2JX3

NMR solution structure of the N-terminal domain of DEK

Summary for 2JX3

• Entry DOI: 10.2210/pdb2jx3/pdb
• Descriptor: Protein DEK (1 entity in total)
• Functional Keywords: alpha helix, saf/sap motif, dna binding, chromosomal rearrangement, dna-binding, nucleus, phosphorylation, proto-oncogene, dna binding protein
• Biological source: Homo sapiens (human)
• Cellular location: Nucleus: P35659
• Total number of polymer chains: 1
• Total formula weight: 15103.93

Authors

Matsuo, H.,Devany, M. (deposition date: 2007-11-02, release date: 2008-02-12, Last modification date: 2024-05-29)

Primary citation

Devany, M.,Kappes, F.,Chen, K.M.,Markovitz, D.M.,Matsuo, H.
Solution NMR structure of the N-terminal domain of the human DEK protein
Protein Sci., 17:205-215, 2008

PubMed Abstract: The human DEK protein has a long-standing association with carcinogenesis since the DEK gene was originally identified in the t(6:9) chromosomal translocation in a subtype of patients with acute myelogenous leukemia (AML). Recent studies have partly unveiled DEK's cellular functions including apoptosis inhibition in primary cells as well as cancer cells, determination of 3' splice site of transcribed RNA, and suppression of transcription initiation by polymerase II. It has been previously shown that the N-terminal region of DEK, spanning residues 68-226, confers important in vitro and in vivo functions of DEK, which include double-stranded DNA (ds-DNA) binding, introduction of constrained positive supercoils into closed dsDNA, and apoptosis inhibition. In this paper, we describe the three-dimensional structure of the N-terminal domain of DEK (DEKntd) as determined using solution NMR. The C-terminal part of DEKntd, which contains a putative DNA-binding motif (SAF/SAP motif), folds into a helix-loop-helix structure. Interestingly, the N-terminal part of DEKntd shows a very similar structure to the C-terminal part, although the N-terminal and the C-terminal part differ distinctively in their amino acid sequences. As a consequence, the structure of DEKntd has a pseudo twofold plane symmetry. In addition, we tested dsDNA binding of DEKntd by monitoring changes of NMR chemical shifts upon addition of dsDNAs. We found that not only the C-terminal part containing the SAF/SAP motif but the N-terminal part is also involved in DEKntd's dsDNA binding. Our study illustrates a new structural variant and reveals novel dsDNA-binding properties for proteins containing the SAP/SAF motif.

PubMed: 18227428
DOI: 10.1110/ps.073244108

Experimental method

SOLUTION NMR