5zcw: Difference between revisions
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==Structure of the Methanosarcina mazei class II CPD-photolyase in complex with intact, phosphodiester linked, CPD-lesion== | |||
<StructureSection load='5zcw' size='340' side='right'caption='[[5zcw]], [[Resolution|resolution]] 2.70Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5zcw]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanosarcina_mazei Methanosarcina mazei] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZCW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZCW 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]] 2.7Å</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=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TTD:CIS-SYN+CYCLOBUTANE+THYMINE+DIMER'>TTD</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=5zcw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zcw OCA], [https://pdbe.org/5zcw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zcw RCSB], [https://www.ebi.ac.uk/pdbsum/5zcw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zcw ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/Q8PYK9_METMA Q8PYK9_METMA] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Cyclobutane pyrimidine dimer (CPD) photolyases harness the energy of blue light to repair UV-induced DNA CPDs. Upon binding, CPD photolyases cause the photodamage to flip out of the duplex DNA and into the catalytic site of the enzyme. This process, called base-flipping, induces a kink in the DNA, as well as an unpaired bubble, which are stabilized by a network of protein-nucleic acid interactions. Previously, several co-crystal structures have been reported in which the binding mode of CPD photolyases has been studied in detail. However, in all cases the internucleoside linkage of the photodamage site was a chemically synthesized formacetal analogue and not the natural phosphodiester. Here, the first crystal structure and conformational analysis via molecular-dynamics simulations of a class II CPD photolyase in complex with photodamaged DNA that contains a natural cyclobutane pyrimidine dimer with an intra-lesion phosphodiester linkage are presented. It is concluded that a highly conserved bubble-intruding region (BIR) mediates stabilization of the open form of CPD DNA when complexed with class II CPD photolyases. | |||
Twist and turn: a revised structural view on the unpaired bubble of class II CPD photolyase in complex with damaged DNA.,Maestre-Reyna M, Yamamoto J, Huang WC, Tsai MD, Essen LO, Bessho Y IUCrJ. 2018 Aug 8;5(Pt 5):608-618. doi: 10.1107/S205225251800996X. eCollection, 2018 Sep 1. PMID:30224964<ref>PMID:30224964</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 5zcw" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Methanosarcina mazei]] | |||
[[Category: Synthetic construct]] | |||
[[Category: Bessho Y]] | |||
[[Category: Maestre-Reyna M]] | |||
Latest revision as of 08:51, 22 November 2023
Structure of the Methanosarcina mazei class II CPD-photolyase in complex with intact, phosphodiester linked, CPD-lesion
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