PDBsum entry 1fuk

Translation

PDB id: 1fuk

Contents

Protein chain

157 a.a. *

Metals

_ZN

Waters ×111

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Crystal structure of yeast initiation factor 4a, A dead-Box RNA helicase.

Authors

J.M.Caruthers, E.R.Johnson, D.B.Mckay.

Ref.

Proc Natl Acad Sci U S A, 2000, 97, 13080-13085. [DOI no: 10.1073/pnas.97.24.13080]

PubMed id

11087862

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.

Figure 1.
Fig. 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 -sheet are labeled sequentially. This and subsequent ribbon drawings were prepared with MOLSCRIPT (34) and rendered with RASTER3D (35). (B) Topology diagram of the structure. -Strands are shown as arrows; -helices, as cylinders. -Strands and -helices are labeled sequentially as 1-7 and [1]- [6], 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.
Fig. 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. 1A.