5caj | pdb_00005caj

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

spinqualitylabelsall models 5caj, resolution 1.65Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 5caj is a 2 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.65Å Ligands: BEN, CL, MSE Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function YAAA_ECOLI Publication Abstract from PubMed DUF328 family proteins are present in many prokaryotes; however, their molecular activities are unknown. The Escherichia coli 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 in vitro 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-A 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. The DUF328 family member YaaA is a DNA-binding protein with a novel fold.,Prahlad J, Yuan Y, Lin J, Chang CW, Iwata-Reuyl D, Liu Y, de Crecy-Lagard V, Wilson MA J Biol Chem. 2020 Oct 9;295(41):14236-14247. doi: 10.1074/jbc.RA120.015055. Epub , 2020 Aug 12. PMID:32796037 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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