8dh5: Difference between revisions

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<table><tr><td colspan='2'>[[8dh5]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_T7 Escherichia phage T7] 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=8DH5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8DH5 FirstGlance]. <br>
<table><tr><td colspan='2'>[[8dh5]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_T7 Escherichia phage T7] 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=8DH5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8DH5 FirstGlance]. <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]] 2.85&#8491;</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]] 2.85&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=S8U:1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-1H-pyrrole-2-carbaldehyde'>S8U</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=S8U:[(2~{R},3~{S},5~{R})-5-(2-methanoylpyrrol-1-yl)-3-oxidanyl-oxolan-2-yl]methyl+dihydrogen+phosphate'>S8U</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=8dh5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8dh5 OCA], [https://pdbe.org/8dh5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8dh5 RCSB], [https://www.ebi.ac.uk/pdbsum/8dh5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8dh5 ProSAT]</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=8dh5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8dh5 OCA], [https://pdbe.org/8dh5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8dh5 RCSB], [https://www.ebi.ac.uk/pdbsum/8dh5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8dh5 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[https://www.uniprot.org/uniprot/RPOL_BPT7 RPOL_BPT7] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Responsible for the transcription of the late genes of T7. It is rifampicin-resistant. It recognizes a specific promoter sequence, unwinds the double-stranded RNA to expose the coding strand for templating, initiates transcription preferentially with a purine.
[https://www.uniprot.org/uniprot/RPOL_BPT7 RPOL_BPT7] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Responsible for the transcription of the late genes of T7. It is rifampicin-resistant. It recognizes a specific promoter sequence, unwinds the double-stranded RNA to expose the coding strand for templating, initiates transcription preferentially with a purine.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Bacteriophage T7 RNA polymerase (T7 RNAP) is widely used for synthesizing RNA molecules with synthetic modifications and unnatural base pairs (UBPs) for a variety of biotechnical and therapeutic applications. However, the molecular basis of transcription recognition of UBPs by T7 RNAP remains poorly understood. Here we focused on a representative UBP, 7-(2-thienyl)-imidazo[4,5-b]pyridine (Ds) and pyrrole 2-carbaldehyde (Pa), and investigated how the hydrophobic Ds-Pa pair is recognized by T7 RNAP. Our kinetic assays revealed that T7 RNAP selectively recognizes the Ds or Pa base in the templates and preferentially incorporates their cognate unnatural base nucleotide substrate (PaTP or DsTP) over natural NTPs. Our structural studies reveal that T7 RNAP recognizes the unnatural substrates at the pre-insertion state in a distinct manner compared to natural substrates. These results provide mechanistic insights into transcription recognition of UBP by T7 RNAP and provide valuable information for designing the next generation of UBPs.


Structural basis of transcription recognition of a hydrophobic unnatural base pair by T7 RNA polymerase.,Oh J, Kimoto M, Xu H, Chong J, Hirao I, Wang D Nat Commun. 2023 Jan 13;14(1):195. doi: 10.1038/s41467-022-35755-8. PMID:36635281<ref>PMID:36635281</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>
</div>
<div class="pdbe-citations 8dh5" style="background-color:#fffaf0;"></div>
== References ==
<references/>
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</StructureSection>
</StructureSection>

Latest revision as of 16:45, 22 July 2026

T7 RNA polymerase elongation complex with unnatural base dPa-ATP mismatch

8dh5, resolution 2.85Å

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