PDBsum entry 1c4j

Deoxyribonucleic acid

PDB id

1c4j

Contents

			DNA/RNA

References listed in PDB file

Key reference

Title

Anchoring an extended htlv-1 rex peptide within an RNA major groove containing junctional base triples.

Authors

F.Jiang, A.Gorin, W.Hu, A.Majumdar, S.Baskerville, W.Xu, A.Ellington, D.J.Patel.

Ref.

Structure, 1999, 7, 1461-1472. [DOI no: 10.1016/S0969-2126(00)88337-9]

PubMed id

10647177

Abstract

BACKGROUND: The Rex protein of the human T cell leukemia virus type 1 (HTLV-1) belongs to a family of proteins that use arginine-rich motifs (ARMs) to recognize their RNA targets. Previously, an in vitro selected RNA aptamer sequence was identified that mediates mRNA transport in vivo when placed in the primary binding site on stem-loop IID of the Rex response element. We present the solution structure of the HTLV-1 arginine-rich Rex peptide bound to its RNA aptamer target determined by multidimensional heteronuclear NMR spectroscopy. RESULTS: The Rex peptide in a predominantly extended conformation threads through a channel formed by the shallow and widened RNA major groove and a looped out guanine. The RNA aptamer contains three stems separated by a pair of two-base bulges, and adopts an unanticipated fold in which both junctional sites are anchored through base triple formation. Binding specificity is associated with intermolecular hydrogen bonding between guanidinium groups of three non-adjacent arginines and the guanine base edges of three adjacent G.C pairs. CONCLUSIONS: The extended S-shaped conformation of the Rex peptide, together with previous demonstrations of a beta-hairpin conformation for the bovine immunodeficiency virus (BIV) Tat peptide and an alpha-helical conformation for the human immunodeficiency virus (HIV) Rev peptide in complex with their respective RNA targets, expands our understanding of the strategies employed by ARMs for adaptive recognition and highlights the importance of RNA tertiary structure in accommodating minimalist elements of protein secondary structure.



	Figure 8. Figure 8. Stacking of adjacent arginine-guanine pairing alignments. (a) Intermolecular interactions between the guanidinium groups of arginines 5, 7 and 13 and the major groove edges of adjacent stacked G8, G24 and G25 residues in a representative refined structure of the Rex peptide-RNA aptamer complex. The G o C-rich stem II segment of the bound RNA is shown in magenta in a space-filling representation with the backbone phosphorus atoms in red. The peptide backbone in yellow is shown in stick representation, whereas the three arginine sidechains in yellow are shown in space-filling representation. The intermolecular arginine-guanine pairing alignments involve (b) R13 with G25, (c) R7 with G24 and (d) R5 with G8. Note that we observe three distinct arginine-guanine pairing alignments in the complex. This figure was prepared using INSIGHT II.

	Headers