PDBsum entry 2k7e

RNA

PDB id: 2k7e

Contents

DNA/RNA

PDB id:

2k7e

Name:

RNA

Title:

Nmr structure of the human trnalys3 bound to the HIV genome loop i

Structure:

RNA (5'-r( Gp Cp Gp Gp Up Gp Up Ap Ap Ap Ap G)-3'). Chain: a. Engineered: yes. Other_details: HIV a-loop. RNA (5'-r( Cp Up (Sur)p Up Up Ap Ap (Psu)p Cp Up Gp C)-3'). Chain: b. Engineered: yes. Other_details: trnalys3 asl

Source:

Synthetic: yes. Synthetic: yes

NMR struc:

10 models

Authors:

Y.Bilbille,F.P.A.Vendeix,R.Guenther,A.Malkiewicz,X.Ariza,J.Vilarrasa, P.Agris

Key ref:

Y.Bilbille et al. (2009). The structure of the human tRNALys3 anticodon bound to the HIV genome is stabilized by modified nucleosides and adjacent mismatch base pairs. Nucleic Acids Res, 37, 3342-3353. PubMed id: 19324888

Date:

09-Aug-08 Release date: 07-Oct-08

DNA/RNA chains

G-C-G-G-U-G-U-A-A-A-A-G 12 bases

C-U-SUR-U-U-A-A-PSU-C-U-G-C 12 bases

Nucleic Acids Res 37:3342-3353 (2009)

PubMed id: 19324888

The structure of the human tRNALys3 anticodon bound to the HIV genome is stabilized by modified nucleosides and adjacent mismatch base pairs.

Y.Bilbille, F.A.Vendeix, R.Guenther, A.Malkiewicz, X.Ariza, J.Vilarrasa, P.F.Agris.

ABSTRACT

Replication of human immunodeficiency virus (HIV) requires base pairing of the reverse transcriptase primer, human tRNA(Lys3), to the viral RNA. Although the major complementary base pairing occurs between the HIV primer binding sequence (PBS) and the tRNA's 3'-terminus, an important discriminatory, secondary contact occurs between the viral A-rich Loop I, 5'-adjacent to the PBS, and the modified, U-rich anticodon domain of tRNA(Lys3). The importance of individual and combined anticodon modifications to the tRNA/HIV-1 Loop I RNA's interaction was determined. The thermal stabilities of variously modified tRNA anticodon region sequences bound to the Loop I of viral sub(sero)types G and B were analyzed and the structure of one duplex containing two modified nucleosides was determined using NMR spectroscopy and restrained molecular dynamics. The modifications 2-thiouridine, s(2)U(34), and pseudouridine, Psi(39), appreciably stabilized the interaction of the anticodon region with the viral subtype G and B RNAs. The structure of the duplex results in two coaxially stacked A-form RNA stems separated by two mismatched base pairs, U(162)*Psi(39) and G(163)*A(38), that maintained a reasonable A-form helix diameter. The tRNA's s(2)U(34) stabilized the interaction between the A-rich HIV Loop I sequence and the U-rich anticodon, whereas the tRNA's Psi(39) stabilized the adjacent mismatched pairs.