1kjk: Difference between revisions

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-[[Image:1kjk.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1kjk", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
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-{{STRUCTURE_1kjk|  PDB=1kjk  |  SCENE=  }}
-'''Solution structure of the lambda integrase amino-terminal domain'''
+==Solution structure of the lambda integrase amino-terminal domain==
+<StructureSection load='1kjk' size='340' side='right'caption='[[1kjk]]' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1kjk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_Lambda Escherichia virus Lambda]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KJK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KJK FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1kjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kjk OCA], [https://pdbe.org/1kjk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kjk RCSB], [https://www.ebi.ac.uk/pdbsum/1kjk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kjk ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/VINT_LAMBD VINT_LAMBD] Integrase is necessary for integration of the phage into the host genome by site-specific recombination. In conjunction with excisionase, integrase is also necessary for excision of the prophage from the host genome.
+== 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/kj/1kjk_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=1kjk ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The integrase protein (Int) from bacteriophage lambda catalyzes the insertion and excision of the viral genome into and out of Escherichia coli. It is a member of the lambda-Int family of site-specific recombinases that catalyze a diverse array of DNA rearrangements in archaebacteria, eubacteria, and yeast and belongs to the subset of this family that possesses two autonomous DNA-binding domains. The heterobivalent properties of Int can be decomposed into a carboxyl-terminal domain that executes the DNA cleavage and ligation reactions and a smaller amino-terminal domain that binds to an array of conserved DNA sites within the phage arms, thereby arranging Int protomers within the higher-order recombinogenic complex. We have determined that residues Met-1 to Leu-64 of Int constitute the minimal arm-type DNA-binding domain (INT-DBD(1-64)) and solved the solution structure by using NMR. We show that the INT-DBD(1-64) is a novel member of the growing family of three-stranded beta-sheet DNA-binding proteins, because it supplements this motif with a disordered amino-terminal basic tail that is important for arm-site binding. A model of the arm-DNA-binding domain recognizing its cognate DNA site is proposed on the basis of similarities with the analogous domain of Tn916 Int and is discussed in relation to other features of the protein.
-==Overview==
+Arm-site binding by lambda -integrase: solution structure and functional characterization of its amino-terminal domain.,Wojciak JM, Sarkar D, Landy A, Clubb RT Proc Natl Acad Sci U S A. 2002 Mar 19;99(6):3434-9. PMID:11904406<ref>PMID:11904406</ref>
-The integrase protein (Int) from bacteriophage lambda catalyzes the insertion and excision of the viral genome into and out of Escherichia coli. It is a member of the lambda-Int family of site-specific recombinases that catalyze a diverse array of DNA rearrangements in archaebacteria, eubacteria, and yeast and belongs to the subset of this family that possesses two autonomous DNA-binding domains. The heterobivalent properties of Int can be decomposed into a carboxyl-terminal domain that executes the DNA cleavage and ligation reactions and a smaller amino-terminal domain that binds to an array of conserved DNA sites within the phage arms, thereby arranging Int protomers within the higher-order recombinogenic complex. We have determined that residues Met-1 to Leu-64 of Int constitute the minimal arm-type DNA-binding domain (INT-DBD(1-64)) and solved the solution structure by using NMR. We show that the INT-DBD(1-64) is a novel member of the growing family of three-stranded beta-sheet DNA-binding proteins, because it supplements this motif with a disordered amino-terminal basic tail that is important for arm-site binding. A model of the arm-DNA-binding domain recognizing its cognate DNA site is proposed on the basis of similarities with the analogous domain of Tn916 Int and is discussed in relation to other features of the protein.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-KJK is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_lambda Enterobacteria phage lambda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KJK OCA].
+</div>
+<div class="pdbe-citations 1kjk" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Arm-site binding by lambda -integrase: solution structure and functional characterization of its amino-terminal domain., Wojciak JM, Sarkar D, Landy A, Clubb RT, Proc Natl Acad Sci U S A. 2002 Mar 19;99(6):3434-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11904406 11904406]
+*[[Retroviral integrase 3D structures|Retroviral integrase 3D structures]]
-[[Category: Enterobacteria phage lambda]]
+== References ==
-[[Category: Single protein]]
+<references/>
-[[Category: Clubb, R T.]]
+__TOC__
-[[Category: Landy, A.]]
+</StructureSection>
-[[Category: Sarkar, D.]]
+[[Category: Escherichia virus Lambda]]
-[[Category: Wojciak, J M.]]
+[[Category: Large Structures]]
-[[Category: Dna recombination]]
+[[Category: Clubb RT]]
-[[Category: Dna-binding domain]]
+[[Category: Landy A]]
-[[Category: Integrase]]
+[[Category: Sarkar D]]
-[[Category: Three-stranded beta-sheet]]
+[[Category: Wojciak JM]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 22:49:07 2008''