This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
5zcw
From Proteopedia
(Difference between revisions)
m (Protected "5zcw" [edit=sysop:move=sysop]) |
|||
| (4 intermediate revisions not shown.) | |||
| Line 1: | Line 1: | ||
| - | '''Unreleased structure''' | ||
| - | + | ==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]] | ||
Current revision
Structure of the Methanosarcina mazei class II CPD-photolyase in complex with intact, phosphodiester linked, CPD-lesion
| |||||||||||
