2vtb: Difference between revisions

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-[[Image:2vtb.png|left|200px]]
-<!--
+==Structure of cryptochrome 3 - DNA complex==
-The line below this paragraph, containing "STRUCTURE_2vtb", creates the "Structure Box" on the page.
+<StructureSection load='2vtb' size='340' side='right'caption='[[2vtb]], [[Resolution|resolution]] 2.01&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2vtb]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VTB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VTB FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.01&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MHF:5,10-METHENYL-6,7,8-TRIHYDROFOLIC+ACID'>MHF</scene>, <scene name='pdbligand=TCP:5-METHYLTHYMIDINE'>TCP</scene></td></tr>
-{{STRUCTURE_2vtb|  PDB=2vtb  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vtb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vtb OCA], [https://pdbe.org/2vtb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vtb RCSB], [https://www.ebi.ac.uk/pdbsum/2vtb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vtb ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CRYD_ARATH CRYD_ARATH] May have a photoreceptor function. Binds ss- and ds-DNA in a sequence non-specific manner. Has a photolyase activity specific for cyclobutane pyrimidine dimers in ssDNA.<ref>PMID:17062752</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/vt/2vtb_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=2vtb ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+DNA photolyases and cryptochromes (cry) form a family of flavoproteins that use light energy in the blue/UV-A region for the repair of UV-induced DNA lesions or for signaling, respectively. Very recently, it was shown that members of the DASH cryptochrome subclade repair specifically cyclobutane pyrimidine dimers (CPDs) in UV-damaged single-stranded DNA. Here, we report the crystal structure of Arabidopsis cryptochrome 3 with an in-situ-repaired CPD substrate in single-stranded DNA. The structure shows a binding mode similar to that of conventional DNA photolyases. Furthermore, CPD lesions in double-stranded DNA are bound and repaired with similar efficiency as in single-stranded DNA if the CPD lesion is present in a loop structure. Together, these data reveal that DASH cryptochromes catalyze light-driven DNA repair like conventional photolyases but lack an efficient flipping mechanism for interaction with CPD lesions within duplex DNA.
-===STRUCTURE OF CRYPTOCHROME 3 - DNA COMPLEX===
+Recognition and repair of UV lesions in loop structures of duplex DNA by DASH-type cryptochrome.,Pokorny R, Klar T, Hennecke U, Carell T, Batschauer A, Essen LO Proc Natl Acad Sci U S A. 2008 Dec 30;105(52):21023-7. Epub 2008 Dec 12. PMID:19074258<ref>PMID:19074258</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2vtb" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19074258}}, adds the Publication Abstract to the page
+*[[Cryptochrome 3D structures|Cryptochrome 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19074258 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19074258}}
+__TOC__
+</StructureSection>
-==About this Structure==
-[[2vtb]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VTB OCA].
-==Reference==
-<ref group="xtra">PMID:19074258</ref><ref group="xtra">PMID:17188299</ref><references group="xtra"/>
 [[Category: Arabidopsis thaliana]]
-[[Category: Deoxyribodipyrimidine photo-lyase]]
+[[Category: Homo sapiens]]
-[[Category: Batschauer, A.]]
+[[Category: Large Structures]]
-[[Category: Carell, T.]]
+[[Category: Batschauer A]]
-[[Category: Essen, L O.]]
+[[Category: Carell T]]
-[[Category: Hennecke, U.]]
+[[Category: Essen L-O]]
-[[Category: Klar, T.]]
+[[Category: Hennecke U]]
-[[Category: Pokorny, R.]]
+[[Category: Klar T]]
-[[Category: Chloroplast]]
+[[Category: Pokorny R]]
-[[Category: Chromophore]]
-[[Category: Cryptochrome]]
-[[Category: Cyclobutane-pyrimidine dimer]]
-[[Category: Dna]]
-[[Category: Dna-binding]]
-[[Category: Fad]]
-[[Category: Flavin adenine dinucleotide]]
-[[Category: Flavoprotein]]
-[[Category: Lyase dna complex]]
-[[Category: Lyase/dna complex]]
-[[Category: Mitochondrion]]
-[[Category: Photolyase]]
-[[Category: Plastid]]
-[[Category: Single-stranded dna]]
-[[Category: Transit peptide]]