title: Asymmetric photocross-linking pattern of restriction endonuclease EcoRII to the DNA recognition sequence.
abstract: The EcoRII homodimer engages two of its recognition sequences (5'-CCWGG) simultaneously and is therefore a type IIE restriction endonuclease. To identify the amino acids of EcoRII that interact specifically with the recognition sequence, we photocross-linked EcoRII with oligonucleotide substrates that contained only one recognition sequence for EcoRII. In this recognition sequence, we substituted either 5-iododeoxycytidine for each C or 5-iododeoxyuridine for A, G, or T. These iodo-pyrimidine bases were excited using a UV laser to result in covalent cross-linking products. The yield of EcoRII photocross-linked to the 5'-C of the 5'-CCAGG strand of the recognition sequence was 45%. However, we could not photocross-link EcoRII to the 5'-C of the 5'-CCTGG strand. Thus, the contact of EcoRII to the bases of the recognition sequence appears to be asymmetric, unlike that expected for most type II restriction endonucleases. Tryptic digestion of free and of cross-linked EcoRII, followed by high performance liquid chromatography (HPLC) separation of the individual peptides and Edman degradation, identified amino acids 25-49 of EcoRII as the cross-linking peptide. Mutational analysis of the electron-rich amino acids His(36) and Tyr(41) of this peptide indicates that Tyr(41) is the amino acid involved in the cross-link and that it therefore contributes to specific DNA recognition by EcoRII.
authors.affiliation: Institut für Virologie, Medizinische Fakultät der Humboldt-Universität zu Berlin (Charité), D-10098 Berlin, Germany.
authors.forename: Merlind
authors.initials: M
authors.lastname: Mücke
authors.forename: Vera
authors.initials: V
authors.lastname: Pingoud
authors.forename: Gerlinde
authors.initials: G
authors.lastname: Grelle
authors.forename: Regine
authors.initials: R
authors.lastname: Kraft
authors.forename: Detlev H
authors.initials: DH
authors.lastname: Krüger
authors.forename: Monika
authors.initials: M
authors.lastname: Reuter
mesh_terms: D001483:Base Sequence; D002851:Chromatography, High Pressure Liquid; D003432:Cross-Linking Reagents / Q000494:pharmacology*; D004247:DNA / Q000378:metabolism*; D004252:DNA Mutational Analysis; D015252:Deoxyribonucleases, Type II Site-Specific / Q000737:chemistry* / Q000378:metabolism*; D004591:Electrophoresis, Polyacrylamide Gel; D006639:Histidine / Q000737:chemistry; D008969:Molecular Sequence Data; D009154:Mutation; D009841:Oligonucleotides / Q000737:chemistry; D010455:Peptides / Q000737:chemistry; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D013997:Time Factors; D014364:Tryptophan / Q000737:chemistry
chemical_list: D003432:Cross-Linking Reagents; D009841:Oligonucleotides; D010455:Peptides; D006639:Histidine; D014364:Tryptophan; D004247:DNA; C046545:CCWGG-specific type II deoxyribonucleases; D015252:Deoxyribonucleases, Type II Site-Specific