3BBC

Crystal structure of R88A mutant of the NM23-H2 transcription factor

Summary for 3BBC

• Entry DOI: 10.2210/pdb3bbc/pdb
• Related: 1NUE 3BBB 3BBF
• Descriptor: Nucleoside diphosphate kinase B (2 entities in total)
• Functional Keywords: transcriptional factor, kinase, nm23 gen, hexamer, cancer, activator, anti-oncogene, atp-binding, cell cycle, dna-binding, magnesium, metal-binding, nucleotide metabolism, nucleotide-binding, nucleus, phosphorylation, transcription regulation, transferase
• Biological source: Homo sapiens (Human)
• Cellular location: Cytoplasm: P22392
• Total number of polymer chains: 6
• Total formula weight: 102640.46

Authors

Weichsel, A.,Montfort, W.R. (deposition date: 2007-11-09, release date: 2008-09-23, Last modification date: 2023-08-30)

Primary citation

Dexheimer, T.S.,Carey, S.S.,Zuohe, S.,Gokhale, V.M.,Hu, X.,Murata, L.B.,Maes, E.M.,Weichsel, A.,Sun, D.,Meuillet, E.J.,Montfort, W.R.,Hurley, L.H.
NM23-H2 may play an indirect role in transcriptional activation of c-myc gene expression but does not cleave the nuclease hypersensitive element III1.
Mol.Cancer Ther., 8:1363-1377, 2009

PubMed Abstract: The formation of G-quadruplex structures within the nuclease hypersensitive element (NHE) III(1) region of the c-myc promoter and the ability of these structures to repress c-myc transcription have been well established. However, just how these extremely stable DNA secondary structures are transformed to activate c-myc transcription is still unknown. NM23-H2/nucleoside diphosphate kinase B has been recognized as an activator of c-myc transcription via interactions with the NHE III(1) region of the c-myc gene promoter. Through the use of RNA interference, we confirmed the transcriptional regulatory role of NM23-H2. In addition, we find that further purification of NM23-H2 results in loss of the previously identified DNA strand cleavage activity, but retention of its DNA binding activity. NM23-H2 binds to both single-stranded guanine- and cytosine-rich strands of the c-myc NHE III(1) and, to a lesser extent, to a random single-stranded DNA template. However, it does not bind to or cleave the NHE III(1) in duplex form. Significantly, potassium ions and compounds that stabilize the G-quadruplex and i-motif structures have an inhibitory effect on NM23-H2 DNA-binding activity. Mutation of Arg(88) to Ala(88) (R88A) reduced both DNA and nucleotide binding but had minimal effect on the NM23-H2 crystal structure. On the basis of these data and molecular modeling studies, we have proposed a stepwise trapping-out of the NHE III(1) region in a single-stranded form, thus allowing single-stranded transcription factors to bind and activate c-myc transcription. Furthermore, this model provides a rationale for how the stabilization of the G-quadruplex or i-motif structures formed within the c-myc gene promoter region can inhibit NM23-H2 from activating c-myc gene expression.

PubMed: 19435876
DOI: 10.1158/1535-7163.MCT-08-1093

Experimental method

X-RAY DIFFRACTION (1.7 Å)