Proton NMR studies of DNA recognition by the glucocorticoid receptor: complex of the DNA binding domain with a half-site response element

Biochemistry ◽  
1991 ◽  
Vol 30 (50) ◽  
pp. 11620-11624 ◽  
Author(s):  
M. L. Remerowski ◽  
E. Kellenbach ◽  
R. Boelens ◽  
G. A. Van der Marel ◽  
J. H. Van Boom ◽  
...  
Keyword(s):  
Dna Binding ◽  
Glucocorticoid Receptor ◽  
Site Response ◽  
Dna Recognition ◽  
Proton Nmr ◽  
Receptor Complex ◽  
Dna Binding Domain ◽  
Nmr Studies ◽  
Response Element ◽  
Half Site

Proton NMR studies of the glucocorticoid receptor DNA-binding domain: sequential assignments and identification of secondary structure elements

Biochemistry ◽  
1990 ◽  
Vol 29 (38) ◽  
pp. 9015-9023 ◽  
Author(s):  
T. Haerd ◽  
E. Kellenbach ◽  
R. Boelens ◽  
K. Dahlman ◽  
J. Carlstedt-Duke ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Dna Binding ◽  
Glucocorticoid Receptor ◽  
Proton Nmr ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Nmr Studies

The DNA-binding domain of BenM reveals the structural basis for the recognition of a T-N11-A sequence motif by LysR-type transcriptional regulators

2013 ◽  
Vol 69 (10) ◽  
pp. 1995-2007 ◽  
Author(s):  
Amer M. Alanazi ◽  
Ellen L. Neidle ◽  
Cory Momany
Keyword(s):  
Amino Acids ◽  
Dna Binding ◽  
Dna Recognition ◽  
Transcriptional Regulators ◽  
Binding Domain ◽  
Structural Basis ◽  
Binding Motif ◽  
Sequence Motif ◽  
Dna Binding Domain ◽  
Half Site

LysR-type transcriptional regulators (LTTRs) play critical roles in metabolism and constitute the largest family of bacterial regulators. To understand protein–DNA interactions, atomic structures of the DNA-binding domain and linker-helix regions of a prototypical LTTR, BenM, were determined by X-ray crystallography. BenM structures with and without bound DNA reveal a set of highly conserved amino acids that interact directly with DNA bases. At the N-terminal end of the recognition helix (α3) of a winged-helix–turn–helix DNA-binding motif, several residues create hydrophobic pockets (Pro30, Pro31 and Ser33). These pockets interact with the methyl groups of two thymines in the DNA-recognition motif and its complementary strand, T-N11-A. This motif usually includes some dyad symmetry, as exemplified by a sequence that binds two subunits of a BenM tetramer (ATAC-N7-GTAT). Gln29 forms hydrogen bonds to adenine in the first position of the recognition half-site (ATAC). Another hydrophobic pocket defined by Ala28, Pro30 and Pro31 interacts with the methyl group of thymine, complementary to the base at the third position of the half-site. Arg34 interacts with the complementary base of the 3′ position. Arg53, in the wing, provides AT-tract recognition in the minor groove. For DNA recognition, LTTRs use highly conserved interactions between amino acids and nucleotide bases as well as numerous less-conserved secondary interactions.

Cadmium-113 NMR studies of the DNA binding domain of the mammalian glucocorticoid receptor

Biochemistry ◽  
1990 ◽  
Vol 29 (39) ◽  
pp. 9218-9225 ◽  
Author(s):  
Tao Pan ◽  
Leonard P. Freedman ◽  
Joseph E. Coleman
Keyword(s):  
Dna Binding ◽  
Glucocorticoid Receptor ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Nmr Studies

scholarly journals Cooperative interaction of oestrogen receptor ‘zinc finger’ domain polypeptides on DNA binding

1995 ◽  
Vol 305 (3) ◽  
pp. 805-810 ◽  
Author(s):  
P F Predki ◽  
B Sarkar
Keyword(s):  
Retinoic Acid ◽  
Dna Binding ◽  
Oestrogen Receptor ◽  
Binding Domain ◽  
The Other ◽  
Cooperative Interaction ◽  
Dna Binding Domain ◽  
Response Element ◽  
Response Elements ◽  
Half Site

The consensus oestrogen response element (ERE) contains two inverted copies of an AGGTCA consensus hexameric half-site, spaced by three base pairs. It differs from many other hormone response elements, such as consensus thyroid (TREp) and retinoic acid (DR-5 RARE) response elements, only in the relative spacing and orientation of these sequences. In the present study we report values for cooperativity (omega) of an oestrogen receptor DNA-binding domain polypeptide upon binding to these sequences. The polypeptide binds with negative cooperativity, or without cooperativity to retinoic acid and thyroid response elements respectively, but with high cooperativity to the ERE. We have also examined cooperativity upon binding of the polypeptide to an ERE variant. Since naturally occurring EREs commonly contain one hexamer which is considerably more degenerate than the other, we designed a hybrid response element in which one hexamer is a consensus ERE, while specific mutations were introduced into the other. We chose to mutate the second half-site to a glucocorticoid response element (GRE) half-site sequence (AGAACA), since normally no binding of the DNA-binding domain polypeptide to a GRE hexamer alone can be detected. In the hybrid response element, however, the GRE half-site is recognized with relatively high affinity, although binding to this sequence is dependent on the previous binding of a polypeptide to the ERE hexamer. Thus, cooperative interactions are capable of mediating the recognition of ERE sequence degeneracy. The ability of protein-protein interactions to mediate recognition of DNA sequence degeneracy may also have implications for transcription factors in general.

NMR studies of the R2 repeat and related peptide fragments of the DNA binding domain of c-Myb. New light on the structure and folding of R2.

1999 ◽  
Vol 96 (9/10) ◽  
pp. 1580-1584 ◽  
Author(s):  
I. Ségalas ◽  
S. Desjardins ◽  
H. Oulyadi ◽  
Y. Prigent ◽  
S. Tribouillard ◽  
...  
Keyword(s):  
Dna Binding ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Peptide Fragments ◽  
Nmr Studies ◽  
Related Peptide
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