Cyanobacterial response regulator PatA contains a conserved N-terminal domain (PATAN) with an alpha-helical insertion

• Published in: Bioinformatics Vol. 22; no. 11; pp. 1297 - 1301
• Main Authors: Makarova, Kira S., Koonin, Eugene V., Haselkorn, Robert, Galperin, Michael Y.
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 01.06.2006; Oxford Publishing Limited (England)
• Subjects: Amino Acid Sequence; Anabaena; Anabaena - metabolism; Archaea; Bacterial Physiological Phenomena; Bacterial Proteins - chemistry; Bacterial Proteins - physiology; Biological and medical sciences; Cell Differentiation; Cell Movement; Computational Biology - methods; Conserved Sequence; Cyanobacteria; Cyanophyta; Fundamental and applied biological sciences. Psychology; General aspects; Geobacter sulfurreducens; Helix-Turn-Helix Motifs; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Molecular Sequence Data; Myxococcus xanthus; Nitrogen fixation; Nostoc; Protein Binding; Protein Structure, Secondary; Protein Structure, Tertiary; Proteobacteria; Sequence Homology, Amino Acid; Synechocystis; Helicidae; Copy number; Interaction; Sequence alignment; Insertion; Mobility; Gastropoda; Regulator; Cell differentiation; Protein; Original document; Conserved sequence; Association; Pulmonata; Cyanobacteria; Helix; Bacteria; Invertebrata; Mollusca; Bioinformatics
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btl096

The cyanobacterium Anabaena (Nostoc) PCC 7120 responds to starvation for nitrogen compounds by differentiating approximately every 10th cell in the filament into nitrogen-fixing cells called heterocysts. Heterocyst formation is subject to complex regulation, which involves an unusual response regulator PatA that contains a CheY-like phosphoacceptor (receiver, REC) domain at its C-terminus. PatA-like response regulators are widespread in cyanobacteria; one of them regulates phototaxis in Synechocystis PCC 6803. Sequence analysis of PatA revealed, in addition to the REC domain, a previously undetected, conserved domain, which we named PATAN (after PatA N-terminus), and a potential helix–turn–helix (HTH) domain. PATAN domains are encoded in a variety of environmental bacteria and archaea, often in several copies per genome, and are typically associated with REC, Roadblock and other signal transduction domains, or with DNA-binding HTH domains. Many PATAN domains contain insertions of a small additional domain, termed α-clip, which is predicted to form a four-helix bundle. PATAN domains appear to participate in protein–protein interactions that regulate gliding motility and processes of cell development and differentiation in cyanobacteria and some proteobacteria, such as Myxococcus xanthus and Geobacter sulfurreducens. Contact: galperin@ncbi.nlm.nih.gov Supplementary information: