title: The Ku-Mar zinc finger: A segment-swapped zinc ribbon in MarR-like transcription regulators related to the Ku bridge.
abstract: Two putative oxidative-stress sensor proteins from Pseudomonas aeruginosa, PA1607 and PA1374, belong to the MarR family of transcription regulators and possess a unique mode of dimerization. In these proteins, in addition to the α-helices involved in dimerization, inter-subunit contacts are strengthened by additional C-terminal β-strands. Using sequence and structure analysis we show that these β-strands constitute a novel segment-swapped zinc ribbon domain. We detect the presence of the zinc ribbon domain in MarR proteins from many bacterial homologs. While the metal-chelating residues of the zinc ribbons are absent in most members of this family, we could however identify several species of Proteobacteria, Actinobacteria and Firmicutes that possess intact zinc-chelating sites. Conservation pattern of metal-chelating residues together with the extensive structural resemblance to zinc ribbons, in particular to the bridge-region of the dsDNA break repair protein Ku, suggests that the C-terminal β-rich region of these proteins is a zinc ribbon. Sequence analysis also supports a distant evolutionary connection between the zinc ribbons of the MarR and Ku families. However, unlike Ku where the segment-swapped zinc ribbons play a role in DNA-binding and obligate dimerization, their primary role in MarR appears to be in dimerization and strengthening of inter-subunit contacts.
authors.affiliation: CSIR-Institute of Microbial Technology (IMTECH), Sector 39-A, Chandigarh 160036, India. Electronic address: gurmeetkaur@imtech.res.in.
authors.forename: Gurmeet
authors.initials: G
authors.lastname: Kaur
authors.affiliation: CSIR-Institute of Microbial Technology (IMTECH), Sector 39-A, Chandigarh 160036, India. Electronic address: krishna@imtech.res.in.
authors.forename: Srikrishna
authors.initials: S
authors.lastname: Subramanian
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000235:genetics*; D004268:DNA-Binding Proteins / Q000235:genetics; D019281:Dimerization; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary; D011550:Pseudomonas aeruginosa / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D014158:Transcription, Genetic / Q000235:genetics*; D015032:Zinc / Q000378:metabolism*; D016335:Zinc Fingers / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; D015032:Zinc
keywords: DNA-binding proteins; Dimerization; Helix-turn-helix domain; Multidrug resistance; Segment-swapping; Zinc ribbon