title: Bioinformatic analysis of ClpS, a protein module involved in prokaryotic and eukaryotic protein degradation.
abstract: ClpS is a small protein, usually encoded immediately upstream of ClpA in the genomes of proteobacteria. Recent results show that it is a molecular adaptor for substrate recognition by ClpA in Escherichia coli. We analyzed ClpS by bioinformatic methods and found that ClpS homologs are also found in organisms that lack ClpA, such as actinobacteria, cyanobacteria, and plant chloroplasts. Furthermore, ClpS is homologous to a domain in the eukaryotic E3 ubiquitin ligase, N-recognin. This domain has previously been described as responsible for the recognition of type 2 N-end rule substrates. Despite very low levels of sequence similarity to proteins of known structure, there appears to be substantial structural similarity between ClpS and the C-terminal domain of ribosomal protein L7/12 (1CTF).
authors.affiliation: Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, Spemannstr. 35, D-72076 Tübingen, Germany. andrei.lupas@tuebingen.mpg.de
authors.forename: Andrei N
authors.initials: AN
authors.lastname: Lupas
authors.forename: Kristin K
authors.initials: KK
authors.lastname: Koretke
mesh_terms: D000251:Adenosine Triphosphatases / Q000737:chemistry; D000595:Amino Acid Sequence; D002352:Carrier Proteins / Q000737:chemistry*; D019295:Computational Biology / Q000379:methods*; D018360:Crystallography, X-Ray; D019992:Databases as Topic; D049071:Endopeptidase Clp; D004926:Escherichia coli / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry*; D008025:Ligases / Q000737:chemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry; D017386:Sequence Homology, Amino Acid; D012697:Serine Endopeptidases / Q000737:chemistry; D044767:Ubiquitin-Protein Ligases
chemical_list: D002352:Carrier Proteins; C454820:ClpS protein, E coli; D029968:Escherichia coli Proteins; D029701:Saccharomyces cerevisiae Proteins; C066066:UBR1 protein, S cerevisiae; D044767:Ubiquitin-Protein Ligases; D012697:Serine Endopeptidases; C483568:ClpA protease, E coli; D049071:Endopeptidase Clp; D000251:Adenosine Triphosphatases; D008025:Ligases