A universal protein-protein interaction motif in the eubacterial DNA replication and repair systems.
The interaction between DNA polymerases and sliding clamp proteins confers processivity in DNA synthesis. This interaction is critical for most DNA replication machines from viruses and prokaryotes to higher eukaryotes. The clamp proteins also participate in a variety of dynamic and competing protein-protein interactions. However, clamp-protein binding sequences have not so far been identified in the eubacteria. Here we show from three lines of evidence, bioinformatics, yeast two-hybrid analysis, and inhibition of protein-protein interaction by modified peptides, that variants of a pentapeptide motif (consensus QL[SD]LF) are sufficient to enable interaction of a number of proteins with an archetypal eubacterial sliding clamp (the beta subunit of Escherichia coli DNA polymerase III holoenzyme). Representatives of this motif are present in most sequenced members of the eubacterial DnaE, PolC, PolB, DinB, and UmuC families of DNA polymerases and the MutS1 mismatch repair protein family. The component tripeptide DLF inhibits the binding of the alpha (DnaE) subunit of E. coli DNA polymerase III to beta at microM concentration, identifying key residues. Comparison of the eubacterial, eukaryotic, and archaeal sliding clamp binding motifs suggests that the basic interactions have been conserved across the evolutionary landscape.
Dalrymple
B P
BP
Commonwealth Scientific and Industrial Research Organisation Livestock Industries, 120 Meiers Road, Indooroopilly QLD 4068, Australia.
Kongsuwan
K
K
Wijffels
G
G
Dixon
N E
NE
Jennings
P A
PA
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D001665:Binding Sites; D002876:Chromosomes, Bacterial / Q000235:genetics; D004258:DNA Polymerase III / Q000235:genetics / Q000378:metabolism; D004260:DNA Repair; D004261:DNA Replication; D016208:Databases, Factual; D015246:Deoxyribonuclease EcoRI / Q000378:metabolism; D018259:Herpesvirus 1, Human / Q000235:genetics; D007700:Kinetics; D008969:Molecular Sequence Data; D005810:Multigene Family; D016254:Mutagenesis, Insertional; D016297:Mutagenesis, Site-Directed; D016133:Polymerase Chain Reaction; D018809:Proliferating Cell Nuclear Antigen / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D014176:Protein Biosynthesis; D021122:Protein Subunits; D011993:Recombinant Fusion Proteins / Q000378:metabolism; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D012697:Serine Endopeptidases / Q000235:genetics / Q000378:metabolism; D000099160:LexA Repressor Protein
D001426:Bacterial Proteins; D004258:DNA Polymerase III; D015246:Deoxyribonuclease EcoRI; D018809:Proliferating Cell Nuclear Antigen; D021122:Protein Subunits; D011993:Recombinant Fusion Proteins; D012697:Serine Endopeptidases; D000099160:LexA Repressor Protein; C074904:DNA polymerase III, alpha subunit