5LFA

Crystal structure of iron-sulfur cluster containing bacterial (6-4) photolyase PhrB - Y424F mutant with impaired DNA repair activity

Summary for 5LFA

• Entry DOI: 10.2210/pdb5lfa/pdb
• Related: 4DJA
• Descriptor: (6-4) photolyase, FLAVIN-ADENINE DINUCLEOTIDE, 1-deoxy-1-(6,7-dimethyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl)-D-ribitol, ... (6 entities in total)
• Functional Keywords: photolyase, dna repair, lyase, iron-sulfur cluster, flavoprotein
• Biological source: Agrobacterium fabrum (strain C58 / ATCC 33970)
• Total number of polymer chains: 1
• Total formula weight: 60947.64

Authors

Kwiatkowski, D.,Zhang, F.,Krauss, N.,Lamparter, T.,Scheerer, P. (deposition date: 2016-06-30, release date: 2017-01-11, Last modification date: 2024-01-10)

Primary citation

Zhang, F.,Ma, H.,Bowatte, K.,Kwiatkowski, D.,Mittmann, E.,Qasem, H.,Krau, 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., 93:304-314, 2017

PubMed Abstract: 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 PhrB mutant showed reduced binding of lesion DNA and loss of DNA repair. The mutant PhrB 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 PhrB revealed a water network extending to His366, which are part of the lesion-binding site. The crystal structure of PhrB shows how the bulky Trp leads to structural rearrangements in the DMRL chromophore pocket. Spectral characterizations of PhrB 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.

PubMed: 27992645
DOI: 10.1111/php.12699

Experimental method

X-RAY DIFFRACTION (2.5 Å)