Structure and function of the c-myc DNA-unwinding element-binding protein DUE-B.
Local zones of easily unwound DNA are characteristic of prokaryotic and eukaryotic replication origins. The DNA-unwinding element of the human c-myc replication origin is essential for replicator activity and is a target of the DNA-unwinding element-binding protein DUE-B in vivo. We present here the 2.0A crystal structure of DUE-B and complementary biochemical characterization of its biological activity. The structure corresponds to a dimer of the N-terminal domain of the full-length protein and contains many of the structural elements of the nucleotide binding fold. A single magnesium ion resides in the putative active site cavity, which could serve to facilitate ATP hydrolytic activity of this protein. The structure also demonstrates a notable similarity to those of tRNA-editing enzymes. Consistent with this structural homology, the N-terminal core of DUE-B is shown to display both D-aminoacyl-tRNA deacylase activity and ATPase activity. We further demonstrate that the C-terminal portion of the enzyme is disordered and not essential for dimerization. However, this region is essential for DNA binding in vitro and becomes ordered in the presence of DNA.
Kemp
Michael
M
Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio 45435, USA.
Bae
Brian
B
Yu
John Paul
JP
Ghosh
Maloy
M
Leffak
Michael
M
Nair
Satish K
SK
D000251:Adenosine Triphosphatases / Q000737:chemistry / Q000378:metabolism; D000255:Adenosine Triphosphate / Q000737:chemistry / Q000378:metabolism; D000818:Animals; D018360:Crystallography, X-Ray; D004261:DNA Replication / Q000502:physiology; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D019281:Dimerization; D006801:Humans; D011485:Protein Binding / Q000502:physiology; D017510:Protein Folding; D020836:Protein Structure, Quaternary; D017434:Protein Structure, Tertiary / Q000502:physiology; D016271:Proto-Oncogene Proteins c-myc / Q000737:chemistry / Q000378:metabolism; D017393:RNA Editing / Q000502:physiology; D040681:Structural Homology, Protein; D013329:Structure-Activity Relationship
D004268:DNA-Binding Proteins; C500359:DTD1 protein, human; D016271:Proto-Oncogene Proteins c-myc; D000255:Adenosine Triphosphate; D000251:Adenosine Triphosphatases