3c3l

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==X-ray crystal structure of the N4 mini-vRNAP P2 promoter complex==
==X-ray crystal structure of the N4 mini-vRNAP P2 promoter complex==
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<StructureSection load='3c3l' size='340' side='right' caption='[[3c3l]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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<StructureSection load='3c3l' size='340' side='right'caption='[[3c3l]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3c3l]] 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=3C3L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3C3L FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3c3l]] is a 4 chain structure with sequence from [https://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=3C3L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C3L FirstGlance]. <br>
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</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3c2p|3c2p]], [[3c42|3c42]], [[3c46|3c46]], [[3c47|3c47]]</td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">vRNAP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10752 Escherichia phage N4])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3c3l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c3l OCA], [https://pdbe.org/3c3l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c3l RCSB], [https://www.ebi.ac.uk/pdbsum/3c3l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c3l ProSAT]</span></td></tr>
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<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>
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<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=3c3l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c3l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3c3l RCSB], [http://www.ebi.ac.uk/pdbsum/3c3l PDBsum]</span></td></tr>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[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>
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Coliphage N4 virion-encapsidated RNA polymerase (vRNAP) is a member of the phage T7-like single-subunit RNA polymerase (RNAP) family. Its central domain (mini-vRNAP) contains all RNAP functions of the full-length vRNAP, which recognizes a 5 to 7 base pair stem and 3 nucleotide loop hairpin DNA promoter. Here, we report the X-ray crystal structures of mini-vRNAP bound to promoters. Mini-vRNAP uses four structural motifs to recognize DNA sequences at the hairpin loop and stem and to unwind DNA. Despite their low sequence similarity, three out of four motifs are shared with T7 RNAP that recognizes a double-stranded DNA promoter. The binary complex structure and results of engineered disulfide linkage experiments reveal that the plug and motif B loop, which block the access of template DNA to the active site in the apo-form mini-vRNAP, undergo a large-scale conformational change upon promoter binding, explaining the restricted promoter specificity that is critical for N4 phage early transcription.
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Structural basis for DNA-hairpin promoter recognition by the bacteriophage N4 virion RNA polymerase.,Gleghorn ML, Davydova EK, Rothman-Denes LB, Murakami KS Mol Cell. 2008 Dec 5;32(5):707-17. PMID:19061645<ref>PMID:19061645</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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==See Also==
==See Also==
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*[[RNA polymerase|RNA polymerase]]
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*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: DNA-directed RNA polymerase]]
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[[Category: Escherichia phage N4]]
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[[Category: Escherichia phage n4]]
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[[Category: Large Structures]]
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[[Category: Gleghorn, M L]]
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[[Category: Gleghorn ML]]
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[[Category: Murakami, K S]]
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[[Category: Murakami KS]]
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[[Category: Dna-hairpin]]
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[[Category: Nucleotidyltransferase]]
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[[Category: Promoter binary complex]]
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[[Category: Protein-dna complex]]
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[[Category: Transferase-dna complex]]
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[[Category: Virion rna polymerase]]
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Current revision

X-ray crystal structure of the N4 mini-vRNAP P2 promoter complex

PDB ID 3c3l

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