1iqr: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:1iqr.png|left|200px]]
-<!--
+==Crystal structure of DNA photolyase from Thermus thermophilus==
-The line below this paragraph, containing "STRUCTURE_1iqr", creates the "Structure Box" on the page.
+<StructureSection load='1iqr' size='340' side='right'caption='[[1iqr]], [[Resolution|resolution]] 2.10&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'>[[1iqr]] 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=1IQR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IQR 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]] 2.1&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-{{STRUCTURE_1iqr|  PDB=1iqr  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1iqr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iqr OCA], [https://pdbe.org/1iqr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1iqr RCSB], [https://www.ebi.ac.uk/pdbsum/1iqr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1iqr ProSAT], [https://www.topsan.org/Proteins/RSGI/1iqr TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PHR_THET8 PHR_THET8] Involved in repair of UV radiation-induced DNA damage. Catalyzes the light-dependent monomerization (300-600 nm) of cyclobutyl pyrimidine dimers (in cis-syn configuration), which are formed between adjacent bases on the same DNA strand upon exposure to ultraviolet radiation (By similarity).
+== 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/iq/1iqr_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=1iqr ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+DNA photolyase is a pyrimidine-dimer repair enzyme that uses visible light. Photolyase generally contains two chromophore cofactors. One is a catalytic cofactor directly contributing to the repair of a pyrimidine-dimer. The other is a light-harvesting cofactor, which absorbs visible light and transfers energy to the catalytic cofactor. Photolyases are classified according to their second cofactor into either a folate- or deazaflavin-type. The native structures of both types of photolyases have already been determined, but the mechanism of substrate recognition remains largely unclear because of the lack of structural information regarding the photolyase-substrate complex. Photolyase from Thermus thermophilus, the first thermostable class I photolyase found, is favorable for function analysis, but even the type of the second cofactor has not been identified. Here, we report the crystal structures of T. thermophilus photolyase in both forms of the native enzyme and the complex along with a part of its substrate, thymine. A structural comparison with other photolyases suggests that T. thermophilus photolyase has structural features allowing for thermostability and that its light-harvesting cofactor binding site bears a close resemblance to a deazaflavin-type photolyase. One thymine base is found at the hole, a putative substrate-binding site near the catalytic cofactor in the complex form. This structural data for the photolyase-thymine complex allow us to propose a detailed model for the pyrimidine-dimer recognition mechanism.
-===Crystal structure of DNA photolyase from Thermus thermophilus===
+Crystal structure of thermostable DNA photolyase: pyrimidine-dimer recognition mechanism.,Komori H, Masui R, Kuramitsu S, Yokoyama S, Shibata T, Inoue Y, Miki K Proc Natl Acad Sci U S A. 2001 Nov 20;98(24):13560-5. Epub 2001 Nov 13. PMID:11707580<ref>PMID:11707580</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_11707580}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1iqr" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 11707580 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_11707580}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-IQR 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=1IQR OCA].
-==Reference==
-Crystal structure of thermostable DNA photolyase: pyrimidine-dimer recognition mechanism., Komori H, Masui R, Kuramitsu S, Yokoyama S, Shibata T, Inoue Y, Miki K, Proc Natl Acad Sci U S A. 2001 Nov 20;98(24):13560-5. Epub 2001 Nov 13. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11707580 11707580]
-[[Category: Deoxyribodipyrimidine photo-lyase]]
-[[Category: Single protein]]
 [[Category: Thermus thermophilus]]
-[[Category: Inoue, Y.]]
+[[Category: Inoue Y]]
-[[Category: Kuramitsu, S.]]
+[[Category: Komori H]]
-[[Category: Masui, R.]]
+[[Category: Kuramitsu S]]
-[[Category: Miki, K.]]
+[[Category: Masui R]]
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+[[Category: Miki K]]
-[[Category: Shibata, T.]]
+[[Category: Shibata T]]
-[[Category: Yokoyama, S.]]
+[[Category: Yokoyama S]]
-[[Category: Komori, H.]]
-[[Category: Dna repair]]
-[[Category: Dna-binding]]
-[[Category: Fad]]
-[[Category: Photoreactivating enzyme]]
-[[Category: Riken structural genomics/proteomics initiative]]
-[[Category: Rsgi]]
-[[Category: Structural genomic]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul  1 13:49:33 2008''