1qyp: Difference between revisions

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==THERMOCOCCUS CELER RPB9, NMR, 25 STRUCTURES==
==THERMOCOCCUS CELER RPB9, NMR, 25 STRUCTURES==
<StructureSection load='1qyp' size='340' side='right' caption='[[1qyp]], [[NMR_Ensembles_of_Models | 25 NMR models]]' scene=''>
<StructureSection load='1qyp' size='340' side='right'caption='[[1qyp]]' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1qyp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermococcus_celer Thermococcus celer]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QYP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QYP FirstGlance]. <br>
<table><tr><td colspan='2'>[[1qyp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_celer Thermococcus celer]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QYP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QYP FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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">Solution NMR</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=1qyp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qyp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qyp RCSB], [http://www.ebi.ac.uk/pdbsum/1qyp PDBsum]</span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=1qyp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qyp OCA], [https://pdbe.org/1qyp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qyp RCSB], [https://www.ebi.ac.uk/pdbsum/1qyp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qyp ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/RPOM_THECE RPOM_THECE]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.  
[https://www.uniprot.org/uniprot/TFS_THECE TFS_THECE] Induces RNA cleavage activity in the RNA polymerase. In its presence, the cleavage activity of the RNA polymerase truncates the RNA back to position +15 in a stepwise manner by releasing mainly dinucleotides from the 3'-end of the nascent RNA. The truncated RNAs are able to continue elongation. Involved in transcriptional proofreading and fidelity. Misincorporation of nucleotides during elongation of transcription leads to arrested elongation complexes which are rescued by TFS-promoted removal of a dinucleotide from the 3'-end. TFS is able to induce a cleavage resynthesis cycle in stalled elongation complexes (resulting from the next missing nucleotide or a reduced incorporation rate of a wrong nucleotide) preventing misincorporation and enabling proofreading in a post-incorporation manner. Pausing of elongation complexes is the main determinant of TFS-induced RNA cleavage.[UniProtKB:Q9P9I8]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qy/1qyp_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qy/1qyp_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </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].
</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/main_output.php?pdb_ID=1qyp ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
BACKGROUND: Transcriptional initiation and elongation provide control points in gene expression. Eukaryotic RNA polymerase II subunit 9 (RPB9) regulates start-site selection and elongational arrest. RPB9 contains Cys4 Zn(2+)-binding motifs which are conserved in archaea and homologous to those of the general transcription factors TFIIB and TFIIS. RESULTS: The structure of an RPB9 domain from the hyperthermophilic archaeon Thermococcus celer was determined at high resolution by NMR spectroscopy. The structure consists of an apical tetrahedral Zn(2+)-binding site, central beta sheet and disordered loop. Although the structure lacks a globular hydrophobic core, the two surfaces of the beta sheet each contain well ordered aromatic rings engaged in serial edge-to-face interactions. Basic sidechains are clustered near the Zn(2+)-binding site. The disordered loop contains sidechains conserved in TFIIS, including acidic residues essential for the stimulation of transcriptional elongation. CONCLUSIONS: The planar architecture of the RPB9 zinc ribbon-distinct from that of a conventional globular domain-can accommodate significant differences in the alignment of polar, non-polar and charged sidechains. Such divergence is associated with local and non-local changes in structure. The RPB9 structure is distinguished by a fourth beta strand (extending the central beta sheet) in a well ordered N-terminal segment and also differs from TFIIS (but not TFIIB) in the orientation of its apical Zn(2+)-binding site. Cys4 Zn(2+)-binding sites with distinct patterns of polar, non-polar and charged residues are conserved among unrelated RNAP subunits and predicted to form variant zinc ribbons.
High-resolution structure of an archaeal zinc ribbon defines a general architectural motif in eukaryotic RNA polymerases.,Wang B, Jones DN, Kaine BP, Weiss MA Structure. 1998 May 15;6(5):555-69. PMID:9634694<ref>PMID:9634694</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>


==See Also==
==See Also==
*[[RNA polymerase|RNA polymerase]]
*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Thermococcus celer]]
[[Category: Thermococcus celer]]
[[Category: Jones, D N.M]]
[[Category: Jones DNM]]
[[Category: Kaine, B P]]
[[Category: Kaine BP]]
[[Category: Wang, B]]
[[Category: Wang B]]
[[Category: Weiss, M A]]
[[Category: Weiss MA]]
[[Category: Extremophile]]
[[Category: Hyperthermophilic]]
[[Category: Rna polymerase ii subunit]]
[[Category: Rpb9]]
[[Category: Transcription]]
[[Category: Zn ribbon]]

Latest revision as of 09:08, 17 April 2024

THERMOCOCCUS CELER RPB9, NMR, 25 STRUCTURESTHERMOCOCCUS CELER RPB9, NMR, 25 STRUCTURES

Structural highlights

1qyp is a 1 chain structure with sequence from Thermococcus celer. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Solution NMR
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TFS_THECE Induces RNA cleavage activity in the RNA polymerase. In its presence, the cleavage activity of the RNA polymerase truncates the RNA back to position +15 in a stepwise manner by releasing mainly dinucleotides from the 3'-end of the nascent RNA. The truncated RNAs are able to continue elongation. Involved in transcriptional proofreading and fidelity. Misincorporation of nucleotides during elongation of transcription leads to arrested elongation complexes which are rescued by TFS-promoted removal of a dinucleotide from the 3'-end. TFS is able to induce a cleavage resynthesis cycle in stalled elongation complexes (resulting from the next missing nucleotide or a reduced incorporation rate of a wrong nucleotide) preventing misincorporation and enabling proofreading in a post-incorporation manner. Pausing of elongation complexes is the main determinant of TFS-induced RNA cleavage.[UniProtKB:Q9P9I8]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

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