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2pij

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[[Image:2pij.jpg|left|200px]]
 
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{{Structure
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==Structure of the Cro protein from prophage Pfl 6 in Pseudomonas fluorescens Pf-5==
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|PDB= 2pij |SIZE=350|CAPTION= <scene name='initialview01'>2pij</scene>, resolution 1.700&Aring;
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<StructureSection load='2pij' size='340' side='right'caption='[[2pij]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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|SITE= <scene name='pdbsite=AC1:So4+Binding+Site+For+Residue+B+501'>AC1</scene>, <scene name='pdbsite=AC2:So4+Binding+Site+For+Residue+A+502'>AC2</scene>, <scene name='pdbsite=AC3:So4+Binding+Site+For+Residue+B+503'>AC3</scene>, <scene name='pdbsite=AC4:So4+Binding+Site+For+Residue+B+504'>AC4</scene>, <scene name='pdbsite=AC5:Bct+Binding+Site+For+Residue+A+601'>AC5</scene> and <scene name='pdbsite=AC6:Dtt+Binding+Site+For+Residue+B+701'>AC6</scene>
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
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<table><tr><td colspan='2'>[[2pij]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Psef5 Psef5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PIJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PIJ FirstGlance]. <br>
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|ACTIVITY=
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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|GENE= Prophage Pfl 6 Cro ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 Pseudomonas fluorescens])
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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|DOMAIN=
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3bd1|3bd1]]</div></td></tr>
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|RELATEDENTRY=[[3bd1|3BD1]]
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Prophage Pfl 6 Cro ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=220664 PSEF5])</td></tr>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2pij FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pij OCA], [http://www.ebi.ac.uk/pdbsum/2pij PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2pij RCSB]</span>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2pij FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pij OCA], [https://pdbe.org/2pij PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pij RCSB], [https://www.ebi.ac.uk/pdbsum/2pij PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pij ProSAT]</span></td></tr>
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}}
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</table>
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== Evolutionary Conservation ==
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'''Structure of the Cro protein from prophage Pfl 6 in Pseudomonas fluorescens Pf-5'''
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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==Overview==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pi/2pij_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2pij ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
Proteins that share common ancestry may differ in structure and function because of divergent evolution of their amino acid sequences. For a typical diverse protein superfamily, the properties of a few scattered members are known from experiment. A satisfying picture of functional and structural evolution in relation to sequence changes, however, may require characterization of a larger, well chosen subset. Here, we employ a "stepping-stone" method, based on transitive homology, to target sequences intermediate between two related proteins with known divergent properties. We apply the approach to the question of how new protein folds can evolve from preexisting folds and, in particular, to an evolutionary change in secondary structure and oligomeric state in the Cro family of bacteriophage transcription factors, initially identified by sequence-structure comparison of distant homologs from phages P22 and lambda. We report crystal structures of two Cro proteins, Xfaso 1 and Pfl 6, with sequences intermediate between those of P22 and lambda. The domains show 40% sequence identity but differ by switching of alpha-helix to beta-sheet in a C-terminal region spanning approximately 25 residues. Sedimentation analysis also suggests a correlation between helix-to-sheet conversion and strengthened dimerization.
Proteins that share common ancestry may differ in structure and function because of divergent evolution of their amino acid sequences. For a typical diverse protein superfamily, the properties of a few scattered members are known from experiment. A satisfying picture of functional and structural evolution in relation to sequence changes, however, may require characterization of a larger, well chosen subset. Here, we employ a "stepping-stone" method, based on transitive homology, to target sequences intermediate between two related proteins with known divergent properties. We apply the approach to the question of how new protein folds can evolve from preexisting folds and, in particular, to an evolutionary change in secondary structure and oligomeric state in the Cro family of bacteriophage transcription factors, initially identified by sequence-structure comparison of distant homologs from phages P22 and lambda. We report crystal structures of two Cro proteins, Xfaso 1 and Pfl 6, with sequences intermediate between those of P22 and lambda. The domains show 40% sequence identity but differ by switching of alpha-helix to beta-sheet in a C-terminal region spanning approximately 25 residues. Sedimentation analysis also suggests a correlation between helix-to-sheet conversion and strengthened dimerization.
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==About this Structure==
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Transitive homology-guided structural studies lead to discovery of Cro proteins with 40% sequence identity but different folds.,Roessler CG, Hall BM, Anderson WJ, Ingram WM, Roberts SA, Montfort WR, Cordes MH Proc Natl Acad Sci U S A. 2008 Feb 19;105(7):2343-8. Epub 2008 Jan 28. PMID:18227506<ref>PMID:18227506</ref>
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2PIJ is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PIJ OCA].
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==Reference==
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Transitive homology-guided structural studies lead to discovery of Cro proteins with 40% sequence identity but different folds., Roessler CG, Hall BM, Anderson WJ, Ingram WM, Roberts SA, Montfort WR, Cordes MH, Proc Natl Acad Sci U S A. 2008 Feb 19;105(7):2343-8. Epub 2008 Jan 28. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18227506 18227506]
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[[Category: Protein complex]]
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[[Category: Pseudomonas fluorescens]]
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[[Category: Cordes, M H.J.]]
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[[Category: Montfort, W R.]]
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[[Category: Roberts, S A.]]
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[[Category: Roessler, C G.]]
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[[Category: helix-turn-helix]]
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[[Category: prophage]]
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[[Category: structural evolution]]
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[[Category: transcription factor]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:36:20 2008''
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2pij" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Psef5]]
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[[Category: Cordes, M H.J]]
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[[Category: Montfort, W R]]
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[[Category: Roberts, S A]]
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[[Category: Roessler, C G]]
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[[Category: Helix-turn-helix]]
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[[Category: Prophage]]
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[[Category: Structural evolution]]
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[[Category: Transcription]]
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[[Category: Transcription factor]]

Current revision

Structure of the Cro protein from prophage Pfl 6 in Pseudomonas fluorescens Pf-5

PDB ID 2pij

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