The Met Repressor‐Operator Complex: DNA Recognition by β‐Strands^a

Abstract

The crystal structure of the E. coli met repressor in complex with a synthetic 19-base pair oligonucleotide reveals two dimeric repressor molecules bound to adjacent sites on the DNA. The oligonucleotide contains two adjacent repeats of an 8-mer known as a met-box, which represents the consensus of the met operator sites. Each met repressor dimer is centered on a met box and interacts with the adjacent dimer through antiparallel alpha-helices, which explained the observed cooperative nature of the binding. DNA binding takes place through the insertion of a beta-ribbon into the major groove of B-form DNA, representing a novel DNA binding motif. Sequence specificity arises from direct interactions between side chains of the beta-strands and the edges of the bases in the major groove. The local DNA conformation confers additional specificity through interactions between protein and the phosphate backbone. The repressor is activated through binding of S-adenosyl methionine (SAM), the corepressor, to the face opposite to that used for DNA binding. The lack of significant conformational change upon SAM binding, together with electrostatic calculations, suggests that DNA binding enhancement occurs through long-range electrostatic interactions.

Structural Basis of the Role of the NikA Ribbon-Helix-Helix Domain in Initiating Bacterial Conjugation

“…10,31,43 The mutation of the Arg residue on its antiparallel β-strands confirmed that NikA interacts also with the major groove of double-stranded B-form DNA in repeat A with the antiparallel β-strands. Most RHH proteins bind as tetramers with two dimeric DNA-binding domains to an operator sequence containing two tandem binding sites, usually arranged as an inverted repeat, which allows a mismatch of a few nucleotides.…”

HIV Tat, its TARgets and the control of viral gene expression

“…For example, BIV Tat has been observed to switch from a looser structure allowing for several non‐specific nucleic acid contacts to a defined β ribbon conformation only upon TAR binding[18]. Interestingly, this structural motif bears similarities to the 17‐residue β ribbon structure used by the bacterial Met repressor for recognition of target DNA[19]. This structural flexibility is also observable in the bacteriophage N protein, which, either free in solution or as a complex with non‐specific RNA, lacks recognizable structure and binds RNA sequences indiscriminately.…”

Effect of traY amber mutations on F-plasmid traY promoter activity in vivo

“…TraY belongs to a family of genetic regulatory proteins that are distinguished by DNA-binding domains composed of antiparallel ␤-sheets and including the Arc, Mnt, and MetJ repressor proteins (4,5,23,27). However, direct evidence that TraY has a genetic regulatory function is lacking.…”