4q4z: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(5 intermediate revisions by the same user not shown)
Line 1: Line 1:
==RPase complex 1==
 
<StructureSection load='4q4z' size='340' side='right' caption='[[4q4z]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
==Thermus thermophilus RNA polymerase de novo transcription initiation complex==
<StructureSection load='4q4z' size='340' side='right'caption='[[4q4z]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4q4z]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q4Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Q4Z FirstGlance]. <br>
<table><tr><td colspan='2'>[[4q4z]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] and [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q4Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Q4Z FirstGlance]. <br>
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2TM:5-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]METHYL}PHOSPHORYL]CYTIDINE'>2TM</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9&#8491;</td></tr>
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4q5a|4q5a]], [[4q5s|4q5s]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2TM:5-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]METHYL}PHOSPHORYL]CYTIDINE'>2TM</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr><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=4q4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q4z OCA], [https://pdbe.org/4q4z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4q4z RCSB], [https://www.ebi.ac.uk/pdbsum/4q4z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4q4z ProSAT]</span></td></tr>
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4q4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q4z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4q4z RCSB], [http://www.ebi.ac.uk/pdbsum/4q4z PDBsum]</span></td></tr>
</table>
<table>
== Function ==
<div style="background-color:#fffaf0;">
[https://www.uniprot.org/uniprot/RPOA_THETH RPOA_THETH] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.
== Publication Abstract from PubMed ==
The bacterial RNA polymerase (RNAP) holoenzyme containing sigma factor initiates transcription at specific promoter sites by de novo RNA priming, the first step of RNA synthesis where RNAP accepts two initiating ribonucleoside triphosphates (iNTPs) and performs the first phosphodiester bond formation. We present the structure of de novo transcription initiation complex that reveals unique contacts of the iNTPs bound at the transcription start site with the template DNA and also with RNAP, and demonstrate the importance of these contacts for transcription initiation. To get further insight into the mechanism of RNA priming, we determined the structure of initially transcribing complex of RNAP holoenzyme with 6-mer RNA, obtained by in crystallo transcription approach. The structure highlights RNAP-RNA contacts that stabilize the short RNA transcript in the active site and demonstrates that the RNA 5-end displaces sigma region 3.2 from its position near the active site, which likely plays a key role in sigma ejection during the initiation-to-elongation transition. Given the structural conservation of the RNAP active site, the mechanism of de novo RNA priming appears to be conserved in all cellular RNAPs.
 
Structural Basis of Transcription Initiation by Bacterial RNA Polymerase holoenzyme.,Basu RS, Warner BA, Molodtsov V, Pupov D, Esyunina D, Fernandez-Tornero C, Kulbachinskiy A, Murakami KS J Biol Chem. 2014 Jun 27. pii: jbc.M114.584037. PMID:24973216<ref>PMID:24973216</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
==See Also==
</div>
*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
== References ==
*[[Sigma factor 3D structures|Sigma factor 3D structures]]
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: DNA-directed RNA polymerase]]
[[Category: Large Structures]]
[[Category: Thermus thermophilus]]
[[Category: Thermus thermophilus]]
[[Category: Murakami, K S.]]
[[Category: Thermus thermophilus HB8]]
[[Category: Dna and ntp]]
[[Category: Murakami KS]]
[[Category: Transcription]]
[[Category: Transcription-dna complex]]

Latest revision as of 15:44, 1 March 2024

Thermus thermophilus RNA polymerase de novo transcription initiation complexThermus thermophilus RNA polymerase de novo transcription initiation complex

Structural highlights

4q4z is a 8 chain structure with sequence from Thermus thermophilus and Thermus thermophilus HB8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.9Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RPOA_THETH DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.

See Also

4q4z, resolution 2.90Å

Drag the structure with the mouse to rotate

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

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=4q4z&oldid=4075994"