1ir6: Difference between revisions

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-[[Image:1ir6.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1ir6", creates the "Structure Box" on the page.
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-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_1ir6|  PDB=1ir6  |  SCENE=  }}
-'''Crystal structure of exonuclease RecJ bound to manganese'''
+==Crystal structure of exonuclease RecJ bound to manganese==
+<StructureSection load='1ir6' size='340' side='right'caption='[[1ir6]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1ir6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IR6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IR6 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></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=1ir6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ir6 OCA], [https://pdbe.org/1ir6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ir6 RCSB], [https://www.ebi.ac.uk/pdbsum/1ir6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ir6 ProSAT], [https://www.topsan.org/Proteins/RSGI/1ir6 TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RECJ_THET8 RECJ_THET8] Single-stranded-DNA-specific exonuclease acting in a 5' to 3' direction; has no detectable activity on ssRNA.<ref>PMID:21087930</ref>
+== 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/ir/1ir6_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=1ir6 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+RecJ, a 5' to 3' exonuclease specific for single-stranded DNA, functions in DNA repair and recombination systems. We determined the crystal structure of RecJ bound to Mn(2+) ion essential for its activity. RecJ has a novel fold in which two domains are interconnected by a long helix, forming a central groove. Mn(2+) is located on the wall of the groove and is coordinated by conserved residues characteristic of a family of phosphoesterases that includes RecJ proteins. The groove is composed of residues conserved among RecJ proteins and is positively charged. These findings and the narrow width of the groove indicate that the groove binds single- instead of double-stranded DNA.
-==Overview==
+The crystal structure of exonuclease RecJ bound to Mn2+ ion suggests how its characteristic motifs are involved in exonuclease activity.,Yamagata A, Kakuta Y, Masui R, Fukuyama K Proc Natl Acad Sci U S A. 2002 Apr 30;99(9):5908-12. Epub 2002 Apr 23. PMID:11972066<ref>PMID:11972066</ref>
-RecJ, a 5' to 3' exonuclease specific for single-stranded DNA, functions in DNA repair and recombination systems. We determined the crystal structure of RecJ bound to Mn(2+) ion essential for its activity. RecJ has a novel fold in which two domains are interconnected by a long helix, forming a central groove. Mn(2+) is located on the wall of the groove and is coordinated by conserved residues characteristic of a family of phosphoesterases that includes RecJ proteins. The groove is composed of residues conserved among RecJ proteins and is positively charged. These findings and the narrow width of the groove indicate that the groove binds single- instead of double-stranded DNA.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-IR6 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IR6 OCA].
+</div>
+<div class="pdbe-citations 1ir6" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-The crystal structure of exonuclease RecJ bound to Mn2+ ion suggests how its characteristic motifs are involved in exonuclease activity., Yamagata A, Kakuta Y, Masui R, Fukuyama K, Proc Natl Acad Sci U S A. 2002 Apr 30;99(9):5908-12. Epub 2002 Apr 23. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11972066 11972066]
+*[[Exonuclease 3D structures|Exonuclease 3D structures]]
-[[Category: Single protein]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Thermus thermophilus]]
-[[Category: Fukuyama, K.]]
+[[Category: Fukuyama K]]
-[[Category: Kakuta, Y.]]
+[[Category: Kakuta Y]]
-[[Category: Masui, R.]]
+[[Category: Masui R]]
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+[[Category: Yamagata A]]
-[[Category: Yamagata, A.]]
-[[Category: Dna recombination]]
-[[Category: Dna repair]]
-[[Category: Manganese]]
-[[Category: Nuclease]]
-[[Category: Riken structural genomics/proteomics initiative]]
-[[Category: Rsgi]]
-[[Category: Single-stranded dna]]
-[[Category: Structural genomic]]
-[[Category: Two domains interconnected by alpha-helix]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 20:18:53 2008''