This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

8dh0

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

T7 RNA polymerase elongation complex with unnatural base dDs

Structural highlights

8dh0 is a 14 chain structure with sequence from Escherichia phage T7 and Synthetic construct. 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

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Oh J, Kimoto M, Xu H, Chong J, Hirao I, Wang D. Structural basis of transcription recognition of a hydrophobic unnatural base pair by T7 RNA polymerase. Nat Commun. 2023 Jan 13;14(1):195. doi: 10.1038/s41467-022-35755-8. PMID:36635281 doi:http://dx.doi.org/10.1038/s41467-022-35755-8

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/8dh0"

Categories: Escherichia phage T7 | Large Structures | Synthetic construct | Oh J | Wang D

@@ Line 4: / Line 4: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[8dh0]] is a 14 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=8DH0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8DH0 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=91N:[(2~{R},3~{S},5~{R})-3-oxidanyl-5-(7-thiophen-2-ylimidazo[4,5-b]pyridin-3-yl)oxolan-2-yl]methyl+dihydrogen+phosphate'>91N</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2.9&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=91N:[(2~{R},3~{S},5~{R})-3-oxidanyl-5-(7-thiophen-2-ylimidazo[4,5-b]pyridin-3-yl)oxolan-2-yl]methyl+dihydrogen+phosphate'>91N</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=8dh0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8dh0 OCA], [https://pdbe.org/8dh0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8dh0 RCSB], [https://www.ebi.ac.uk/pdbsum/8dh0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8dh0 ProSAT]</span></td></tr>
 </table>

8dh0

From Proteopedia

Current revision

T7 RNA polymerase elongation complex with unnatural base dDs

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox