4nc8: Difference between revisions
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==N-terminal domain of delta-subunit of RNA polymerase complexed with nickel ions== | ==N-terminal domain of delta-subunit of RNA polymerase complexed with nickel ions== | ||
<StructureSection load='4nc8' size='340' side='right' caption='[[4nc8]], [[Resolution|resolution]] 2.17Å' scene=''> | <StructureSection load='4nc8' size='340' side='right'caption='[[4nc8]], [[Resolution|resolution]] 2.17Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4nc8]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NC8 OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[4nc8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NC8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NC8 FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.17Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4nc8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nc8 OCA], [https://pdbe.org/4nc8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nc8 RCSB], [https://www.ebi.ac.uk/pdbsum/4nc8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nc8 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/RPOE_BACSU RPOE_BACSU] Participates in both the initiation and recycling phases of transcription. In the presence of the delta subunit, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling. May function in sigma factor switching. It displaces RNA bound to RNA polymerase in a binary complex. | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 4nc8" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[RNA polymerase 3D structures|RNA polymerase 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Demo | [[Category: Bacillus subtilis subsp. subtilis str. 168]] | ||
[[Category: Komarek | [[Category: Large Structures]] | ||
[[Category: Krasny | [[Category: Demo G]] | ||
[[Category: Papouskova | [[Category: Komarek J]] | ||
[[Category: Rabatinova | [[Category: Krasny L]] | ||
[[Category: Sanderova | [[Category: Papouskova V]] | ||
[[Category: Sklenar | [[Category: Rabatinova A]] | ||
[[Category: Wimmerova | [[Category: Sanderova H]] | ||
[[Category: Zidek | [[Category: Sklenar V]] | ||
[[Category: Wimmerova M]] | |||
[[Category: Zidek L]] | |||
Latest revision as of 19:52, 20 September 2023
N-terminal domain of delta-subunit of RNA polymerase complexed with nickel ionsN-terminal domain of delta-subunit of RNA polymerase complexed with nickel ions
Structural highlights
FunctionRPOE_BACSU Participates in both the initiation and recycling phases of transcription. In the presence of the delta subunit, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling. May function in sigma factor switching. It displaces RNA bound to RNA polymerase in a binary complex. Publication Abstract from PubMedThe crystal structure of the N-terminal domain of the RNA polymerase delta subunit (Ndelta) from Bacillus subtilis solved at a resolution of 2.0A is compared with the NMR structure determined previously. The molecule crystallizes in the space group C222(1) with a dimer in the asymmetric unit. Importantly, the X-ray structure exhibits significant differences from the lowest energy NMR structure. In addition to the overall structure differences, structurally important beta sheets found in the NMR structure are not present in the crystal structure. We systematically investigated the cause of the discrepancies between the NMR and X-ray structures of Ndelta, addressing the pH dependence, presence of metal ions, and crystal packing forces. We convincingly showed that the crystal packing forces, together with the presence of Ni2+ ions, are the main reason for such a difference. In summary, the study illustrates that the two structural approaches may give unequal results, which need to be interpreted with care to obtain reliable structural information in terms of biological relevance. X-ray vs. NMR structure of N-terminal domain of delta-subunit of RNA polymerase.,Demo G, Papouskova V, Komarek J, Kaderavek P, Otrusinova O, Srb P, Rabatinova A, Krasny L, Zidek L, Sklenar V, Wimmerova M J Struct Biol. 2014 Jun 14. pii: S1047-8477(14)00137-3. doi:, 10.1016/j.jsb.2014.06.001. PMID:24937760[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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