6p0s: Difference between revisions

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<StructureSection load='6p0s' size='340' side='right'caption='[[6p0s]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
<StructureSection load='6p0s' size='340' side='right'caption='[[6p0s]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6p0s]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteriophage_lambda Bacteriophage lambda] and [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P0S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6P0S FirstGlance]. <br>
<table><tr><td colspan='2'>[[6p0s]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli], [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] and [https://en.wikipedia.org/wiki/Escherichia_virus_Lambda Escherichia virus Lambda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P0S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6P0S FirstGlance]. <br>
</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">fis, b3261, JW3229 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), xis ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10710 Bacteriophage lambda])</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6p0s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p0s OCA], [http://pdbe.org/6p0s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p0s RCSB], [http://www.ebi.ac.uk/pdbsum/6p0s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p0s 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=6p0s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p0s OCA], [https://pdbe.org/6p0s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6p0s RCSB], [https://www.ebi.ac.uk/pdbsum/6p0s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6p0s ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/VXIS_LAMBD VXIS_LAMBD]] Excisionase and integrase are necessary for the excision of prophage from the host genome by site-specific recombination at the att site. [[http://www.uniprot.org/uniprot/FIS_ECOLI FIS_ECOLI]] Activates ribosomal RNA transcription, as well other genes. Plays a direct role in upstream activation of rRNA promoters. Binds to a recombinational enhancer sequence that is required to stimulate hin-mediated DNA inversion. Prevents initiation of DNA replication from oriC.<ref>PMID:2209559</ref> <ref>PMID:8836178</ref>
[https://www.uniprot.org/uniprot/FIS_ECOLI FIS_ECOLI] Activates ribosomal RNA transcription, as well other genes. Plays a direct role in upstream activation of rRNA promoters. Binds to a recombinational enhancer sequence that is required to stimulate hin-mediated DNA inversion. Prevents initiation of DNA replication from oriC.<ref>PMID:2209559</ref> <ref>PMID:8836178</ref>  
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacteriophage lambda]]
[[Category: Escherichia coli]]
[[Category: Ecoli]]
[[Category: Escherichia coli K-12]]
[[Category: Escherichia virus Lambda]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Cascio, D]]
[[Category: Cascio D]]
[[Category: Hancock, S P]]
[[Category: Hancock SP]]
[[Category: Johnson, R C]]
[[Category: Johnson RC]]
[[Category: Cooperative binding]]
[[Category: Dna binding protein]]
[[Category: Dna binding protein-dna complex]]
[[Category: Dna shape]]
[[Category: Protein-dna ternary complex]]

Latest revision as of 10:20, 11 October 2023

Crystal structure of ternary DNA complex "FX2" containing E. coli Fis and phage lambda XisCrystal structure of ternary DNA complex "FX2" containing E. coli Fis and phage lambda Xis

Structural highlights

6p0s is a 5 chain structure with sequence from Escherichia coli, Escherichia coli K-12 and Escherichia virus Lambda. 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

FIS_ECOLI Activates ribosomal RNA transcription, as well other genes. Plays a direct role in upstream activation of rRNA promoters. Binds to a recombinational enhancer sequence that is required to stimulate hin-mediated DNA inversion. Prevents initiation of DNA replication from oriC.[1] [2]

Publication Abstract from PubMed

Localized arrays of proteins cooperatively assemble onto chromosomes to control DNA activity in many contexts. Binding cooperativity is often mediated by specific protein-protein interactions, but cooperativity through DNA structure is becoming increasingly recognized as an additional mechanism. During the site-specific DNA recombination reaction that excises phage lambda from the chromosome, the bacterial DNA architectural protein Fis recruits multiple lambda-encoded Xis proteins to the attR recombination site. Here, we report X-ray crystal structures of DNA complexes containing Fis + Xis, which show little, if any, contacts between the two proteins. Comparisons with structures of DNA complexes containing only Fis or Xis, together with mutant protein and DNA binding studies, support a mechanism for cooperative protein binding solely by DNA allostery. Fis binding both molds the minor groove to potentiate insertion of the Xis beta-hairpin wing motif and bends the DNA to facilitate Xis-DNA contacts within the major groove. The Fis-structured minor groove shape that is optimized for Xis binding requires a precisely positioned pyrimidine-purine base-pair step, whose location has been shown to modulate minor groove widths in Fis-bound complexes to different DNA targets.

Cooperative DNA binding by proteins through DNA shape complementarity.,Hancock SP, Cascio D, Johnson RC Nucleic Acids Res. 2019 Sep 19;47(16):8874-8887. doi: 10.1093/nar/gkz642. PMID:31616952[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Ross W, Thompson JF, Newlands JT, Gourse RL. E.coli Fis protein activates ribosomal RNA transcription in vitro and in vivo. EMBO J. 1990 Nov;9(11):3733-42. PMID:2209559
  2. ↑ Wold S, Crooke E, Skarstad K. The Escherichia coli Fis protein prevents initiation of DNA replication from oriC in vitro. Nucleic Acids Res. 1996 Sep 15;24(18):3527-32. PMID:8836178
  3. ↑ Hancock SP, Cascio D, Johnson RC. Cooperative DNA binding by proteins through DNA shape complementarity. Nucleic Acids Res. 2019 Sep 19;47(16):8874-8887. doi: 10.1093/nar/gkz642. PMID:31616952 doi:http://dx.doi.org/10.1093/nar/gkz642

6p0s, resolution 2.70Å

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