Multiple Conformations of the Cytidine Repressor DNA-Binding Domain Coalesce to One upon Recognition of a Specific DNA Surface

Biochemistry ◽  
2011 ◽  
Vol 50 (31) ◽  
pp. 6622-6632 ◽  
Author(s):  
Colleen L. Moody ◽  
Vira Tretyachenko-Ladokhina ◽  
Thomas M. Laue ◽  
Donald F. Senear ◽  
Melanie J. Cocco
Keyword(s):  
Dna Binding ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Cytidine Repressor ◽  
Multiple Conformations

scholarly journals Structure and Dynamics of the Cytidine Repressor DNA-Binding Domain

2010 ◽  
Vol 98 (3) ◽  
pp. 660a
Author(s):  
Colleen L. Moody ◽  
Vira Tretyachenko-Ladokhina ◽  
Donald F. Senear ◽  
Melanie J. Cocco
Keyword(s):  
Dna Binding ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Structure And Dynamics ◽  
Cytidine Repressor

scholarly journals Dynamic Consequences of Specificity within the Cytidine Repressor DNA-Binding Domain

2021 ◽  
Vol 120 (3) ◽  
pp. 17a
Author(s):  
Jenaro Soto ◽  
Colleen Moody ◽  
Donald F. Senear ◽  
Melanie J. Cocco
Keyword(s):  
Dna Binding ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Cytidine Repressor

scholarly journals Dynamic Consequences of Specificity within the Cytidine Repressor DNA-Binding Domain

2021 ◽  
Author(s):  
Colleen L Moody ◽  
Jenaro Soto ◽  
Vira Tretyachenko-Ladokhina ◽  
Donald F Senear ◽  
Melanie J Cocco
Keyword(s):  
Dna Binding ◽  
Hydrogen Exchange ◽  
Intrinsically Disordered Protein ◽  
Structural Features ◽  
Binding Domain ◽  
Free State ◽  
Dna Binding Domain ◽  
Intrinsically Disordered ◽  
Cytidine Repressor ◽  
Half Site

The E. coli cytidine repressor (CytR) is a member of the LacR family of bacterial repressors that regulates nine operons with distinct spacing and orientations of recognition sites. Understanding the structural features of the CytR DNA-binding domain (DBD) when bound to DNA is critical to understanding differential mechanisms of gene regulation. We previously reported the structure of the CytR DBD monomer bound specifically to half-site DNA and found that the DBD exists as a three-helix bundle containing a canonical helix-turn-helix motif, similar to other proteins that interact with DNA [Moody, et al (2011), Biochemistry 50:6622-32]. We also studied the free state of the monomer and found that since NMR spectra show it populates up to four distinct conformations, the free state exists as an intrinsically disordered protein (IDP). Here, we present further analysis of the DBD structure and dynamics in the context of full-site operator or nonspecific DNA. DBDs bound to full-site DNA show one set of NMR signals, consistent with fast exchange between the two binding sites. When bound to full-length DNA, we observed only slight changes in structure compared to the monomer structure and no folding of the hinge helix. Notably, the CytR DBD behaves quite differently when bound to nonspecific DNA compared to LacR. A dearth of NOEs and complete lack of protection from hydrogen exchange are consistent with the protein populating a flexible, molten state when associated with DNA nonspecifically, similar to fuzzy complexes. The CytR DBD structure is significantly more stable when bound specifically to the udp half-site substrate. For CytR, the transition from nonspecific association to specific recognition results in substantial changes in protein mobility that are coupled to structural rearrangements. These effects are more pronounced in the CytR DBD compared to other LacR family members.

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

scholarly journals Primary structure of a glycosylated DNA-binding domain in human plasma fibronectin.

1985 ◽  
Vol 260 (4) ◽  
pp. 2301-2306
Author(s):  
H Pande ◽  
J Calaycay ◽  
D Hawke ◽  
C M Ben-Avram ◽  
J E Shively
Keyword(s):  
Dna Binding ◽  
Human Plasma ◽  
Primary Structure ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Plasma Fibronectin

scholarly journals Functional mechanisms of MYRF DNA-binding domain mutations implicated in birth defects

2021 ◽  
Vol 296 ◽  
pp. 100612
Author(s):  
Chuandong Fan ◽  
Hongjoo An ◽  
Mohamed Sharif ◽  
Dongkyeong Kim ◽  
Yungki Park
Keyword(s):  
Dna Binding ◽  
Birth Defects ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Functional Mechanisms
Sign in / Sign up

Export Citation Format

Share Document