4DJA

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

Summary for 4DJA

• Entry DOI: 10.2210/pdb4dja/pdb
• Descriptor: Photolyase, FLAVIN-ADENINE DINUCLEOTIDE, 1-deoxy-1-(6,7-dimethyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl)-D-ribitol, ... (7 entities in total)
• Functional Keywords: photolyase, dna repair, lyase, iron-sulfur cluster, flavoprotein
• Biological source: Agrobacterium tumefaciens
• Total number of polymer chains: 1
• Total formula weight: 60894.54

Authors

Scheerer, P.,Zhang, F.,Oberpichler, I.,Lamparter, T.,Krauss, N. (deposition date: 2012-02-01, release date: 2013-04-17, Last modification date: 2024-04-03)

Primary citation

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.USA, 110:7217-7222, 2013

PubMed Abstract: 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 Å 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.

PubMed: 23589886
DOI: 10.1073/pnas.1302377110

Experimental method

X-RAY DIFFRACTION (1.45 Å)