1d5y: Difference between revisions

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[[Image:1d5y.gif|left|200px]]


{{Structure
==CRYSTAL STRUCTURE OF THE E. COLI ROB TRANSCRIPTION FACTOR IN COMPLEX WITH DNA==
|PDB= 1d5y |SIZE=350|CAPTION= <scene name='initialview01'>1d5y</scene>, resolution 2.7&Aring;
<StructureSection load='1d5y' size='340' side='right'caption='[[1d5y]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>
<table><tr><td colspan='2'>[[1d5y]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D5Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D5Y FirstGlance]. <br>
|ACTIVITY=
</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>
|GENE=
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d5y OCA], [https://pdbe.org/1d5y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d5y RCSB], [https://www.ebi.ac.uk/pdbsum/1d5y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d5y ProSAT]</span></td></tr>
|DOMAIN=
</table>
|RELATEDENTRY=
== Function ==
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1d5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d5y OCA], [http://www.ebi.ac.uk/pdbsum/1d5y PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1d5y RCSB]</span>
[https://www.uniprot.org/uniprot/ROB_ECOLI ROB_ECOLI] Binds to the right arm of the replication origin oriC of the chromosome. Rob binding may influence the formation of the nucleoprotein structure, required for oriC function in the initiation of replication.
}}
== Evolutionary Conservation ==
 
[[Image:Consurf_key_small.gif|200px|right]]
'''CRYSTAL STRUCTURE OF THE E. COLI ROB TRANSCRIPTION FACTOR IN COMPLEX WITH DNA'''
Check<jmol>
 
  <jmolCheckbox>
 
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d5/1d5y_consurf.spt"</scriptWhenChecked>
==Overview==
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
The Escherichia coli Rob protein is a transcription factor belonging to the AraC/XylS protein family that regulates genes involved in resistance to antibiotics, organic solvents and heavy metals. The genes encoding these proteins are activated by the homologous proteins MarA and SoxS, although the level of activation can vary for the different transcription factors. Here we report a 2.7 A crystal structure of Rob in complex with the micF promoter that reveals an unusual mode of binding to DNA. The Rob-DNA complex differs from the previously reported structure of MarA bound to the mar promoter, in that only one of Rob's dual helix-turn-helix (HTH) motifs engages the major groove of the binding site. Biochemical studies show that sequence specific interactions involving only one of Rob's HTH motifs are sufficient for high affinity binding to DNA. The two different modes of DNA binding seen in crystal structures of Rob and MarA also match the distinctive patterns of DNA protection by AraC at several sites within the pBAD promoter. These and other findings suggest that gene activation by AraC/XylS transcription factors might involve two alternative modes of binding to DNA in different promoter contexts.
    <text>to colour the structure by Evolutionary Conservation</text>
 
  </jmolCheckbox>
==About this Structure==
</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=1d5y ConSurf].
1D5Y is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D5Y OCA].  
<div style="clear:both"></div>
 
__TOC__
==Reference==
</StructureSection>
Crystal structure of the Escherichia coli Rob transcription factor in complex with DNA., Kwon HJ, Bennik MH, Demple B, Ellenberger T, Nat Struct Biol. 2000 May;7(5):424-30. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10802742 10802742]
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Bennik, M H.J.]]
[[Category: Bennik MHJ]]
[[Category: Demple, B.]]
[[Category: Demple B]]
[[Category: Ellenberger, T.]]
[[Category: Ellenberger T]]
[[Category: Kwon, H J.]]
[[Category: Kwon HJ]]
[[Category: dna]]
[[Category: protein-dna complex]]
[[Category: rob transcription factor]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:35:18 2008''

Latest revision as of 09:49, 7 February 2024

CRYSTAL STRUCTURE OF THE E. COLI ROB TRANSCRIPTION FACTOR IN COMPLEX WITH DNACRYSTAL STRUCTURE OF THE E. COLI ROB TRANSCRIPTION FACTOR IN COMPLEX WITH DNA

Structural highlights

1d5y is a 8 chain structure with sequence from Escherichia coli. 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

ROB_ECOLI Binds to the right arm of the replication origin oriC of the chromosome. Rob binding may influence the formation of the nucleoprotein structure, required for oriC function in the initiation of replication.

Evolutionary Conservation

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

1d5y, resolution 2.70Å

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