title: A unique uracil-DNA binding protein of the uracil DNA glycosylase superfamily.
abstract: Uracil DNA glycosylases (UDGs) are an important group of DNA repair enzymes, which pioneer the base excision repair pathway by recognizing and excising uracil from DNA. Based on two short conserved sequences (motifs A and B), UDGs have been classified into six families. Here we report a novel UDG, UdgX, from Mycobacterium smegmatis and other organisms. UdgX specifically recognizes uracil in DNA, forms a tight complex stable to sodium dodecyl sulphate, 2-mercaptoethanol, urea and heat treatment, and shows no detectable uracil excision. UdgX shares highest homology to family 4 UDGs possessing Fe-S cluster. UdgX possesses a conserved sequence, KRRIH, which forms a flexible loop playing an important role in its activity. Mutations of H in the KRRIH sequence to S, G, A or Q lead to gain of uracil excision activity in MsmUdgX, establishing it as a novel member of the UDG superfamily. Our observations suggest that UdgX marks the uracil-DNA for its repair by a RecA dependent process. Finally, we observed that the tight binding activity of UdgX is useful in detecting uracils in the genomes.
authors: Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India.
authors: Pau Biak
authors: PB
authors: Sang
authors: Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India.
authors: Thiruneelakantan
authors: T
authors: Srinath
authors: Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India.
authors: Aravind Goud
authors: AG
authors: Patil
authors: Functional Genomic Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahakro, Yuseongu, Daejeon, South Korea.
authors: Eui-Jeon
authors: EJ
authors: Woo
authors: Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, 560064, India varshney@mcbl.iisc.ernet.in.
authors: Umesh
authors: U
authors: Varshney
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D004260:DNA Repair; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D009154:Mutation; D020102:Mycobacterium smegmatis / Q000201:enzymology; D011938:Rec A Recombinases / Q000378:metabolism; D017386:Sequence Homology, Amino Acid; D040681:Structural Homology, Protein; D014498:Uracil / Q000378:metabolism*; D051981:Uracil-DNA Glycosidase / Q000737:chemistry / Q000145:classification / Q000235:genetics / Q000378:metabolism*; D014764:Viral Proteins / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; D014764:Viral Proteins; C027619:uracil-DNA glycosylase inhibitor protein, B. subtilis bacteriophage; D014498:Uracil; D004247:DNA; D011938:Rec A Recombinases; D051981:Uracil-DNA Glycosidase