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Issue 2, 2005
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Identification of base-specific contacts in protein–DNA complexes by photocrosslinking and mass spectrometry: a case study using the restriction endonuclease SsoII

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Abstract

Specific protein–nucleic acid interactions are of paramount importance for the propagation, maintenance and expression of genetic information. Restriction endonucleases serve as model systems to study the mechanisms of DNA recognition by proteins. SsoII is a Type II restriction endonuclease that recognizes the double stranded sequence ↓CCNGG and cleaves it in the presence of Mg2+-ions, as indicated. SsoII shows sequence similarity over a stretch of ∼70 amino acid residues with several other restriction endonucleases that recognize a similar sequence as SsoII (Cfr10I, EcoRII, NgoMIV, PspGI). In NgoMIV this stretch is involved in DNA recognition and cleavage, as shown by the crystal structure analysis of an enzyme–product complex. To find out whether the presumptive DNA recognition region in SsoII is indeed in contact with DNA we have photocrosslinked SsoII with an oligodeoxyribonucleotide in which the first guanine of the recognition sequence was replaced by 5-iodouracil. Following digestion by trypsin, the peptide–oligodeoxyribonucleotide conjugate was purified by Fe3+-IMAC and then incubated with hydrogen fluoride, which hydrolyzes the oligodeoxyribonucleotide to yield the peptide–deoxyuridine conjugate. The site of photocrosslinking was identified by MALDI-TOF-MS and MALDI-TOF-MS/MS to be Trp189, adjacent to Arg188, which aligns with Arg194 in NgoMIV, involved in recognition of the second guanine in the NgoMIV recognition sequence G↓CCGGC. This result confirms previously published conclusions drawn on the basis of a mutational analysis of SsoII. The methodology that was employed here can be used in principle to identify the DNA binding site of any protein.

Graphical abstract: Identification of base-specific contacts in protein–DNA complexes by photocrosslinking and mass spectrometry: a case study using the restriction endonuclease SsoII

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Publication details

The article was received on 03 Mar 2005, accepted on 20 May 2005 and first published on 09 Jun 2005


Article type: Method
DOI: 10.1039/B503091A
Mol. BioSyst., 2005,1, 135-141

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    Identification of base-specific contacts in protein–DNA complexes by photocrosslinking and mass spectrometry: a case study using the restriction endonuclease SsoII

    V. Pingoud, H. Geyer, R. Geyer, E. Kubareva, J. M. Bujnicki and A. Pingoud, Mol. BioSyst., 2005, 1, 135
    DOI: 10.1039/B503091A

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