4qjv

From Proteopedia

(Difference between revisions)

Revision as of 09:17, 24 April 2019

The X-ray crystal structure of Rpo3/Rpo11 heterodimer of euryarchaeal RNA polymerase from Thermococcus kodakarensis

Structural highlights

4qjv is a 4 chain structure with sequence from Pyrococcus kodakaraensis (strain kod1). Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:	rpoD, TK1503 (Pyrococcus kodakaraensis (strain KOD1)), rpoL, TK1167 (Pyrococcus kodakaraensis (strain KOD1))
Activity:	DNA-directed RNA polymerase, with EC number 2.7.7.6
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RPOD_THEKO] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [RPOL_THEKO] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.

Publication Abstract from PubMed

The archaeal transcription apparatus is closely related to the eukaryotic RNA polymerase II (Pol II) system. Archaeal RNA polymerase (RNAP) and Pol II evolved from a common ancestral structure and the euryarchaeal RNAP is the simplest member of the extant archaeal-eukaryotic RNAP family. Here we report the first crystal structure of euryarchaeal RNAP from Thermococcus kodakarensis (Tko). This structure reveals that the clamp domain is able to swing away from the main body of RNAP in the presence of the Rpo4/Rpo7 stalk by coordinated movements of these domains. More detailed structure-function analysis of yeast Pol II and Tko RNAP identifies structural additions to Pol II that correspond to the binding sites of Pol II-specific general transcription factors including TFIIF, TFIIH and Mediator. Such comparisons provide a framework for dissecting interactions between RNAP and these factors during formation of the pre-initiation complex.

The X-ray crystal structure of the euryarchaeal RNA polymerase in an open-clamp configuration.,Jun SH, Hirata A, Kanai T, Santangelo TJ, Imanaka T, Murakami KS Nat Commun. 2014 Oct 14;5:5132. doi: 10.1038/ncomms6132. PMID:25311937^[1]

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

References

↑ Jun SH, Hirata A, Kanai T, Santangelo TJ, Imanaka T, Murakami KS. The X-ray crystal structure of the euryarchaeal RNA polymerase in an open-clamp configuration. Nat Commun. 2014 Oct 14;5:5132. doi: 10.1038/ncomms6132. PMID:25311937 doi:http://dx.doi.org/10.1038/ncomms6132

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/4qjv"

@@ Line 1: / Line 1: @@
 ==The X-ray crystal structure of Rpo3/Rpo11 heterodimer of euryarchaeal RNA polymerase from Thermococcus kodakarensis==
-<StructureSection load='4qjv' size='340' side='right' caption='[[4qjv]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+<StructureSection load='4qjv' size='340' side='right'caption='[[4qjv]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4qjv]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QJV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QJV FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4qjv]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_kodakaraensis_(strain_kod1) Pyrococcus kodakaraensis (strain kod1)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QJV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QJV FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rpoD, TK1503 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=69014 Pyrococcus kodakaraensis (strain KOD1)]), rpoL, TK1167 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=69014 Pyrococcus kodakaraensis (strain KOD1)])</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=4qjv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qjv OCA], [http://pdbe.org/4qjv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qjv RCSB], [http://www.ebi.ac.uk/pdbsum/4qjv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qjv ProSAT]</span></td></tr>
@@ Line 27: / Line 28: @@
 </StructureSection>
 [[Category: DNA-directed RNA polymerase]]
+[[Category: Large Structures]]
 [[Category: Hirata, A]]
 [[Category: Murakami, K S]]

4qjv

From Proteopedia

Revision as of 09:17, 24 April 2019

The X-ray crystal structure of Rpo3/Rpo11 heterodimer of euryarchaeal RNA polymerase from Thermococcus kodakarensis

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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