Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa

From Proteopedia

PDB ID 2db3 Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image
2db3 asymmetric unit, resolution 2.20Å Click to display the biological molecule.
Ligands:	,
Gene:	VASA (Drosophila melanogaster)
Activity:	Adenosinetriphosphatase, with EC number 3.6.1.3
Structural annotation: Resources: InterPro : Ipr014014, Ipr014021, Ipr014001, Ipr011545, Ipr000629, Ipr001650 Pfam : PF00271, PF00270 UniProt : P09052
Functional annotation: Cellular component: polar granule Biological process: germarium-derived oocyte fate determination germarium-derived egg chamber formation pole plasm RNA localization positive regulation of oskar mRNA translation cell differentiation positive regulation of translation intracellular mRNA localization dorsal appendage formation multicellular organismal development karyosome formation oocyte anterior/posterior axis determination oogenesis pole plasm assembly germ-line cyst formation regulation of oskar mRNA translation mRNA polyadenylation Molecular function: helicase activity nucleotide binding protein binding ATP-dependent helicase activity RNA binding nucleic acid binding RNA helicase activity ATP binding hydrolase activity
Evolutionary conservation: Toggle Conservation Colors: Rows = identical sequences: Further Information: Caveats, Explanation, Complete Results at ConSurfDB
Resources:	FirstGlance, OCA, PDBsum, RCSB, TOPSAN
Coordinates:	save as pdb, mmCIF, xml

Vasa is a DEAD-box RNA helicase and the determination of the structure of the Vasa protein bound to RNA and a nonhydrolyzable ATP analog provided great insight into how this family of helicases unwinds RNA.

The crystallographic asymmetric unit of

.

according to figure 1 of the paper describing the structure. .

[Note: this view generates a surface area which may take half a minute to calculate.]

Motifs I and II bind the triphosphate of the ATP analog directly and through and water. A located ~3.25Å away, situated ideally for a nucleophilic in-line attack. from the negative charge of the phosphates. , specifying ATP vs. GTP.

Details of Structure Featured

The crystallographic structure containing Vasa bound to RNA, 2db3, is a 8 chains structure of sequences from Drosophila melanogaster. Full crystallographic information is available from OCA.

Reference for the structure

• Sengoku T, Nureki O, Nakamura A, Kobayashi S, Yokoyama S. Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa. Cell. 2006 Apr 21;125(2):287-300. PMID:16630817 doi:10.1016/j.cell.2006.01.054

See Also

• Helicase
• Asymmetric Unit

Content Donators

Created with the participation of Luis E Ramirez-Tapia, Wayne Decatur.