7BV9

The NMR structure of the BEN domain from human NAC1

Summary for 7BV9

• Entry DOI: 10.2210/pdb7bv9/pdb
• NMR Information: BMRB: 36342
• Descriptor: Nucleus accumbens-associated protein 1 (1 entity in total)
• Functional Keywords: dna-binding cancer stem cell, nuclear protein
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 1
• Total formula weight: 18637.48

Authors

Nagata, T.,Kobayashi, N.,Nakayama, N.,Obayashi, E.,Urano, T. (deposition date: 2020-04-09, release date: 2021-02-17, Last modification date: 2024-05-15)

Primary citation

Nakayama, N.,Sakashita, G.,Nagata, T.,Kobayashi, N.,Yoshida, H.,Park, S.Y.,Nariai, Y.,Kato, H.,Obayashi, E.,Nakayama, K.,Kyo, S.,Urano, T.
Nucleus Accumbens-Associated Protein 1 Binds DNA Directly through the BEN Domain in a Sequence-Specific Manner.
Biomedicines, 8:-, 2020

PubMed Abstract: Nucleus accumbens-associated protein 1 (NAC1) is a nuclear protein that harbors an amino-terminal BTB domain and a carboxyl-terminal BEN domain. NAC1 appears to play significant and diverse functions in cancer and stem cell biology. Here we demonstrated that the BEN domain of NAC1 is a sequence-specific DNA-binding domain. We selected the palindromic 6 bp motif ACATGT as a target sequence by using a PCR-assisted random oligonucleotide selection approach. The interaction between NAC1 and target DNA was characterized by gel shift assays, pull-down assays, isothermal titration calorimetry (ITC), chromatin-immunoprecipitation assays, and NMR chemical shifts perturbation (CSP). The solution NMR structure revealed that the BEN domain of human NAC-1 is composed of five conserved α helices and two short β sheets, with an additional hitherto unknown N-terminal α helix. In particular, ITC clarified that there are two sequential events in the titration of the BEN domain of NAC1 into the target DNA. The ITC results were further supported by CSP data and structure analyses. Furthermore, live cell photobleaching analyses revealed that the BEN domain of NAC1 alone was unable to interact with chromatin/other proteins in cells.

PubMed: 33327466
DOI: 10.3390/biomedicines8120608

Experimental method

SOLUTION NMR