3jxc

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:05, 6 September 2023) (edit) (undo)
 
(6 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:3jxc.png|left|200px]]
 
-
<!--
+
==Crystal structure of the P22 c2 repressor protein in complex with synthetic operator 9T in the presence of Tl+==
-
The line below this paragraph, containing "STRUCTURE_3jxc", creates the "Structure Box" on the page.
+
<StructureSection load='3jxc' size='340' side='right'caption='[[3jxc]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[3jxc]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_virus_P22 Salmonella virus P22]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JXC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3JXC FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TL:THALLIUM+(I)+ION'>TL</scene></td></tr>
-
{{STRUCTURE_3jxc| PDB=3jxc | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3jxc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jxc OCA], [https://pdbe.org/3jxc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3jxc RCSB], [https://www.ebi.ac.uk/pdbsum/3jxc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3jxc ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/RPC2_BPP22 RPC2_BPP22] This protein allows the phage to reside inactively in the chromosome of its host bacterium. This lysogenic state is maintained by binding of regulatory protein C2 to the OR and OL operators, preventing transcription of proteins necessary for lytic development.
 +
== 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/jx/3jxc_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=3jxc ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The binding of proteins to specific sequences of DNA is an important feature of virtually all DNA transactions. Proteins recognize specific DNA sequences using both direct readout (sensing types and positions of DNA functional groups) and indirect readout (sensing DNA conformation and deformability). Previously we showed that the P22 c2 repressor N-terminal domain (P22R NTD) forces the central non-contacted 5'-ATAT-3' sequence of the DNA operator into the B' state, a state known to affect DNA hydration, rigidity and bending. Usually the B' state, with a narrow minor groove and a spine of hydration, is reserved for A-tract DNA (TpA steps disrupt A-tracts). Here, we have co-crystallized P22R NTD with an operator containing a central 5'-ACGT-3' sequence in the non-contacted region. C.G base pairs have not previously been observed in the B' state and are thought to prevent it. However, P22R NTD induces a narrow minor groove and a spine of hydration to 5'-ACGT-3'. We observe that C.G base pairs have distinctive destabilizing and disordering effects on the spine of hydration. It appears that the reduced stability of the spine results in a higher energy cost for the B to B' transition. The differential effect of DNA sequence on the barrier to this transition allows the protein to sense the non-contacted DNA sequence.
-
===Crystal structure of the P22 c2 repressor protein in complex with synthetic operator 9T in the presence of Tl+===
+
Sequence recognition of DNA by protein-induced conformational transitions.,Watkins D, Mohan S, Koudelka GB, Williams LD J Mol Biol. 2010 Mar 5;396(4):1145-64. Epub 2010 Jan 4. PMID:20053356<ref>PMID:20053356</ref>
-
 
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
<!--
+
</div>
-
The line below this paragraph, {{ABSTRACT_PUBMED_20053356}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 3jxc" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 20053356 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_20053356}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Large Structures]]
-
3JXC is a 4 chains structure with sequences from [http://en.wikipedia.org/wiki/Enterobacteria_phage_p22 Enterobacteria phage p22]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JXC OCA].
+
[[Category: Salmonella virus P22]]
-
 
+
[[Category: Koudelka GB]]
-
==Reference==
+
[[Category: Watkins D]]
-
<ref group="xtra">PMID:20053356</ref><references group="xtra"/>
+
[[Category: Williams LD]]
-
[[Category: Enterobacteria phage p22]]
+
-
[[Category: Koudelka, G B.]]
+
-
[[Category: Watkins, D.]]
+
-
[[Category: Williams, L D.]]
+
-
[[Category: Dna-binding]]
+
-
[[Category: Protein-dna complex]]
+
-
[[Category: Repressor]]
+
-
[[Category: Transcription]]
+
-
[[Category: Transcription regulation]]
+
-
[[Category: Transcription regulator]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 3 14:50:09 2010''
+

Current revision

Crystal structure of the P22 c2 repressor protein in complex with synthetic operator 9T in the presence of Tl+

PDB ID 3jxc

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3jxc"
Personal tools