3q22

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Current revision (10:45, 21 February 2024) (edit) (undo)
 
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<StructureSection load='3q22' size='340' side='right'caption='[[3q22]], [[Resolution|resolution]] 2.11&Aring;' scene=''>
<StructureSection load='3q22' size='340' side='right'caption='[[3q22]], [[Resolution|resolution]] 2.11&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3q22]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bpn4 Bpn4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3Q22 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3Q22 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3q22]] 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=3Q22 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3Q22 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2HP:DIHYDROGENPHOSPHATE+ION'>2HP</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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]] 2.11&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3q0a|3q0a]], [[3q23|3q23]], [[3q24|3q24]]</div></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2HP:DIHYDROGENPHOSPHATE+ION'>2HP</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">gp50 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10752 BPN4])</td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=3q22 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q22 OCA], [https://pdbe.org/3q22 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3q22 RCSB], [https://www.ebi.ac.uk/pdbsum/3q22 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3q22 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=3q22 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q22 OCA], [https://pdbe.org/3q22 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3q22 RCSB], [https://www.ebi.ac.uk/pdbsum/3q22 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3q22 ProSAT]</span></td></tr>
</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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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.
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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>
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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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<div class="pdbe-citations 3q22" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Bpn4]]
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[[Category: Escherichia virus N4]]
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[[Category: DNA-directed RNA polymerase]]
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[[Category: Large Structures]]
[[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: De novo transcription initiation]]
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[[Category: Dna-hairpin]]
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[[Category: Initiation complex]]
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[[Category: Nucleotidyltransferase]]
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[[Category: Phosphate ion]]
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[[Category: Protein-dna complex]]
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[[Category: Rna polymerase]]
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[[Category: Transferase-dna complex]]
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[[Category: Two-metal catalysis]]
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[[Category: Virion rna polymerase]]
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Current revision

X-ray crystal structure of the N4 mini-VRNAP and P2_7a promoter transcription initiation complex with GTP and Magnesium: substrate complex I

PDB ID 3q22

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