1dzf: Difference between revisions

Revision as of 11:05, 3 October 2014

RPB5 from S.cerevisiae

Structural highlights

1dzf is a 1 chain structure with sequence from Atcc 18824. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Gene:	YBR154C OR YBR1204 (ATCC 18824)
Activity:	DNA-directed RNA polymerase, with EC number 2.7.7.6
Resources:	FirstGlance, OCA, RCSB, PDBsum

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

Eukaryotic nuclei contain three different types of RNA polymerases (RNAPs), each consisting of 12-18 different subunits. The evolutionarily highly conserved RNAP subunit RPB5 is shared by all three enzymes and therefore represents a key structural/functional component of all eukaryotic RNAPs. Here we present the crystal structure of the RPB5 subunit from Saccharomyces cerevisiae. The bipartite structure includes a eukaryote-specific N-terminal domain and a C-terminal domain resembling the archaeal RNAP subunit H. RPB5 has been implicated in direct protein-protein contacts with transcription factor IIB, one of the components of the RNAP(II) basal transcriptional machinery, and gene-specific activator proteins, such as the hepatitis B virus transactivator protein X. The experimentally mapped regions of RPB5 involved in these interactions correspond to distinct and surface-exposed alpha-helical structures.

Crystal structure of RPB5, a universal eukaryotic RNA polymerase subunit and transcription factor interaction target.,Todone F, Weinzierl RO, Brick P, Onesti S Proc Natl Acad Sci U S A. 2000 Jun 6;97(12):6306-10. PMID:10841537^[1]

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

References

↑ Todone F, Weinzierl RO, Brick P, Onesti S. Crystal structure of RPB5, a universal eukaryotic RNA polymerase subunit and transcription factor interaction target. Proc Natl Acad Sci U S A. 2000 Jun 6;97(12):6306-10. PMID:10841537

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Todone F, Weinzierl RO, Brick P, Onesti S. Crystal structure of RPB5, a universal eukaryotic RNA polymerase subunit and transcription factor interaction target. Proc Natl Acad Sci U S A. 2000 Jun 6;97(12):6306-10. PMID:10841537

[1]

@@ Line 1: / Line 1: @@
-{{STRUCTURE_1dzf|  PDB=1dzf  |  SCENE=  }}
+==RPB5 from S.cerevisiae==
-===RPB5 from S.cerevisiae===
+<StructureSection load='1dzf' size='340' side='right' caption='[[1dzf]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
-{{ABSTRACT_PUBMED_10841537}}
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1dzf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DZF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DZF FirstGlance]. <br>
+</td></tr><tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">YBR154C OR YBR1204 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
+<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1dzf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dzf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dzf RCSB], [http://www.ebi.ac.uk/pdbsum/1dzf PDBsum]</span></td></tr>
+<table>
+== 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/dz/1dzf_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].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Eukaryotic nuclei contain three different types of RNA polymerases (RNAPs), each consisting of 12-18 different subunits. The evolutionarily highly conserved RNAP subunit RPB5 is shared by all three enzymes and therefore represents a key structural/functional component of all eukaryotic RNAPs. Here we present the crystal structure of the RPB5 subunit from Saccharomyces cerevisiae. The bipartite structure includes a eukaryote-specific N-terminal domain and a C-terminal domain resembling the archaeal RNAP subunit H. RPB5 has been implicated in direct protein-protein contacts with transcription factor IIB, one of the components of the RNAP(II) basal transcriptional machinery, and gene-specific activator proteins, such as the hepatitis B virus transactivator protein X. The experimentally mapped regions of RPB5 involved in these interactions correspond to distinct and surface-exposed alpha-helical structures.
-==Function==
+Crystal structure of RPB5, a universal eukaryotic RNA polymerase subunit and transcription factor interaction target.,Todone F, Weinzierl RO, Brick P, Onesti S Proc Natl Acad Sci U S A. 2000 Jun 6;97(12):6306-10. PMID:10841537<ref>PMID:10841537</ref>
-[[http://www.uniprot.org/uniprot/RPAB1_YEAST RPAB1_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process (By similarity).
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[1dzf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DZF OCA].
+</div>
 ==See Also==
 *[[RNA polymerase|RNA polymerase]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:010841537</ref><references group="xtra"/><references/>
+__TOC__
+</StructureSection>
 [[Category: Atcc 18824]]
 [[Category: DNA-directed RNA polymerase]]

1dzf: Difference between revisions

Revision as of 11:05, 3 October 2014

RPB5 from S.cerevisiae

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

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