2fio: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2fio]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_virus_phi29 Bacillus virus phi29]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FIO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FIO FirstGlance]. <br>
<table><tr><td colspan='2'>[[2fio]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_virus_phi29 Bacillus virus phi29]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FIO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FIO FirstGlance]. <br>
</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=2fio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fio OCA], [https://pdbe.org/2fio PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fio RCSB], [https://www.ebi.ac.uk/pdbsum/2fio PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fio ProSAT]</span></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]] 2.7&#8491;</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=2fio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fio OCA], [https://pdbe.org/2fio PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fio RCSB], [https://www.ebi.ac.uk/pdbsum/2fio PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fio ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[https://www.uniprot.org/uniprot/TF4_BPPH2 TF4_BPPH2] Mediates, together with protein p6, the early to late transcriptional switch by stabilizing the binding of host RNA polymerase (RNAP) to the late A3 promoter. Activates transcription from the late A3 promoter and represses the main early promoters A2b and A2c by modifying the topology of the sequences encompassing early promoters A2c and A2b and late promoter A3 in a hairpin. Proteins p6 and p4 bind cooperatively to an approximately 200 bp DNA region located between the late A3 and the early A2c promoters. Binding of p4 molecules induces the reorganization of the binding of protein p6, giving rise to the nucleoprotein complex responsible for the switch from early to late transcription.<ref>PMID:11689446</ref> <ref>PMID:12426390</ref> <ref>PMID:14757050</ref> <ref>PMID:2107318</ref> <ref>PMID:21614197</ref> <ref>PMID:8617213</ref> <ref>PMID:9784366</ref>  
[https://www.uniprot.org/uniprot/TF4_BPPH2 TF4_BPPH2] Mediates, together with protein p6, the early to late transcriptional switch by stabilizing the binding of host RNA polymerase (RNAP) to the late A3 promoter. Activates transcription from the late A3 promoter and represses the main early promoters A2b and A2c by modifying the topology of the sequences encompassing early promoters A2c and A2b and late promoter A3 in a hairpin. Proteins p6 and p4 bind cooperatively to an approximately 200 bp DNA region located between the late A3 and the early A2c promoters. Binding of p4 molecules induces the reorganization of the binding of protein p6, giving rise to the nucleoprotein complex responsible for the switch from early to late transcription.<ref>PMID:11689446</ref> <ref>PMID:12426390</ref> <ref>PMID:14757050</ref> <ref>PMID:2107318</ref> <ref>PMID:21614197</ref> <ref>PMID:8617213</ref> <ref>PMID:9784366</ref>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Protein p4 affects the transcriptional switch that divides bacteriophage phi29 infection in early and late phases. The synthesis of DNA replication proteins and p4 takes place in the early phase, while structural, morphogenesis, and lysis proteins are synthesized in the late phase. Transcriptional switch by p4 is achieved by activating the late promoter A3 and repressing the early promoters A2b and A2c. The crystal structure of p4 alone and in complex with a 41 bp DNA, including the A3 promoter binding site, helps us to understand how the phage cycle is controlled. Protein p4 has a unique alpha/beta fold that includes a DNA recognition motif consisting of two N-terminal beta turn substructures, or N-hooks, located at the tips of an elongated protein homodimer. The two N-hooks enter the major groove of the double helix, establishing base-specific contacts. A high DNA curvature allows p4 N-hooks to reach two major groove areas three helical turns apart, like a bow and its string.
The structure of phage phi29 transcription regulator p4-DNA complex reveals an N-hook motif for DNA.,Badia D, Camacho A, Perez-Lago L, Escandon C, Salas M, Coll M Mol Cell. 2006 Apr 7;22(1):73-81. PMID:16600871<ref>PMID:16600871</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2fio" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>

Latest revision as of 12:23, 14 February 2024

Phage phi29 transcription regulator p4-DNA complexPhage phi29 transcription regulator p4-DNA complex

Structural highlights

2fio is a 4 chain structure with sequence from Bacillus virus phi29. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.7Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TF4_BPPH2 Mediates, together with protein p6, the early to late transcriptional switch by stabilizing the binding of host RNA polymerase (RNAP) to the late A3 promoter. Activates transcription from the late A3 promoter and represses the main early promoters A2b and A2c by modifying the topology of the sequences encompassing early promoters A2c and A2b and late promoter A3 in a hairpin. Proteins p6 and p4 bind cooperatively to an approximately 200 bp DNA region located between the late A3 and the early A2c promoters. Binding of p4 molecules induces the reorganization of the binding of protein p6, giving rise to the nucleoprotein complex responsible for the switch from early to late transcription.[1] [2] [3] [4] [5] [6] [7]

References

  1. ↑ Camacho A, Salas M. Mechanism for the switch of phi29 DNA early to late transcription by regulatory protein p4 and histone-like protein p6. EMBO J. 2001 Nov 1;20(21):6060-70. doi: 10.1093/emboj/20.21.6060. PMID:11689446 doi:http://dx.doi.org/10.1093/emboj/20.21.6060
  2. ↑ Calles B, Salas M, Rojo F. The phi29 transcriptional regulator contacts the nucleoid protein p6 to organize a repression complex. EMBO J. 2002 Nov 15;21(22):6185-94. doi: 10.1093/emboj/cdf623. PMID:12426390 doi:http://dx.doi.org/10.1093/emboj/cdf623
  3. ↑ Camacho A, Salas M. Molecular interplay between RNA polymerase and two transcriptional regulators in promoter switch. J Mol Biol. 2004 Feb 13;336(2):357-68. doi: 10.1016/j.jmb.2003.12.039. PMID:14757050 doi:http://dx.doi.org/10.1016/j.jmb.2003.12.039
  4. ↑ Rojo F, Zaballos A, Salas M. Bend induced by the phage phi 29 transcriptional activator in the viral late promoter is required for activation. J Mol Biol. 1990 Feb 20;211(4):713-25. doi: 10.1016/0022-2836(90)90072-t. PMID:2107318 doi:http://dx.doi.org/10.1016/0022-2836(90)90072-t
  5. ↑ Camacho A, Salas M. Molecular interactions and protein-induced DNA hairpin in the transcriptional control of bacteriophage o29 DNA. Int J Mol Sci. 2010;11(12):5129-42. doi: 10.3390/ijms11125129. Epub 2010 Dec 13. PMID:21614197 doi:http://dx.doi.org/10.3390/ijms11125129
  6. ↑ Monsalve M, Mencia M, Rojo F, Salas M. Activation and repression of transcription at two different phage phi29 promoters are mediated by interaction of the same residues of regulatory protein p4 with RNA polymerase. EMBO J. 1996 Jan 15;15(2):383-91. PMID:8617213
  7. ↑ Monsalve M, Calles B, Mencia M, Rojo F, Salas M. Binding of phage phi29 protein p4 to the early A2c promoter: recruitment of a repressor by the RNA polymerase. J Mol Biol. 1998 Oct 30;283(3):559-69. doi: 10.1006/jmbi.1998.2084. PMID:9784366 doi:http://dx.doi.org/10.1006/jmbi.1998.2084

2fio, resolution 2.70Å

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