1per: Difference between revisions

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New page: left|200px<br /> <applet load="1per" size="450" color="white" frame="true" align="right" spinBox="true" caption="1per, resolution 2.500Å" /> '''THE COMPLEX BETWEE...
 
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[[Image:1per.gif|left|200px]]<br />
<applet load="1per" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1per, resolution 2.500&Aring;" />
'''THE COMPLEX BETWEEN PHAGE 434 REPRESSION DNA-BINDING DOMAIN AND OPERATOR SITE OR3: STRUCTURAL DIFFERENCES BETWEEN CONSENSUS AND NON-CONSENSUS HALF-SITES'''<br />


==Overview==
==THE COMPLEX BETWEEN PHAGE 434 REPRESSION DNA-BINDING DOMAIN AND OPERATOR SITE OR3: STRUCTURAL DIFFERENCES BETWEEN CONSENSUS AND NON-CONSENSUS HALF-SITES==
BACKGROUND: The repressor of phage 434 binds to a set of operator sites as, a homodimer. Its relative affinities for these sites determine the switch, from lysogenic to lytic growth. The six 434 operator sites (OR1, OR2, OR3, OL1, OL2 and OL3) have a particularly simple organization; all are 14 base, pairs long, with a conserved 5'-ACAA sequence symmetrically placed at, either end, and a variable central six base pairs. OR3 is unique among, naturally-occurring 434 operator sites in that it contains a non-consensus, base pair, G.C, at the fourth position of the otherwise invariant 5'-ACAA, sequence. Comparisons among structures of the 434 repressor DNA-binding, domain, R1-69, bound to various operator sites, allow us to analyze, differential specificity in regulatory complexes of this kind. RESULTS: We, have determined the structure at 2.5 A resolution of a complex of R1-69, with DNA containing the OR3 site and compared it with previously studied, complexes of R1-69 bound to OR1 and OR2. There are surprisingly extensive, structural differences between the consensus and non-consensus half-sites, of OR3 with respect to their interactions with R1-69, including a shift in, the DNA backbone and a small rotation of the entire R1-69 monomer., CONCLUSIONS: Recognition of the base pair difference that is critical for, the 434 regulatory switch involves a number of amino acid residues, not, just the one or two side chains in direct contact with the G-C base pair., Moreover, the repressor imposes a somewhat altered DNA conformation on the, non-consensus half-site.
<StructureSection load='1per' size='340' side='right'caption='[[1per]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1per]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Phage_434 Phage 434]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PER OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PER FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#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=1per FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1per OCA], [https://pdbe.org/1per PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1per RCSB], [https://www.ebi.ac.uk/pdbsum/1per PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1per ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RPC1_BP434 RPC1_BP434] Binds to two sets of three contiguous operator sites in the phage genome.
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pe/1per_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1per ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1PER is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_434 Bacteriophage 434]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1PER OCA].
*[[Bacteriophage repressor|Bacteriophage repressor]]
 
__TOC__
==Reference==
</StructureSection>
The complex between phage 434 repressor DNA-binding domain and operator site OR3: structural differences between consensus and non-consensus half-sites., Rodgers DW, Harrison SC, Structure. 1993 Dec 15;1(4):227-40. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8081737 8081737]
[[Category: Large Structures]]
[[Category: Bacteriophage 434]]
[[Category: Phage 434]]
[[Category: Single protein]]
[[Category: Harrison SC]]
[[Category: Harrison, S.C.]]
[[Category: Rodgers DW]]
[[Category: Rodgers, D.W.]]
[[Category: protein-dna complex]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Thu Nov  8 12:41:47 2007''

Latest revision as of 08:07, 14 February 2024

THE COMPLEX BETWEEN PHAGE 434 REPRESSION DNA-BINDING DOMAIN AND OPERATOR SITE OR3: STRUCTURAL DIFFERENCES BETWEEN CONSENSUS AND NON-CONSENSUS HALF-SITES

1per, resolution 2.50Å

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