4dja

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== Structural highlights ==
== 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>
<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>
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</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>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.45&#8491;</td></tr>
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<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>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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>
<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>
</table>
== Function ==
== Function ==
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[[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>
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[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>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 4dja" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>

Current revision

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

PDB ID 4dja

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