5ipm: Difference between revisions
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==SigmaS-transcription initiation complex with 4-nt nascent RNA== | ==SigmaS-transcription initiation complex with 4-nt nascent RNA== | ||
<StructureSection load='5ipm' size='340' side='right' caption='[[5ipm]], [[Resolution|resolution]] 4.20Å' scene=''> | <StructureSection load='5ipm' size='340' side='right'caption='[[5ipm]], [[Resolution|resolution]] 4.20Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5ipm]] is a 9 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IPM OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[5ipm]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IPM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IPM 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]] 4.2Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <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=5ipm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ipm OCA], [https://pdbe.org/5ipm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ipm RCSB], [https://www.ebi.ac.uk/pdbsum/5ipm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ipm ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/RPOA_ECOLI RPOA_ECOLI] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. This subunit plays an important role in subunit assembly since its dimerization is the first step in the sequential assembly of subunits to form the holoenzyme.[HAMAP-Rule:MF_00059] | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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</div> | </div> | ||
<div class="pdbe-citations 5ipm" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 5ipm" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[RNA polymerase 3D structures|RNA polymerase 3D structures]] | |||
*[[Sigma factor 3D structures|Sigma factor 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Escherichia coli]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Synthetic construct]] | ||
[[Category: | [[Category: Liu B]] | ||
[[Category: | [[Category: Steitz TA]] | ||
[[Category: | [[Category: Zuo Y]] | ||
Latest revision as of 12:00, 23 October 2024
SigmaS-transcription initiation complex with 4-nt nascent RNASigmaS-transcription initiation complex with 4-nt nascent RNA
Structural highlights
FunctionRPOA_ECOLI DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. This subunit plays an important role in subunit assembly since its dimerization is the first step in the sequential assembly of subunits to form the holoenzyme.[HAMAP-Rule:MF_00059] Publication Abstract from PubMedIn bacteria, multiple sigma factors compete to associate with the RNA polymerase (RNAP) core enzyme to form a holoenzyme that is required for promoter recognition. During transcription initiation RNAP remains associated with the upstream promoter DNA via sequence-specific interactions between the sigma factor and the promoter DNA while moving downstream for RNA synthesis. As RNA polymerase repetitively adds nucleotides to the 3'-end of the RNA, a pyrophosphate ion is generated after each nucleotide incorporation. It is currently unknown how the release of pyrophosphate affects transcription. Here we report the crystal structures ofEcolitranscription initiation complexes (TICs) containing the stress-responsive sigmaSfactor, a de novo synthesized RNA oligonucleotide, and a complete transcription bubble (sigmaS-TIC) at about 3.9-A resolution. The structures show the 3D topology of the sigmaSfactor and how it recognizes the promoter DNA, including likely specific interactions with the template-strand residues of the -10 element. In addition, sigmaS-TIC structures display a highly stressed pretranslocated initiation complex that traps a pyrophosphate at the active site that remains closed. The position of the pyrophosphate and the unusual phosphodiester linkage between the two terminal RNA residues suggest an unfinished nucleotide-addition reaction that is likely at equilibrium between nucleotide addition and pyrophosphorolysis. Although these sigmaS-TIC crystals are enzymatically active, they are slow in nucleotide addition, as suggested by an NTP soaking experiment. Pyrophosphate release completes the nucleotide addition reaction and is associated with extensive conformational changes around the secondary channel but causes neither active site opening nor transcript translocation. Structures of E. coli sigmaS-transcription initiation complexes provide new insights into polymerase mechanism.,Liu B, Zuo Y, Steitz TA Proc Natl Acad Sci U S A. 2016 Mar 28. pii: 201520555. PMID:27035955[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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