2po4: Difference between revisions

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==X-ray crystal structure of polymerase domain of the bacteriophage N4 virion RNA polymerase==
==X-ray crystal structure of polymerase domain of the bacteriophage N4 virion RNA polymerase==
<StructureSection load='2po4' size='340' side='right' caption='[[2po4]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='2po4' size='340' side='right'caption='[[2po4]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2po4]] is a 1 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=2PO4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PO4 FirstGlance]. <br>
<table><tr><td colspan='2'>[[2po4]] is a 1 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=2PO4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PO4 FirstGlance]. <br>
</td></tr><tr><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>
</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&#8491;</td></tr>
<tr><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>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2po4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2po4 OCA], [https://pdbe.org/2po4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2po4 RCSB], [https://www.ebi.ac.uk/pdbsum/2po4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2po4 ProSAT]</span></td></tr>
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2po4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2po4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2po4 RCSB], [http://www.ebi.ac.uk/pdbsum/2po4 PDBsum]</span></td></tr>
</table>
<table>
== Function ==
<div style="background-color:#fffaf0;">
[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>  
== Publication Abstract from PubMed ==
Coliphage N4 virion RNA polymerase (vRNAP), which is injected into the host upon infection, transcribes the phage early genes from promoters that have a 5-bp stem-3 nt loop hairpin structure. Here, we describe the 2.0-A resolution x-ray crystal structure of N4 mini-vRNAP, a member of the T7-like, single-unit RNAP family and the minimal component having all RNAP functions of the full-length vRNAP. The structure resembles a "fisted right hand" with Fingers, Palm and Thumb subdomains connected to an N-terminal domain. We established that the specificity loop extending from the Fingers along with W129 of the N-terminal domain play critical roles in hairpin-promoter recognition. A comparison with the structure of the T7 RNAP initiation complex reveals that the pathway of the DNA to the active site is blocked in the apo-form vRNAP, indicating that vRNAP must undergo a large-scale conformational change upon promoter DNA binding and explaining the highly restricted promoter specificity of vRNAP that is essential for phage early transcription.
 
X-ray crystal structure of the polymerase domain of the bacteriophage N4 virion RNA polymerase.,Murakami KS, Davydova EK, Rothman-Denes LB Proc Natl Acad Sci U S A. 2008 Mar 24;. PMID:18362338<ref>PMID:18362338</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: DNA-directed RNA polymerase]]
[[Category: Escherichia virus N4]]
[[Category: Escherichia phage n4]]
[[Category: Large Structures]]
[[Category: Davydova, E K.]]
[[Category: Davydova EK]]
[[Category: Murakami, K S.]]
[[Category: Murakami KS]]
[[Category: Rothman-Denes, L B.]]
[[Category: Rothman-Denes LB]]
[[Category: Right hand shape]]
[[Category: Transferase]]

Latest revision as of 12:10, 21 February 2024

X-ray crystal structure of polymerase domain of the bacteriophage N4 virion RNA polymeraseX-ray crystal structure of polymerase domain of the bacteriophage N4 virion RNA polymerase

Structural highlights

2po4 is a 1 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 2Å
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

2po4, resolution 2.00Å

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