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

From Proteopedia

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2db3 asymmetric unit, resolution 2.20Å Click here to display the biological molecule.
Ligands:	ANP, MG
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 the solved structure contains 4 monomers of Vasa.

Each monomer of Vasa in the structure is bound to RNA and an ATP analog; this is presumed to represent the biological molecule.

Each monomer of Vasa has an N-terminal domain that binds the 3' side of the RNA and a C-terminal domain that binds the 5' side of the RNA.

The 11 conserved motifs colored according to figure 1 of the paper describing the structure. Fancy, high-quality cartoons on/off.

The wedge helix (overlapping with Motif Ib) clashes with the RNA continuing on in normal helix and forces a bend between nucleotide 5 and 6 in 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 a magnesium ion and water. A red broken line connects the gamma-phosphorous atom and a well-ordered water located ~3.25Å away, situated ideally for a nucleophilic in-line attack. Two arginines and a histidine shield the active site from the negative charge of the phosphates. Gln272 recognizes the adenosine base moiety, 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.