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==X-ray crystal structure of the transcription initiation complex of the N4 mini-vRNAP with P2 promoter: Mismatch complex==
==X-ray crystal structure of the transcription initiation complex of the N4 mini-vRNAP with P2 promoter: Mismatch complex==
<StructureSection load='3q0a' size='340' side='right' caption='[[3q0a]], [[Resolution|resolution]] 2.69&Aring;' scene=''>
<StructureSection load='3q0a' size='340' side='right'caption='[[3q0a]], [[Resolution|resolution]] 2.69&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3q0a]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_phage_n4 Escherichia phage n4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3Q0A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3Q0A FirstGlance]. <br>
<table><tr><td colspan='2'>[[3q0a]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_N4 Escherichia virus N4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3Q0A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3Q0A FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.69&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3q22|3q22]], [[3q23|3q23]], [[3q24|3q24]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">gp50 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10752 Escherichia phage N4])</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=3q0a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q0a OCA], [https://pdbe.org/3q0a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3q0a RCSB], [https://www.ebi.ac.uk/pdbsum/3q0a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3q0a 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=3q0a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q0a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3q0a RCSB], [http://www.ebi.ac.uk/pdbsum/3q0a PDBsum]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/RPOLV_BPN4 RPOLV_BPN4] DNA-dependent RNA polymerase, which is injected into the host upon infection and transcribes the phage early genes from promoters that have a 5-bp stem-3 nt loop hairpin structure.<ref>PMID:18362338</ref> <ref>PMID:19061645</ref>  
We have determined the X-ray crystal structures of the pre- and postcatalytic forms of the initiation complex of bacteriophage N4 RNA polymerase that provide the complete set of atomic images depicting the process of transcript initiation by a single-subunit RNA polymerase. As observed during T7 RNA polymerase transcript elongation, substrate loading for the initiation process also drives a conformational change of the O helix, but only the correct base pairing between the +2 substrate and DNA base is able to complete the O-helix conformational transition. Substrate binding also facilitates catalytic metal binding that leads to alignment of the reactive groups of substrates for the nucleotidyl transfer reaction. Although all nucleic acid polymerases use two divalent metals for catalysis, they differ in the requirements and the timing of binding of each metal. In the case of bacteriophage RNA polymerase, we propose that catalytic metal binding is the last step before the nucleotidyl transfer reaction.
 
X-ray crystal structures elucidate the nucleotidyl transfer reaction of transcript initiation using two nucleotides.,Gleghorn ML, Davydova EK, Basu R, Rothman-Denes LB, Murakami KS Proc Natl Acad Sci U S A. 2011 Feb 14. PMID:21321236<ref>PMID:21321236</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>


==See Also==
==See Also==
*[[RNA polymerase|RNA polymerase]]
*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Escherichia phage n4]]
[[Category: Escherichia virus N4]]
[[Category: Murakami, K S]]
[[Category: Large Structures]]
[[Category: Rna polymerase]]
[[Category: Murakami KS]]
[[Category: Transcription-dna complex]]

Latest revision as of 13:44, 21 February 2024

X-ray crystal structure of the transcription initiation complex of the N4 mini-vRNAP with P2 promoter: Mismatch complexX-ray crystal structure of the transcription initiation complex of the N4 mini-vRNAP with P2 promoter: Mismatch complex

Structural highlights

3q0a is a 4 chain structure with sequence from Escherichia virus N4. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.69Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RPOLV_BPN4 DNA-dependent RNA polymerase, which is injected into the host upon infection and transcribes the phage early genes from promoters that have a 5-bp stem-3 nt loop hairpin structure.[1] [2]

See Also

References

  1. ↑ Murakami KS, Davydova EK, Rothman-Denes LB. X-ray crystal structure of the polymerase domain of the bacteriophage N4 virion RNA polymerase. Proc Natl Acad Sci U S A. 2008 Mar 24;. PMID:18362338 doi:0712325105
  2. ↑ Gleghorn ML, Davydova EK, Rothman-Denes LB, Murakami KS. Structural basis for DNA-hairpin promoter recognition by the bacteriophage N4 virion RNA polymerase. Mol Cell. 2008 Dec 5;32(5):707-17. PMID:19061645 doi:S1097-2765(08)00777-6

3q0a, resolution 2.69Å

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