3jxb

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of the P22 c2 repressor protein in complex with synthetic operator 9C

Structural highlights

3jxb is a 4 chain structure with sequence from Salmonella virus P22. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.67Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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

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

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.

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^[1]

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

References

↑ Watkins D, Mohan S, Koudelka GB, Williams LD. Sequence recognition of DNA by protein-induced conformational transitions. J Mol Biol. 2010 Mar 5;396(4):1145-64. Epub 2010 Jan 4. PMID:20053356 doi:10.1016/j.jmb.2009.12.050

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3jxb"

Categories: Large Structures | Salmonella virus P22 | Koudelka GB | Watkins D | Williams LD

@@ Line 1: / Line 1: @@
 ==Crystal structure of the P22 c2 repressor protein in complex with synthetic operator 9C==
-<StructureSection load='3jxb' size='340' side='right' caption='[[3jxb]], [[Resolution|resolution]] 1.67&Aring;' scene=''>
+<StructureSection load='3jxb' size='340' side='right'caption='[[3jxb]], [[Resolution|resolution]] 1.67&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3jxb]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpp22 Bpp22]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JXB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3JXB FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3jxb]] 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=3JXB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3JXB FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3jxc|3jxc]], [[3jxd|3jxd]]</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]] 1.67&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">C2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10754 BPP22])</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=3jxb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jxb OCA], [https://pdbe.org/3jxb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3jxb RCSB], [https://www.ebi.ac.uk/pdbsum/3jxb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3jxb ProSAT]</span></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=3jxb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jxb OCA], [http://pdbe.org/3jxb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3jxb RCSB], [http://www.ebi.ac.uk/pdbsum/3jxb PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://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.
+[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/3jxb_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jx/3jxb_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 32: / Line 32: @@
 __TOC__
 </StructureSection>
-[[Category: Bpp22]]
+[[Category: Large Structures]]
-[[Category: Koudelka, G B]]
+[[Category: Salmonella virus P22]]
-[[Category: Watkins, D]]
+[[Category: Koudelka GB]]
-[[Category: Williams, L D]]
+[[Category: Watkins D]]
-[[Category: Dna-binding]]
+[[Category: Williams LD]]
-[[Category: Protein-dna complex]]
-[[Category: Repressor]]
-[[Category: Transcription]]
-[[Category: Transcription regulation]]
-[[Category: Transcription regulator]]

3jxb

From Proteopedia

Current revision

Crystal structure of the P22 c2 repressor protein in complex with synthetic operator 9C

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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