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| | <StructureSection load='5kcm' size='340' side='right'caption='[[5kcm]], [[Resolution|resolution]] 2.15Å' scene=''> | | <StructureSection load='5kcm' size='340' side='right'caption='[[5kcm]], [[Resolution|resolution]] 2.15Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5kcm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Agrfc Agrfc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KCM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KCM FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5kcm]] is a 2 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=5KCM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KCM FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.149Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">phrB, Atu4765 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=176299 AGRFC])</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/(6-4)DNA_photolyase (6-4)DNA photolyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.99.13 4.1.99.13] </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=5kcm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kcm OCA], [https://pdbe.org/5kcm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kcm RCSB], [https://www.ebi.ac.uk/pdbsum/5kcm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kcm ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5kcm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kcm OCA], [http://pdbe.org/5kcm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kcm RCSB], [http://www.ebi.ac.uk/pdbsum/5kcm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kcm ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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> | + | [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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Agrfc]] | + | [[Category: Agrobacterium fabrum str. C58]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Bowatte, K]] | + | [[Category: Bowatte K]] |
| - | [[Category: Lamparter, T]] | + | [[Category: Lamparter T]] |
| - | [[Category: Yang, X]] | + | [[Category: Yang X]] |
| - | [[Category: Zhang, F]] | + | [[Category: Zhang F]] |
| - | [[Category: Fes-bcp]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Mutant]]
| + | |
| Structural highlights
Function
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.[1]
Publication Abstract from PubMed
PhrB from Agrobacterium fabrum is the first prokaryotic photolyase which repairs (6-4) UV DNA-photoproducts. The protein harbors three cofactors, the enzymatically active FAD chromophore, a second chromophore, 6,7-dimethyl-8-ribityllumazine (DMRL) and a cubane-type Fe-S cluster. Tyr424 of PhrB is part of the DNA binding site and could provide an electron link to the Fe-S cluster. The PhrBY424F mutant showed reduced binding of lesion DNA and loss of DNA repair. The mutant PhrBI51W , is characterized by the loss of the DMRL chromophore, reduced photoreduction and reduced DNA repair capacity. We have determined the crystal structures of both mutants and found that both mutations only affect local protein environments whereas the overall fold remained unchanged. The crystal structure of PhrBY424F revealed a water network extending to His366 which are part of the lesion binding site. The crystal structure of PhrBI51W shows how the bulky Trp leads to structural rearrangements in the DMRL chromophore pocket. Spectral characterizations of PhrBI51W suggest that DMRL serves as an antenna chromophore for photoreduction and DNA repair in the wild type. The energy transfer from DMRL to FAD could represent a phylogenetically ancient process. This article is protected by copyright. All rights reserved.
Crystal Structures of Bacterial (6-4) Photolyase Mutants with Impaired DNA Repair Activity.,Zhang F, Ma H, Bowatte K, Kwiatkowski D, Mittmann E, Qasem H, Krauss N, Zeng X, Ren Z, Scheerer P, Yang X, Lamparter T Photochem Photobiol. 2016 Dec 19. doi: 10.1111/php.12699. PMID:27992645[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Zhang F, Scheerer P, Oberpichler I, Lamparter T, Krauss N. Crystal structure of a prokaryotic (6-4) photolyase with an Fe-S cluster and a 6,7-dimethyl-8-ribityllumazine antenna chromophore. 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 doi:10.1073/pnas.1302377110
- ↑ Zhang F, Ma H, Bowatte K, Kwiatkowski D, Mittmann E, Qasem H, Krauss N, Zeng X, Ren Z, Scheerer P, Yang X, Lamparter T. Crystal Structures of Bacterial (6-4) Photolyase Mutants with Impaired DNA Repair Activity. Photochem Photobiol. 2016 Dec 19. doi: 10.1111/php.12699. PMID:27992645 doi:http://dx.doi.org/10.1111/php.12699
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