5elx | pdb_00005elx

S. cerevisiae Dbp5 bound to RNA and mant-ADP BeF3

spinqualitylabelsall models 5elx, resolution 1.81Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 5elx is a 2 chain structure with sequence from [1] and Baker's yeast. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: BEF, M2A, MG, NO3 Related: 3pey Gene: DBP5, RAT8, SCY_5119 (Baker's yeast) Activity: RNA helicase, with EC number 3.6.4.13 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [DBP5_YEAS7] ATP-dependent RNA helicase associated with the nuclear pore complex and essential for mRNA export from the nucleus. May participate in a terminal step of mRNA export through the removal of proteins that accompany mRNA through the nucleopore complex. May also be involved in early transcription (By similarity). Publication Abstract from PubMed mRNA export from the nucleus depends on the ATPase activity of the DEAD-box protein Dbp5/DDX19. Although Dbp5 has measurable ATPase activity alone, several regulatory factors (e.g., RNA, nucleoporin proteins, and the endogenous small molecule InsP6) modulate catalytic activity in vitro and in vivo to facilitate mRNA export. An analysis of the intrinsic and regulator-activated Dbp5 ATPase cycle is necessary to define how these factors control Dbp5 and mRNA export. Here, we report a kinetic and equilibrium analysis of the Saccharomyces cerevisiae Dbp5 ATPase cycle, including the influence of RNA on Dbp5 activity. These data show that ATP binds Dbp5 weakly in rapid equilibrium with a binding affinity (KT~4mM) comparable to the KM for steady-state cycling, while ADP binds an order of magnitude more tightly (KD~0.4mM). The overall intrinsic steady-state cycling rate constant (kcat) is limited by slow, near-irreversible ATP hydrolysis and even slower subsequent phosphate release. RNA increases kcat and rate-limiting Pi release 20-fold, although Pi release continues to limit steady-state cycling in the presence of RNA, in conjunction with RNA binding. Together, this work identifies RNA binding and Pi release as important biochemical transitions within the Dbp5 ATPase cycle and provides a framework for investigating the means by which Dbp5 and mRNA export is modulated by regulatory factors. Pi Release Limits the Intrinsic and RNA-Stimulated ATPase Cycles of DEAD-Box Protein 5 (Dbp5).,Wong EV, Cao W, Voros J, Merchant M, Modis Y, Hackney DD, Montpetit B, De La Cruz EM J Mol Biol. 2016 Jan 29;428(2 Pt B):492-508. doi: 10.1016/j.jmb.2015.12.018. Epub, 2015 Dec 28. PMID:26730886 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Helicase 3D structures

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