2I4I

Crystal Structure of human DEAD-box RNA helicase DDX3X

Summary for 2I4I

• Entry DOI: 10.2210/pdb2i4i/pdb
• Descriptor: ATP-dependent RNA helicase DDX3X, ADENOSINE MONOPHOSPHATE (3 entities in total)
• Functional Keywords: rna, helicase, dead, structural genomics, sgc, structural genomics consortium, hydrolase
• Biological source: Homo sapiens (human)
• Cellular location: Nucleus speckle: O00571
• Total number of polymer chains: 1
• Total formula weight: 47474.07

Authors

Hogbom, M.,Karlberg, T.,Arrowsmith, C.,Berglund, H.,Busam, R.D.,Collins, R.,Edwards, A.,Ehn, M.,Flodin, S.,Flores, A.,Graslund, S.,Hallberg, B.M.,Hammarstrom, M.,Johansson, I.,Kotenyova, T.,Magnusdottir, A.,Nilsson-Ehle, P.,Nordlund, P.,Nyman, T.,Ogg, D.,Persson, C.,Sagemark, J.,Stenmark, P.,Sundstrom, M.,Thorsell, A.G.,Uppenberg, J.,Van Den Berg, S.,Wallden, K.,Weigelt, J.,Welin, M.,Holmberg-Schiavone, L.,Structural Genomics Consortium (SGC) (deposition date: 2006-08-22, release date: 2006-09-05, Last modification date: 2023-08-30)

Primary citation

Hogbom, M.,Collins, R.,van den Berg, S.,Jenvert, R.-M.,Karlberg, T.,Kotenyova, T.,Flores, A.,Karlsson Hedestam, G.B.,Holmberg Schiavone, L.H.
Crystal Structure of Conserved Domains 1 and 2 of the Human DEAD-box Helicase DDX3X in Complex with the Mononucleotide AMP
J.Mol.Biol., 372:150-159, 2007

PubMed Abstract: DExD-box helicases are involved in all aspects of cellular RNA metabolism. Conserved domains 1 and 2 contain nine signature motifs that are responsible for nucleotide binding, RNA binding and ATP hydrolysis. The human DEAD-box helicase DDX3X has been associated with several different cellular processes, such as cell-growth control, mRNA transport and translation, and is suggested to be essential for the export of unspliced/partially spliced HIV mRNAs from the nucleus to the cytoplasm. Here, the crystal structure of conserved domains 1 and 2 of DDX3X, including a DDX3-specific insertion that is not generally found in human DExD-box helicases, is presented. The N-terminal domain 1 and the C-terminal domain 2 both display RecA-like folds comprising a central beta-sheet flanked by alpha-helices. Interestingly, the DDX3X-specific insertion forms a helical element that extends a highly positively charged sequence in a loop, thus increasing the RNA-binding surface of the protein. Surprisingly, although DDX3X was crystallized in the presence of a large excess of ADP or the slowly hydrolyzable ATP analogue ATPgammaS the contaminant AMP was seen in the structure. A fluorescent-based stability assay showed that the thermal stability of DDX3X was increased by the mononucleotide AMP but not by ADP or ATPgammaS, suggesting that DDX3X is stabilized by AMP and elucidating why AMP was found in the nucleotide-binding pocket.

PubMed: 17631897
DOI: 10.1016/j.jmb.2007.06.050

Experimental method

X-RAY DIFFRACTION (2.2 Å)