5ipl

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
m (Protected "5ipl" [edit=sysop:move=sysop])
Current revision (12:35, 6 March 2024) (edit) (undo)
 
(3 intermediate revisions not shown.)
Line 1: Line 1:
==SigmaS-transcription initiation complex with 4-nt nascent RNA==
==SigmaS-transcription initiation complex with 4-nt nascent RNA==
-
<StructureSection load='5ipl' size='340' side='right' caption='[[5ipl]], [[Resolution|resolution]] 3.60&Aring;' scene=''>
+
<StructureSection load='5ipl' size='340' side='right'caption='[[5ipl]], [[Resolution|resolution]] 3.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[5ipl]] is a 9 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IPL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IPL FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[5ipl]] 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=5IPL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IPL FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DPO:DIPHOSPHATE'>DPO</scene>, <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]] 3.6&#8491;</td></tr>
-
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DPO:DIPHOSPHATE'>DPO</scene>, <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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5ipm|5ipm]], [[5ipn|5ipn]]</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=5ipl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ipl OCA], [https://pdbe.org/5ipl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ipl RCSB], [https://www.ebi.ac.uk/pdbsum/5ipl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ipl ProSAT]</span></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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ipl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ipl OCA], [http://pdbe.org/5ipl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ipl RCSB], [http://www.ebi.ac.uk/pdbsum/5ipl PDBsum]</span></td></tr>
+
</table>
</table>
== Function ==
== Function ==
-
[[http://www.uniprot.org/uniprot/RPOC_ECOLI RPOC_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01322] [[http://www.uniprot.org/uniprot/RPOB_ECOLI RPOB_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01321] [[http://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] [[http://www.uniprot.org/uniprot/RPOZ_ECOLI RPOZ_ECOLI]] 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.[HAMAP-Rule:MF_00366] [[http://www.uniprot.org/uniprot/RPOS_ECOLI RPOS_ECOLI]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is the master transcriptional regulator of the stationary phase and the general stress response. Controls, positively or negatively, the expression of several hundred genes, which are mainly involved in metabolism, transport, regulation and stress management.[HAMAP-Rule:MF_00959]<ref>PMID:15558318</ref> <ref>PMID:15716429</ref> <ref>PMID:16511888</ref> <ref>PMID:21398637</ref> <ref>PMID:8475100</ref> Protects stationary phase cells from killing induced by endoribonuclease MazF.<ref>PMID:19251848</ref>
+
[https://www.uniprot.org/uniprot/RPOS_ECOLI RPOS_ECOLI] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is the master transcriptional regulator of the stationary phase and the general stress response. Controls, positively or negatively, the expression of several hundred genes, which are mainly involved in metabolism, transport, regulation and stress management.[HAMAP-Rule:MF_00959]<ref>PMID:15558318</ref> <ref>PMID:15716429</ref> <ref>PMID:16511888</ref> <ref>PMID:21398637</ref> <ref>PMID:8475100</ref> Protects stationary phase cells from killing induced by endoribonuclease MazF.<ref>PMID:19251848</ref>
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
In 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<ref>PMID:27035955</ref>
+
==See Also==
-
 
+
*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
*[[Sigma factor 3D structures|Sigma factor 3D structures]]
-
</div>
+
-
<div class="pdbe-citations 5ipl" style="background-color:#fffaf0;"></div>
+
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: DNA-directed RNA polymerase]]
+
[[Category: Escherichia coli]]
-
[[Category: Liu, B]]
+
[[Category: Large Structures]]
-
[[Category: Steitz, T A]]
+
[[Category: Synthetic construct]]
-
[[Category: Zuo, Y]]
+
[[Category: Liu B]]
-
[[Category: General stress sigma factor]]
+
[[Category: Steitz TA]]
-
[[Category: Pyrophosphate release]]
+
[[Category: Zuo Y]]
-
[[Category: Rna polymerase]]
+
-
[[Category: Transcription]]
+
-
[[Category: Transcription initiation]]
+
-
[[Category: Transferase-dna-rna complex]]
+

Current revision

SigmaS-transcription initiation complex with 4-nt nascent RNA

PDB ID 5ipl

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5ipl"
Personal tools