8YB63_SULSH] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates (By similarity).[HAMAP-Rule:MF_00250] [B8YB61_SULSH] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates (By similarity).[HAMAP-Rule:MF_00192] [B8YB60_SULSH] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates (By similarity).[HAMAP-Rule:MF_00025] [B8YB54_SULSH] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates (By similarity).[HAMAP-Rule:MF_00411] [B8YB56_SULSH] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates (By similarity).[HAMAP-Rule:MF_00320] [B8YB64_SULSH] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates (By similarity).[HAMAP-Rule:MF_00615] [B8YB62_SULSH] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates (By similarity).[HAMAP-Rule:MF_00261]

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^[1]

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

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 4: / Line 4: @@
 <table><tr><td colspan='2'>[[4v8s]] is a 30 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_shibatae_b12 Sulfolobus shibatae b12]. This structure supersedes and combines 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4V8S FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4b1o|4b1o]], [[4b1p|4b1p]], [[2y0s|2y0s]], [[4ayb|4ayb]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2y0s|2y0s]], [[4ayb|4ayb]]</td></tr>
 <tr id='activity'><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 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=4v8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v8s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4v8s RCSB], [http://www.ebi.ac.uk/pdbsum/4v8s PDBsum]</span></td></tr>

4v8s

From Proteopedia

Revision as of 16:13, 1 September 2015

Archaeal RNAP-DNA binary complex at 4.32Ang

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox