4dja: Difference between revisions
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The | ==Crystal structure of a prokaryotic (6-4) photolyase PhrB from Agrobacterium Tumefaciens with an Fe-S cluster and a 6,7-dimethyl-8-ribityllumazine antenna chromophore at 1.45A resolution== | ||
<StructureSection load='4dja' size='340' side='right'caption='[[4dja]], [[Resolution|resolution]] 1.45Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4dja]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_fabrum_str._C58 Agrobacterium fabrum str. C58]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DJA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DJA 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]] 1.45Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DLZ:1-DEOXY-1-(6,7-DIMETHYL-2,4-DIOXO-3,4-DIHYDROPTERIDIN-8(2H)-YL)-D-RIBITOL'>DLZ</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=4dja FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dja OCA], [https://pdbe.org/4dja PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dja RCSB], [https://www.ebi.ac.uk/pdbsum/4dja PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dja ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/PHRB_AGRFC PHRB_AGRFC] Photolyase involved in the repair of UV-induced (6-4) lesions in DNA. Catalyzes the photoreactivation of (6-4) pyrimidine-pyrimidone photoproducts by using blue-light energy. Can repair (6-4) photoproducts in ssDNA as well as in dsDNA.<ref>PMID:23589886</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The (6-4) photolyases use blue light to reverse UV-induced (6-4) photoproducts in DNA. This (6-4) photorepair was thought to be restricted to eukaryotes. Here we report a prokaryotic (6-4) photolyase, PhrB from Agrobacterium tumefaciens, and propose that (6-4) photolyases are broadly distributed in prokaryotes. The crystal structure of photolyase related protein B (PhrB) at 1.45 A resolution suggests a DNA binding mode different from that of the eukaryotic counterparts. A His-His-X-X-Arg motif is located within the proposed DNA lesion contact site of PhrB. This motif is structurally conserved in eukaryotic (6-4) photolyases for which the second His is essential for the (6-4) photolyase function. The PhrB structure contains 6,7-dimethyl-8-ribityllumazine as an antenna chromophore and a [4Fe-4S] cluster bound to the catalytic domain. A significant part of the Fe-S fold strikingly resembles that of the large subunit of eukaryotic and archaeal primases, suggesting that the PhrB-like photolyases branched at the base of the evolution of the cryptochrome/photolyase family. Our study presents a unique prokaryotic (6-4) photolyase and proposes that the prokaryotic (6-4) photolyases are the ancestors of the cryptochrome/photolyase family. | |||
Crystal structure of a prokaryotic (6-4) photolyase with an Fe-S cluster and a 6,7-dimethyl-8-ribityllumazine antenna chromophore.,Zhang F, Scheerer P, Oberpichler I, Lamparter T, Krauss N Proc Natl Acad Sci U S A. 2013 Apr 30;110(18):7217-22. doi:, 10.1073/pnas.1302377110. Epub 2013 Apr 15. PMID:23589886<ref>PMID:23589886</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4dja" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Agrobacterium fabrum str. C58]] | |||
[[Category: Large Structures]] | |||
[[Category: Krauss N]] | |||
[[Category: Lamparter T]] | |||
[[Category: Oberpichler I]] | |||
[[Category: Scheerer P]] | |||
[[Category: Zhang F]] | |||
