5CAJ

Crystal structure of E. coli YaaA, a member of the DUF328/UPF0246 family

Summary for 5CAJ

• Entry DOI: 10.2210/pdb5caj/pdb
• Descriptor: UPF0246 protein YaaA, CHLORIDE ION, BENZAMIDINE, ... (4 entities in total)
• Functional Keywords: unknown function
• Biological source: Escherichia coli
• Total number of polymer chains: 2
• Total formula weight: 64504.76

Authors

Prahlad, J.,Lin, J.,Wilson, M.A. (deposition date: 2015-06-29, release date: 2016-02-24, Last modification date: 2024-11-06)

Primary citation

Prahlad, J.,Yuan, Y.,Lin, J.,Chang, C.W.,Iwata-Reuyl, D.,Liu, Y.,de Crecy-Lagard, V.,Wilson, M.A.
The DUF328 family member YaaA is a DNA-binding protein with a novel fold.
J.Biol.Chem., 295:14236-14247, 2020

PubMed Abstract: DUF328 family proteins are present in many prokaryotes; however, their molecular activities are unknown. The DUF328 protein YaaA is a member of the OxyR regulon and is protective against oxidative stress. Because uncharacterized proteins involved in prokaryotic oxidative stress response are rare, we sought to learn more about the DUF328 family. Using comparative genomics, we found a robust association between the DUF328 family and genes involved in DNA recombination and the oxidative stress response. In some proteins, DUF328 domains are fused to other domains involved in DNA binding, recombination, and repair. Cofitness analysis indicates that DUF328 family genes associate with recombination-mediated DNA repair pathways, particularly the RecFOR pathway. Purified recombinant YaaA binds to dsDNA, duplex DNA containing bubbles of unpaired nucleotides, and Holliday junction constructs with dissociation equilibrium constants of 200-300 nm YaaA binds DNA with positive cooperativity, forming multiple shifted species in electrophoretic mobility shift assays. The 1.65-Å resolution X-ray crystal structure of YaaA reveals that the protein possesses a new fold that we name the cantaloupe fold. YaaA has a positively charged cleft and a helix-hairpin-helix DNA-binding motif found in other DNA repair enzymes. Our results demonstrate that YaaA is a new type of DNA-binding protein associated with the oxidative stress response and that this molecular function is likely conserved in other DUF328 family members.

PubMed: 32796037
DOI: 10.1074/jbc.RA120.015055

Experimental method

X-RAY DIFFRACTION (1.65 Å)