1t5l: Difference between revisions

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-{{STRUCTURE_1t5l|  PDB=1t5l  |  SCENE=  }}
+==Crystal structure of the DNA repair protein UvrB point mutant Y96A revealing a novel fold for domain 2==
-===Crystal structure of the DNA repair protein UvrB point mutant Y96A revealing a novel fold for domain 2===
+<StructureSection load='1t5l' size='340' side='right' caption='[[1t5l]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
-{{ABSTRACT_PUBMED_15192705}}
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1t5l]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_caldotenax Bacillus caldotenax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T5L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T5L FirstGlance]. <br>
+</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
+<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1d9x|1d9x]], [[1d9z|1d9z]], [[1c40|1c40]], [[1d2m|1d2m]], [[1e52|1e52]], [[1qoj|1qoj]]</td></tr>
+<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">UVRB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1395 Bacillus caldotenax])</td></tr>
+<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1t5l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t5l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1t5l RCSB], [http://www.ebi.ac.uk/pdbsum/1t5l PDBsum]</span></td></tr>
+<table>
+== 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/t5/1t5l_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/chain_selection.php?pdb_ID=2ata ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Nucleotide excision repair (NER) is a highly conserved DNA repair mechanism present in all kingdoms of life. UvrB is a central component of the bacterial NER system, participating in damage recognition, strand excision and repair synthesis. None of the three presently available crystal structures of UvrB has defined the structure of domain 2, which is critical for the interaction with UvrA. We have solved the crystal structure of the UvrB Y96A variant, which reveals a new fold for domain 2 and identifies highly conserved residues located on its surface. These residues are restricted to the face of UvrB important for DNA binding and may be critical for the interaction of UvrB with UvrA. We have mutated these residues to study their role in the incision reaction, formation of the pre-incision complex, destabilization of short duplex regions in DNA, binding to UvrA and ATP hydrolysis. Based on the structural and biochemical data, we conclude that domain 2 is required for a productive UvrA-UvrB interaction, which is a pre-requisite for all subsequent steps in nucleotide excision repair.
-==Function==
+Interactions between UvrA and UvrB: the role of UvrB's domain 2 in nucleotide excision repair.,Truglio JJ, Croteau DL, Skorvaga M, DellaVecchia MJ, Theis K, Mandavilli BS, Van Houten B, Kisker C EMBO J. 2004 Jul 7;23(13):2498-509. Epub 2004 Jun 10. PMID:15192705<ref>PMID:15192705</ref>
-[[http://www.uniprot.org/uniprot/UVRB_BACCA UVRB_BACCA]] The UvrABC repair system catalyzes the recognition and processing of DNA lesions. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. Upon binding of the UvrA(2)B(2) complex to a putative damaged site, the DNA wraps around one UvrB monomer. DNA wrap is dependent on ATP binding by UvrB and probably causes local melting of the DNA helix, facilitating insertion of UvrB beta-hairpin between the DNA strands. Then UvrB probes one DNA strand for the presence of a lesion. If a lesion is found the UvrA subunits dissociate and the UvrB-DNA preincision complex is formed. This complex is subsequently bound by UvrC and the second UvrB is released. If no lesion is found, the DNA wraps around the other UvrB subunit that will check the other stand for damage (By similarity).[HAMAP-Rule:MF_00204]
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[1t5l]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_caldotenax Bacillus caldotenax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T5L OCA].
+</div>
 ==See Also==
 *[[UvrABC|UvrABC]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:015192705</ref><references group="xtra"/><references/>
+__TOC__
+</StructureSection>
 [[Category: Bacillus caldotenax]]
 [[Category: Croteau, D L.]]