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Asymmetric photocross-linking pattern of restriction endonuclease EcoRII to the DNA recognition sequence

Item Type:Article
Title:Asymmetric photocross-linking pattern of restriction endonuclease EcoRII to the DNA recognition sequence
Creators Name:Muecke, M. and Pingoud, V. and Grelle, G. and Kraft, R. and Krueger, D.H. and Reuter, M.
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 iodopyrimidine 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 His36 and Tyr41 of this peptide indicates that Tyr41 is the amino acid involved in the cross-link and that it therefore contributes to specific DNA recognition by EcoRII.
Keywords:Base Sequence, Cross-Linking Reagents, DNA, DNA Mutational Analysis, High Pressure Liquid Chromatography, Histidine, Molecular Sequence Data, Mutation, Oligonucleotides, Peptides, Polyacrylamide Gel Electrophoresis, Protein Binding, Tertiary Protein Structure, Time Factors, Tryptophan, Type II Site-Specific Deoxyribonucleases
Source:Journal of Biological Chemistry
Publisher:American Society for Biochemistry and Molecular Biology
Page Range:14288-14293
Date:19 April 2002
Official Publication:https://doi.org/10.1074/jbc.M109311200
PubMed:View item in PubMed

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