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| | ==Structure of Nrd1 CID bound to phosphorylated RNAP II CTD== | | ==Structure of Nrd1 CID bound to phosphorylated RNAP II CTD== |
| - | <StructureSection load='2lo6' size='340' side='right'caption='[[2lo6]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''> | + | <StructureSection load='2lo6' size='340' side='right'caption='[[2lo6]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2lo6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LO6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LO6 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2lo6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LO6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LO6 FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NRD1, YNL251C, N0868 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>
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| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </span></td></tr>
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| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2lo6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lo6 OCA], [https://pdbe.org/2lo6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lo6 RCSB], [https://www.ebi.ac.uk/pdbsum/2lo6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lo6 ProSAT]</span></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=2lo6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lo6 OCA], [https://pdbe.org/2lo6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lo6 RCSB], [https://www.ebi.ac.uk/pdbsum/2lo6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lo6 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/NRD1_YEAST NRD1_YEAST]] Plays a role in sequence-specific regulation of nuclear pre-mRNA abundance. [[https://www.uniprot.org/uniprot/RPB1_YEAST RPB1_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Forms the polymerase active center together with the second largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. During a transcription cycle, Pol II, general transcription factors and the Mediator complex assemble as the preinitiation complex (PIC) at the promoter. 11-15 base pairs of DNA surrounding the transcription start site are melted and the single stranded DNA template strand of the promoter is positioned deeply within the central active site cleft of Pol II to form the open complex. After synthesis of about 30 bases of RNA, Pol II releases its contacts with the core promoter and the rest of the transcription machinery (promoter clearance) and enters the stage of transcription elongation in which it moves on the template as the transcript elongates. Pol II appears to oscillate between inactive and active conformations at each step of nucleotide addition. Elongation is influenced by the phosphorylation status of the C-terminal domain (CTD) of Pol II largest subunit (RPB1), which serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing. Pol II is composed of mobile elements that move relative to each other. The core element with the central large cleft comprises RPB3, RBP10, RPB11, RPB12 and regions of RPB1 and RPB2 forming the active center. The clamp element (portions of RPB1, RPB2 and RPB3) is connected to the core through a set of flexible switches and moves to open and close the cleft. A bridging helix emanates from RPB1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol II by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition. In elongating Pol II, the lid loop (RPB1) appears to act as a wedge to drive apart the DNA and RNA strands at the upstream end of the transcription bubble and guide the RNA strand toward the RNA exit groove located near the base of the largely unstructured CTD domain of RPB1. The rudder loop (RPB1) interacts with single stranded DNA after separation from the RNA strand, likely preventing reassociation with the exiting RNA. The cleft is surrounded by jaws: an upper jaw formed by portions of RBP1, RPB2 and RPB9, and a lower jaw, formed by RPB5 and portions of RBP1. The jaws are thought to grab the incoming DNA template, mainly by RPB5 direct contacts to DNA.
| + | [https://www.uniprot.org/uniprot/NRD1_YEAST NRD1_YEAST] Plays a role in sequence-specific regulation of nuclear pre-mRNA abundance. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Baker's yeast]] | |
| - | [[Category: DNA-directed RNA polymerase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Cerna, H]] | + | [[Category: Saccharomyces cerevisiae S288C]] |
| - | [[Category: Hofr, C]] | + | [[Category: Cerna H]] |
| - | [[Category: Holub, P]] | + | [[Category: Hofr C]] |
| - | [[Category: Hrossova, D]] | + | [[Category: Holub P]] |
| - | [[Category: Kubicek, K]] | + | [[Category: Hrossova D]] |
| - | [[Category: Loehr, F]] | + | [[Category: Kubicek K]] |
| - | [[Category: Pasulka, J]] | + | [[Category: Loehr F]] |
| - | [[Category: Stefl, R]] | + | [[Category: Pasulka J]] |
| - | [[Category: Vanacova, S]] | + | [[Category: Stefl R]] |
| - | [[Category: Carboxy-terminal domain]]
| + | [[Category: Vanacova S]] |
| - | [[Category: Cid]]
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| - | [[Category: Cis-trans isomerization of proline]]
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| - | [[Category: Ctd]]
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| - | [[Category: Ctd-interacting domain]]
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| - | [[Category: Ess1 isomerase]]
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| - | [[Category: Peptide binding protein]]
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| - | [[Category: Rna-processing]]
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| - | [[Category: Transciption termination]]
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| - | [[Category: Transcription]]
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