5ui8: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
 ==structure of sigmaN-holoenzyme==
-<StructureSection load='5ui8' size='340' side='right' caption='[[5ui8]], [[Resolution|resolution]] 3.76&Aring;' scene=''>
+<StructureSection load='5ui8' size='340' side='right'caption='[[5ui8]], [[Resolution|resolution]] 3.76&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5ui8]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UI8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UI8 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5ui8]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_O157:H7 Escherichia coli O157:H7], [https://en.wikipedia.org/wiki/Escherichia_coli_S88 Escherichia coli S88] and [https://en.wikipedia.org/wiki/Klebsiella_pneumoniae Klebsiella pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UI8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UI8 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <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">X-ray diffraction, [[Resolution|Resolution]] 3.76&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5byh|5byh]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='activity'><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 id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5ui8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ui8 OCA], [https://pdbe.org/5ui8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ui8 RCSB], [https://www.ebi.ac.uk/pdbsum/5ui8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ui8 ProSAT]</span></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=5ui8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ui8 OCA], [http://pdbe.org/5ui8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ui8 RCSB], [http://www.ebi.ac.uk/pdbsum/5ui8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ui8 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RPOZ_ECO45 RPOZ_ECO45]] Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits. [[http://www.uniprot.org/uniprot/RPOA_ECO57 RPOA_ECO57]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOC_ECO57 RPOC_ECO57]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOB_ECO45 RPOB_ECO45]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/A0A0J4U551_KLEPN A0A0J4U551_KLEPN]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released.[PIRNR:PIRNR000774]
+[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;">
 == Publication Abstract from PubMed ==
-Transcription by RNA polymerase (RNAP) in bacteria requires specific promoter recognition by sigma factors. The major variant sigma factor (sigma(54)) initially forms a transcriptionally silent complex requiring specialized adenosine triphosphate-dependent activators for initiation. Our crystal structure of the 450-kilodalton RNAP-sigma(54) holoenzyme at 3.8 angstroms reveals molecular details of sigma(54) and its interactions with RNAP. The structure explains how sigma(54) targets different regions in RNAP to exert its inhibitory function. Although sigma(54) and the major sigma factor, sigma(70), have similar functional domains and contact similar regions of RNAP, unanticipated differences are observed in their domain arrangement and interactions with RNAP, explaining their distinct properties. Furthermore, we observe evolutionarily conserved regulatory hotspots in RNAPs that can be targeted by a diverse range of mechanisms to fine tune transcription.
+The bacterial sigma factors confer promoter specificity to the RNA polymerase (RNAP). One alternative sigma factor, sigmaN, is unique in its structure and functional mechanism, forming transcriptionally inactive promoter complexes that require activation by specialized AAA+ ATPases. We report a 3.4-A resolution X-ray crystal structure of a sigmaN fragment in complex with its cognate promoter DNA, revealing the molecular details of promoter recognition by sigmaN The structure allowed us to build and refine an improved sigmaN-holoenzyme model based on previously published 3.8-A resolution X-ray data. The improved sigmaN-holoenzyme model reveals a conserved interdomain interface within sigmaN that, when disrupted by mutations, leads to transcription activity without activator intervention (so-called bypass mutants). Thus, the structure and stability of this interdomain interface are crucial for the role of sigmaN in blocking transcription activity and in maintaining the activator sensitivity of sigmaN.
-TRANSCRIPTION. Structures of the RNA polymerase-sigma54 reveal new and conserved regulatory strategies.,Yang Y, Darbari VC, Zhang N, Lu D, Glyde R, Wang YP, Winkelman JT, Gourse RL, Murakami KS, Buck M, Zhang X Science. 2015 Aug 21;349(6250):882-5. doi: 10.1126/science.aab1478. PMID:26293966<ref>PMID:26293966</ref>
+Crystal structure of Aquifex aeolicus sigmaN bound to promoter DNA and the structure of sigmaN-holoenzyme.,Campbell EA, Kamath S, Rajashankar KR, Wu M, Darst SA Proc Natl Acad Sci U S A. 2017 Feb 21. pii: 201619464. doi:, 10.1073/pnas.1619464114. PMID:28223493<ref>PMID:28223493</ref>
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
 <div class="pdbe-citations 5ui8" 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/>
 __TOC__
 </StructureSection>
-[[Category: DNA-directed RNA polymerase]]
+[[Category: Escherichia coli O157:H7]]
-[[Category: Campbell, E A]]
+[[Category: Escherichia coli S88]]
-[[Category: Darst, S A]]
+[[Category: Klebsiella pneumoniae]]
-[[Category: Bacterial rna polymerase sigman-holoenzyme]]
+[[Category: Large Structures]]
-[[Category: Transcription]]
+[[Category: Campbell EA]]
+[[Category: Darst SA]]