PDBsum entry: 1j2b

Transferase/RNA

PDB id: 1j2b

Contents

Protein chains

576 a.a. *

DNA/RNA

Metals

_MG ×4

_ZN ×2

Waters ×41

* Residue conservation analysis

PDB id:

1j2b

Name:

Transferase/RNA

Title:

Crystal structure of archaeosine tRNA-guanine transglycosylase complexed with lambda-form tRNA(val)

Structure:

tRNA(val). Chain: c, d. Engineered: yes. Archaeosine tRNA-guanine transglycosylase. Chain: a, b. Engineered: yes

Source:

Synthetic: yes. Other_details: synthetic tRNA transcript. Sequence from pyrococcus horikoshii. Organism_taxid: 53953. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Tetramer (from PQS)

Resolution:

3.30Å R-factor: 0.225 R-free: 0.288

Authors:

R.Ishitani,O.Nureki,N.Nameki,N.Okada,S.Nishimura,S.Yokoyama, Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

R.Ishitani et al. (2003). Alternative tertiary structure of tRNA for recognition by a posttranscriptional modification enzyme. Cell, 113, 383-394. PubMed id: 12732145 DOI: 10.1016/S0092-8674(03)00280-0

Date:

29-Dec-02 Release date: 27-May-03

Protein chains

O58843  (ATGT_PYRHO) -  7-cyano-7-deazaguanine tRNA-ribosyltransferase

Seq: 582 a.a.

Struc: 576 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: tRNA processing (3 terms)
• Biochemical function: transferase activity (7 terms)

DOI no: 10.1016/S0092-8674(03)00280-0

Cell 113:383-394 (2003)

PubMed id: 12732145

Alternative tertiary structure of tRNA for recognition by a posttranscriptional modification enzyme.

R.Ishitani, O.Nureki, N.Nameki, N.Okada, S.Nishimura, S.Yokoyama.

ABSTRACT

Transfer RNA (tRNA) canonically has the clover-leaf secondary structure with the acceptor, D, anticodon, and T arms, which are folded into the L-shaped tertiary structure. To strengthen the L form, posttranscriptional modifications occur on nucleotides buried within the core, but the modification enzymes are paradoxically inaccessible to them in the L form. In this study, we determined the crystal structure of tRNA bound with archaeosine tRNA-guanine transglycosylase, which modifies G15 of the D arm in the core. The bound tRNA assumes an alternative conformation ("lambda form") drastically different from the L form. All of the D-arm secondary base pairs and the canonical tertiary interactions are disrupted. Furthermore, a helical structure is reorganized, while the rest of the D arm is single stranded and protruded. Consequently, the enzyme precisely locates the exposed G15 in the active site, by counting the nucleotide number from G1 to G15 in the lambda form.

Selected figure(s)

Figure 1.
Figure 1. A tRNA Modification Enzyme, ArcTGT, Replaces the Base at Position 15 in the D Loop, which Is Deeply Buried in the Canonical L Form of tRNA(A) The secondary and tertiary structures of tRNA in the canonical L form. The acceptor, D, anticodon, and T arms, and the variable loop are colored red, yellow, green, purple, and sky blue, respectively. The secondary structure is shown in the clover-leaf (left) and L-shape (center) diagrams. The RNA backbones are shown with thick lines, while the Watson-Crick base pairs are indicated with short thin lines. In the tertiary structure (right), the RNA backbone is shown as a tube model and the Watson-Crick base pairs are shown with sticks. The ArcTGT target site, G15, which is buried deeply in the tRNA tertiary structure, is circled.(B) Biosynthetic pathway of archaeosine. The guanine moiety of G15 is replaced with preQ[0] by the transglycosylation catalyzed by ArcTGT. Afterwards, the preQ[0] at position 15 is further modified to archaeosine on the polynucleotide chain, by an unknown pathway (Watanabe et al., 1997). The biosynthetic pathway of preQ[0] is also unknown.

Figure 2.
Figure 2. Overall Structure of the P. horikoshii ArcTGT·tRNA^Val Complex(A) Stereo view of the ArcTGT·tRNA^Val complex. ArcTGT and tRNA are shown as ribbon models. The catalytic domain and the C-terminal domains of the ArcTGT subunit A are colored green and brown, while those of subunit B are colored deep blue and purple, respectively. tRNA-I and -II are colored sky blue and pink, respectively.(B and C) Close-ups of the ArcTGT-tRNA interaction interfaces. (B) The anticodon arm and the DV helix are accommodated into the cleft formed between the catalytic and C-terminal domains. (C) U8 to U17 of the protruded D arm are recognized by the C-terminal domains of subunit A and the catalytic domain of subunit B, and G15 is accommodated into the catalytic pocket. The coloring schemes of (B) and (C) are the same as in (A).(D) Schematic diagram of the ArcTGT-tRNA interactions.

The above figures are reprinted by permission from Cell Press: Cell (2003, 113, 383-394) copyright 2003.

Figures were selected by an automated process.