Binding sites of different geometries for the 16-3 phage repressor

Péter P. Papp, Tibor Nagy, Szilamér Ferenczi, Péter Élõ, Zsolt Csiszovszki, Zsuzsanna Buzás, András Patthy, László Orosz

Research output: Contribution to journalArticle

9 Citations (Scopus)


Prokaryotic repressor-operator systems provide exemplars for the sequence-specific interactions between DNA and protein. The crucial atomic contacts of the two macromolecules are attained in a compact, geometrically defined structure of the DNA-protein complex, The pitch of the DNA interface seems an especially sensitive part of this architecture because changes in its length introduce new spacing and rotational relations in one step. We discovered a natural system that may serve as a model for investigating this problem: the repressor of the 16-3 phage of Rhizobium meliloti (helix-turn-helix class protein) possesses inherent ability to accommodate to various DNA twistings. It binds the cognate operators, which are 5′-ACAA-4 bp-TTGT-3′ (OL) and 5′-ACAA-6 bp-TTGT-3′ (OR) and thus differ 2 bp in length, and consequently the two half-sites will be rotated with respect to each other by 72° in the idealized B-DNA (64° by dinucleotide steps calculations). Furthermore, a synthetic intermediate (DNA sequence) 5′-ACAA-5 bp-TTGT-3′ (O5) also binds specifically the repressor. The natural operators and bound repressors can form higher order DNAprotein complexes and perform efficient repression, whereas the synthetic operator-repressor complex cannot do either. The natural operators are bent when complexed with the repressor, whereas the Os operator does not show bending in electrophoretic mobility assay. Possible structures of the complexes are discussed.

Original languageEnglish
Pages (from-to)8790-8795
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number13
Publication statusPublished - Jun 25 2002


  • DNA-protein interactions
  • Repressor-operator binding
  • Rhizobium phage
  • Transcription regulation

ASJC Scopus subject areas

  • General

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