Crystal structure of yeast initiation factor 4A, a DEAD-box RNA helicase - PubMed (original) (raw)

Crystal structure of yeast initiation factor 4A, a DEAD-box RNA helicase

J M Caruthers et al. Proc Natl Acad Sci U S A. 2000.

Abstract

The eukaryotic translation initiation factor 4A (eIF4A) is a member of the DEA(D/H)-box RNA helicase family, a diverse group of proteins that couples an ATPase activity to RNA binding and unwinding. Previous work has provided the structure of the amino-terminal, ATP-binding domain of eIF4A. Extending those results, we have solved the structure of the carboxyl-terminal domain of eIF4A with data to 1.75 A resolution; it has a parallel alpha-beta topology that superimposes, with minor variations, on the structures and conserved motifs of the equivalent domain in other, distantly related helicases. Using data to 2.8 A resolution and molecular replacement with the refined model of the carboxyl-terminal domain, we have completed the structure of full-length eIF4A; it is a "dumbbell" structure consisting of two compact domains connected by an extended linker. By using the structures of other helicases as a template, compact structures can be modeled for eIF4A that suggest (i) helicase motif IV binds RNA; (ii) Arg-298, which is conserved in the DEA(D/H)-box RNA helicase family but is absent from many other helicases, also binds RNA; and (iii) motifs V and VI "link" the carboxyl-terminal domain to the amino-terminal domain through interactions with ATP and the DEA(D/H) motif, providing a mechanism for coupling ATP binding and hydrolysis with conformational changes that modulate RNA binding.

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Figures

Figure 1

Structure of the carboxyl-terminal domain of eIF4A. (A) Stereoview, ribbon drawing of the structure. Conserved motifs are colored as follows: motif IV, VIFCNTRR, residues 263–270, green; “conserved R” motif, residue Arg-298, purple; motif V, RGID, residues 321–324, magenta; motif VI, HRIGRGGR, residues 345–352, cyan. The strands of the β-sheet are labeled sequentially. This and subsequent ribbon drawings were prepared with

molscript

(34) and rendered with

raster

(35). (B) Topology diagram of the structure. β-Strands are shown as arrows; α-helices, as cylinders. β-Strands and α-helices are labeled sequentially as 1–7 and α1– α6, respectively. Sequences of the conserved motifs are shown in boxes; residues whose side chains are illustrated in_A_ and subsequent figures are underlined.

Figure 2

Ribbon drawing of the structure of full-length eIF4A. The amino- and carboxyl-terminal domains are colored silver and gold, respectively; the 11-residue linker connecting them is colored black. The conserved amino-terminal motifs are colored as follows: motif I, Walker A motif ASQSGTGKT, residues 65–72, blue; motif Ia, PTRELA, residues 97–102, yellow; GG, residues 125–126, orange; TPGR, residues 145–148, pink; motif II, Walker B motif DEAD, residues 169–172, red; motif III, SAT, residues 200–202, green. The conserved carboxyl-terminal motifs are colored as described in Fig. 1_A_.

Figure 3

Overlay of amino- and carboxyl-terminal domains of eIF4A onto the equivalent domains of other helicases. The amino-terminal domain of eIF4A is in approximately the same orientation as in Fig. 2. The color convention for the domains and conserved motifs of eIF4A is the same as in Fig. 2. In all cases, the “target” helicase is shown as a transparent tube drawing against the solid eIF4A model. Oligonucleotides are shown as CPK space-filling models. (A) PcrA DNA helicase (PDB ID code 3PJR) with ATP and the single-stranded portion of the DNA. ATP is shown as a ball-and-stick representation. (B) HCV RNA helicase with ssDNA (PDB ID code 1A1V). (C) UvrD DNA helicase (PDB ID code 1D9X).

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Crystal structure of yeast initiation factor 4A, a DEAD-box RNA helicase - PubMed (original) (raw)