scholarly journals Engineering a trifunctional proline utilization A chimaera by fusing a DNA-binding domain to a bifunctional PutA

2016 ◽  
Vol 36 (6) ◽  
Author(s):  
Benjamin W. Arentson ◽  
Erin L. Hayes ◽  
Weidong Zhu ◽  
Harkewal Singh ◽  
John J. Tanner ◽  
...  
Keyword(s):  
Dna Binding ◽  
Modular Design ◽  
Quaternary Structure ◽  
Lipid Binding ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Oligomeric State ◽  
Proline Utilization ◽  
Functional Switching ◽  
Proline Utilization A

Proline utilization A (PutA) is a bifunctional flavoenzyme with proline dehydrogenase (PRODH) and Δ1-pyrroline-5-carboxylate (P5C) dehydrogenase (P5CDH) domains that catalyses the two-step oxidation of proline to glutamate. Trifunctional PutAs also have an N-terminal ribbon–helix–helix (RHH) DNA-binding domain and moonlight as autogenous transcriptional repressors of the put regulon. A unique property of trifunctional PutA is the ability to switch functions from DNA-bound repressor to membrane-associated enzyme in response to cellular nutritional needs and proline availability. In the present study, we attempt to construct a trifunctional PutA by fusing the RHH domain of Escherichia coli PutA (EcRHH) to the bifunctional Rhodobacter capsulatus PutA (RcPutA) in order to explore the modular design of functional switching in trifunctional PutAs. The EcRHH–RcPutA chimaera retains the catalytic properties of RcPutA while acquiring the oligomeric state, quaternary structure and DNA-binding properties of EcPutA. Furthermore, the EcRHH–RcPutA chimaera exhibits proline-induced lipid association, which is a fundamental characteristic of functional switching. Unexpectedly, RcPutA lipid binding is also activated by proline, which shows for the first time that bifunctional PutAs exhibit a limited form of functional switching. Altogether, these results suggest that the C-terminal domain (CTD), which is conserved by trifunctional PutAs and certain bifunctional PutAs, is essential for functional switching in trifunctional PutAs.

scholarly journals Crystal structure of the DNA binding domain of the transcription factor T-bet suggests simultaneous recognition of distant genome sites

2016 ◽  
Vol 113 (43) ◽  
pp. E6572-E6581 ◽  
Author(s):  
Ce Feng Liu ◽  
Gabriel S. Brandt ◽  
Quyen Q. Hoang ◽  
Natalia Naumova ◽  
Vanja Lazarevic ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Transcription Factor ◽  
Dna Binding ◽  
Quaternary Structure ◽  
Regulatory Element ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Chromosome Conformation

The transcription factor T-bet (Tbox protein expressed in T cells) is one of the master regulators of both the innate and adaptive immune responses. It plays a central role in T-cell lineage commitment, where it controls the TH1 response, and in gene regulation in plasma B-cells and dendritic cells. T-bet is a member of the Tbox family of transcription factors; however, T-bet coordinately regulates the expression of many more genes than other Tbox proteins. A central unresolved question is how T-bet is able to simultaneously recognize distant Tbox binding sites, which may be located thousands of base pairs away. We have determined the crystal structure of the Tbox DNA binding domain (DBD) of T-bet in complex with a palindromic DNA. The structure shows a quaternary structure in which the T-bet dimer has its DNA binding regions splayed far apart, making it impossible for a single dimer to bind both sites of the DNA palindrome. In contrast to most other Tbox proteins, a single T-bet DBD dimer binds simultaneously to identical half-sites on two independent DNA. A fluorescence-based assay confirms that T-bet dimers are able to bring two independent DNA molecules into close juxtaposition. Furthermore, chromosome conformation capture assays confirm that T-bet functions in the direct formation of chromatin loops in vitro and in vivo. The data are consistent with a looping/synapsing model for transcriptional regulation by T-bet in which a single dimer of the transcription factor can recognize and coalesce distinct genetic elements, either a promoter plus a distant regulatory element, or promoters on two different genes.

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

scholarly journals Poly(ADP-ribose) synthetase. The DNA binding domain and the automodification domain.

1982 ◽  
Vol 257 (11) ◽  
pp. 6102-6105
Author(s):  
M Nishikimi ◽  
K Ogasawara ◽  
I Kameshita ◽  
T Taniguchi ◽  
Y Shizuta
Keyword(s):  
Dna Binding ◽  
Binding Domain ◽  
Dna Binding Domain

Structural basis of the p53 DNA binding domain and PUMA complex

2021 ◽  
Vol 548 ◽  
pp. 39-46
Author(s):  
Chang Woo Han ◽  
Han Na Lee ◽  
Mi Suk Jeong ◽  
So Young Park ◽  
Se Bok Jang
Keyword(s):  
Dna Binding ◽  
Binding Domain ◽  
Structural Basis ◽  
Dna Binding Domain
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