8KCA

Crystal structure of DDX53 helicase domain

Summary for 8KCA

• Entry DOI: 10.2210/pdb8kca/pdb
• Descriptor: Probable ATP-dependent RNA helicase DDX53 (2 entities in total)
• Functional Keywords: rna helicase, rna binding protein
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 2
• Total formula weight: 44105.64

Authors

Park, S.,Yang, J.B.,Jung, H.S.,Kim, H.Y. (deposition date: 2023-08-06, release date: 2023-08-30, Last modification date: 2024-05-08)

Primary citation

Park, S.,Yang, J.B.,Park, Y.H.,Kim, Y.K.,Jeoung, D.,Kim, H.Y.,Jung, H.S.
Structural insight into crystal structure of helicase domain of DDX53.
Biochem.Biophys.Res.Commun., 677:190-195, 2023

PubMed Abstract: DEAD box helicase proteins are a family of RNA helicases that participate in various RNA metabolisms such as RNA unwinding, RNA processing, and RNPase activities. A particular DEAD box protein, the DDX53 protein, is primarily expressed in cancer cells and plays a crucial role in tumorigenesis. Numerous studies have revealed that DDX53 interacts with various microRNA and Histone deacetylases. However, its molecular structure and the detailed binding interaction between DDX53 and microRNA or HDAC is still unclear. In this study, we used X-ray crystallography to investigate the 3D structure of the hlicase C-terminal domain of DDX53, and successfully determined its crystal structure at a resolution of 1.97 Å. Subsequently, a functional analysis of RNA was conducted by examining the binding properties thereof with DDX53 by transmission electron microscopy and computing-based molecular docking simulation. The defined 3D model of DDX53 not only provides a structural basis for the fundamental understanding of DDX53 but is also expected to contribute to the field of anti-cancer drug discovery such as structure-based drug discovery and computer-aided drug design.

PubMed: 37603933
DOI: 10.1016/j.bbrc.2023.08.022

Experimental method

X-RAY DIFFRACTION (1.97 Å)