A dodecapeptide comprising the extended chain-alpha 4 region of the restriction endonuclease EcoRI specifically binds to the EcoRI recognition site

Regions of endonuclease EcoRII involved in DNA target recognition identified by membrane-bound peptide repertoires

Target sequence-specific DNA binding regions of the restriction endonuclease EcoRII were identified by screening a membrane-bound EcoRII-derived peptide scan with an EcoRII recognition site (CCWGG) oligonucleotide duplex. Dodecapeptides overlapping by nine amino acids and representing the complete protein were prepared by spot synthesis. Two separate DNA binding regions, amino acids 88-102 and amino acids 256-273, which share the consensus motif KXRXXK, emerged. Screening 570 single substitution analogues obtained by exchanging every residue of both binding sites for all other amino acids demonstrated that replacing basic residues in the consensus motifs significantly reduced DNA binding. EcoRII mutant enzymes generated by substituting alanine or glutamic acid for the consensus lysine residues in DNA binding site I expressed attenuated DNA binding, whereas corresponding substitutions in DNA binding site II caused impaired cleavage, but enzyme secondary structure was unaffected. Furthermore, Glu96, which is part of a potential catalytic motif and also locates to DNA binding site I, was demonstrated to be critical for DNA cleavage and binding. Homology studies of DNA binding site II revealed strong local homology to SsoII (recognition sequence, CCNGG) and patterns of sequence conservation, suggesting the existence of functionally related DNA binding sites in diverse restriction endonucleases with recognition sequences containing terminal C:G or G:C pairs.

Asn141 is essential for DNA recognition by EcoRI restriction endonuclease

The amino acid residue Asn141 of the restriction endonuclease EcoRI was proposed to make three hydrogen bonds to both adenine residues within the recognition sequence -GAATTC-. We have mutated Asn141 to alanine, aspartate, serine, and tyrosine. Only the serine mutant is active under normal buffer conditions although 1000-fold less than wild-type EcoRI. The alanine and aspartate mutants can be activated by Mn2+. At acidic pH the latter mutant becomes even more active than the wild-type enzyme in the presence of Mn2+. We conclude that Asn141 is essential for DNA recognition and that serine can partly substitute it.

Recognition and cleavage of DNA by type-II restriction endonucleases

Restriction endonucleases are enzymes which recognize short DNA sequences and cleave the DNA in both strands. Depending on the enzymological properties different types are distinguished. Type II restriction endonucleases are homodimers which recognize short palindromic sequences 4-8 bp in length and, in the presence of Mg2+, cleave the DNA within or next to the recognition site. They are capable of non-specific binding to DNA and make use of linear diffusion to locate their target site. Binding and recognition of the specific site involves contacts to the bases of the recognition sequence and the phosphodiester backbone over approximately 10-12 bp. In general, recognition is highly redundant which explains the extreme specificity of these enzymes. Specific binding is accompanied by conformational changes over both the protein and the DNA. This mutual induced fit leads to the activation of the catalytic centers. The precise mechanism of cleavage has not yet been established for any restriction endonuclease. Currently two models are discussed: the substrate-assisted catalysis mechanism and the two-metal-ion mechanism. Structural similarities identified between EcoRI, EcoRV, BamHI, PvuII and Cfr10I suggest that many type II restriction endonucleases are not only functionally but also evolutionarily related.

Influence of divalent cations on inner-arm mutants of restriction endonuclease EcoRI

To understand the functional role of the inner arm region of EcoRI for the interaction with its DNA substrate, we mutated each of the positively charged amino acid residues Lys130 and Arg131 to Ala or Glu. The resulting cleavage activities are only about tenfold reduced but DNA binding in the absence of divalent cations is totally disrupted for three of the mutants ([Ala130]EcoRI, [Glu130]EcoRI and [Glu131]EcoRI). The binding can be rescued by adding 1 mM Ca2+. This binding behaviour resembles that of the blunt end cutter EcoRV. Furthermore, the cleavage activity of the [Glu130]EcoRI is stimulated by Ca2+. Therefore, a second metal binding site is involved in [Glu130]EcoRI catalyzed DNA cleavage. Its location is postulated to be in the inner arm region at positions 133 and 135 presenting an Asp-Xaa-Asp motif typical for Ca2+ binding. A net positive charge at the tip of the inner arm due to the basic amino acids Lys130 and Arg131 in the wild-type enzyme or due to binding of a divalent cation in the mutants is important for DNA recognition by EcoRI. However, a direct phosphate contact providing an indirect readout is not observed. Implications of the binding and cleavage behaviour with regard to mechanistic differences between blunt end and sticky end cutters and a general catalytic mechanism of restriction enzymes are discussed.

Asp-59 is not important for the catalytic activity of the restriction endonuclease EcoRI

The amino acid Asp-59 was proposed to be involved in EcoRI catalyzed DNA cleavage (Cheng et al., EMBO J. 13, 3927-35, 1994). We have tested this hypothesis by site directed mutagenesis experiments. The four mutants D59A, D59E, D59G, and D59N bind with similar stability to the specific recognition sequence as wild type EcoRI. The D59E mutant cleaves DNA as fast as the wild type enzyme. Specific activities of the other three mutants are five to tenfold lower. Therefore, we conclude that Asp-59 is not involved in catalysis of the EcoRI restriction endonuclease. Consequences for catalytic mechanisms of EcoRI and other restriction enzymes are discussed.