PDBsum entry 1hv8

RNA binding protein

PDB id: 1hv8

Contents

Protein chains

363 a.a. *

Ligands

SO4 ×6

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Crystal structure of a dead box protein from the hyperthermophile methanococcus jannaschii.

Authors

R.M.Story, H.Li, J.N.Abelson.

Ref.

Proc Natl Acad Sci U S A, 2001, 98, 1465-1470. [DOI no: 10.1073/pnas.98.4.1465]

PubMed id

11171974

Abstract

We have determined the structure of a DEAD box putative RNA helicase from the hyperthermophile Methanococcus jannaschii. Like other helicases, the protein contains two alpha/beta domains, each with a recA-like topology. Unlike other helicases, the protein exists as a dimer in the crystal. Through an interaction that resembles the dimer interface of insulin, the amino-terminal domain's 7-strand beta-sheet is extended to 14 strands across the two molecules. Motifs conserved in the DEAD box family cluster in the cleft between domains, and many of their functions can be deduced by mutational data and by comparison with other helicase structures. Several lines of evidence suggest that motif III Ser-Ala-Thr may be involved in binding RNA.

Figure 1.
Fig. 1. Monomer structure. (A) The MjDEAD monomer showing the amino- and carboxyl-terminal domains (labeled N and C in subsequent figures). The linker between the domains can be seen in the middle of the figure. The orientation of the dimer in this view (in this and subsequent figures) is depicted in an Inset, with the equivalent domains colored blue, as in the main figure. Fig. 1A, as well as Fig. 1C, Fig. 2 A and B, and Fig. 3 A and C were made with MOLSCRIPT (41) and RASTER 3D (42). (B) The topological organization of the MjDEAD monomer, illustrating the similarities of the two domains. The "RecA-like core" stretches from -strands 1 and 2 and 4-7 as numbered for the amino-terminal domain and their connecting -helices. Sequence numbers at the edges of secondary structure elements are indicated, as are those loop regions observed to bind the nucleic acid backbone in some or all of known helicase complexes with nucleic acid. The region of polypeptide equivalent to the GG motif (motif 1B) also contacts nucleic acid in the HCV NS3 helicase. -Helix F and -strand no. 7 (that pack against their symmetry-related counterparts to form a dimer) are indicated. (C) Difference in the amino- and carboxyl-terminal domain orientation relative to other proteins. Superposition of only the amino-terminal domain with that of other proteins reveals a structure "opened up" relative to the others (blue domains). Independent superposition of the carboxyl-terminal domain on a "closed" structure (in this case the PcrA DNA and AMPPNP structure) leads to a closing of the MjDEAD structure to a conformation more like that observed for other helicases (blue amino-terminal domain and gold carboxyl-terminal domain). Single-stranded (ss)DNA binds at the top of the two domains in other helicases in this orientation. We assume that this closed structure for MjDEAD will likewise resemble the structure of the DNA/ATP bound form of this enzyme.

Figure 2.
Fig. 2. Dimer Structure. (A) Structure of the MjDEAD dimer found in the asymmetric unit in the crystal with the molecules related by an approximate 2-fold symmetry axis. The individual monomers are shown in blue and green. Two equivalent -strands (no. 7) are hydrogen bonded, effectively extending the -sheet to 14 strands. (B) Closeup of the dimer interface of MjDEAD and its superposition with the B:D interface of insulin (PDB code 1trz). Each interface is created by a similar interaction across a roughly 2-fold symmetry axis of two -helices and two hydrogen-bonded -strands, depicted as coils and arrows. Insulin is colored yellow with red side chains, and MjDEAD is colored cyan with blue side chains. The arrangement of equivalent aromatic residues on the -strands (YsF for MjDEAD, FfY for insulin) is shown.