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2db3

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

Publication Abstract from PubMed

DEAD-box RNA helicases, which regulate various processes involving RNA, have two RecA-like domains as a catalytic core to alter higher-order RNA structures. We determined the 2.2 A resolution structure of the core of the Drosophila DEAD-box protein Vasa in complex with a single-stranded RNA and an ATP analog. The ATP analog intensively interacts with both of the domains, thereby bringing them into the closed form, with many interdomain interactions of conserved residues. The bound RNA is sharply bent, avoiding a clash with a conserved alpha helix in the N-terminal domain. This "wedge" helix should disrupt base pairs by bending one of the strands when a duplex is bound. Mutational analyses indicated that the interdomain interactions couple ATP hydrolysis to RNA unwinding, probably through fine positioning of the duplex relative to the wedge helix. This mechanism, which differs from those for canonical translocating helicases, may enable the targeted modulation of intricate RNA structures.

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

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

About this Structure

2db3 asymmetric unit, resolution 2.20Å
Click to display the biological molecule.
Sites: , , , , , , and
Ligands: ,
Gene: VASA (Drosophila melanogaster)
Activity: Adenosinetriphosphatase, with EC number 3.6.1.3
Resources: FirstGlance, OCA, PDBsum, RCSB, TOPSAN
Coordinates: save as pdb, mmCIF, xml


2DB3 is a 8 chains structure of sequences from Drosophila melanogaster. Full crystallographic information is available from OCA.

.

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.

Reference

  • 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
  • Sengoku T, Nureki O, Dohmae N, Nakamura A, Yokoyama S. Crystallization and preliminary X-ray analysis of the helicase domains of Vasa complexed with RNA and an ATP analogue. Acta Crystallogr D Biol Crystallogr. 2004 Feb;60(Pt 2):320-2. Epub 2004, Jan 23. PMID:14747711 doi:10.1107/S0907444903025897

Original page seeded by OCA on Tue Feb 17 20:22:33 2009

Proteopedia Page Contributors and Editors (what is this?)

Wayne Decatur, OCA

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