1ijw: Difference between revisions

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New page: left|200px<br /><applet load="1ijw" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ijw, resolution 2.40Å" /> '''Testing the Water-Me...
 
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[[Image:1ijw.gif|left|200px]]<br /><applet load="1ijw" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1ijw, resolution 2.40&Aring;" />
'''Testing the Water-Mediated Hin Recombinase DNA Recognition by Systematic Mutations.'''<br />


==Overview==
==Testing the Water-Mediated Hin Recombinase DNA Recognition by Systematic Mutations.==
The Hin recombinase specifically recognizes its DNA-binding site by means, of both major and minor groove interactions. A previous X-ray structure, together with new structures of the Hin DNA-binding domain bound to a, recombination half-site that were solved as part of the present study, have revealed that two ordered water molecules are present within the, major groove interface. In this report, we test the importance of these, waters directly by X-ray crystal structure analysis of complexes with four, mutant DNA sequences. These structures, combined with their Hin-binding, properties, provide strong support for the critical importance of one of, the intermediate waters. A lesser but demonstrable role is ascribed to the, second water molecule. The mutant structures also illustrate the prominent, roles of thymine methyls both in stabilizing intermediate waters and in, interfering with water or amino acid side chain interactions with DNA.
<StructureSection load='1ijw' size='340' side='right'caption='[[1ijw]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1ijw]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IJW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IJW 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]] 2.4&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CBR:5-BROMO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>CBR</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></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=1ijw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ijw OCA], [https://pdbe.org/1ijw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ijw RCSB], [https://www.ebi.ac.uk/pdbsum/1ijw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ijw ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/HIN_SALTY HIN_SALTY] A DNA fragment of approximately 900 base pairs, adjacent to the fljB (H2) gene, which specifies the synthesis of phase-2 flagellin, can exist in either orientation with respect to fljB. The orientation of the inversion region controls expression of fljB. The hin gene occupies about two-thirds of the inversion region; it is required for the inversion of the fljB controlling region.
== 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/ij/1ijw_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=1ijw ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1IJW is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/ ] with TRS as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1IJW OCA].
*[[Resolvase 3D structures|Resolvase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Testing water-mediated DNA recognition by the Hin recombinase., Chiu TK, Sohn C, Dickerson RE, Johnson RC, EMBO J. 2002 Feb 15;21(4):801-14. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11847127 11847127]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]]
[[Category: Chiu, T.K.]]
[[Category: Chiu TK]]
[[Category: Dickerson, R.E.]]
[[Category: Dickerson RE]]
[[Category: Johnson, R.C.]]
[[Category: Johnson RC]]
[[Category: Sohn, C.]]
[[Category: Sohn C]]
[[Category: TRS]]
[[Category: br18]]
[[Category: hin recombinase]]
[[Category: protein-dna complex]]
[[Category: water-mediated recognition]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 17:27:33 2007''

Latest revision as of 10:36, 7 February 2024

Testing the Water-Mediated Hin Recombinase DNA Recognition by Systematic Mutations.Testing the Water-Mediated Hin Recombinase DNA Recognition by Systematic Mutations.

Structural highlights

1ijw is a 3 chain structure with sequence from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.4Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

HIN_SALTY A DNA fragment of approximately 900 base pairs, adjacent to the fljB (H2) gene, which specifies the synthesis of phase-2 flagellin, can exist in either orientation with respect to fljB. The orientation of the inversion region controls expression of fljB. The hin gene occupies about two-thirds of the inversion region; it is required for the inversion of the fljB controlling region.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1ijw, resolution 2.40Å

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