1J2B

Crystal Structure Of Archaeosine tRNA-Guanine Transglycosylase Complexed With lambda-form tRNA(Val)

Summary for 1J2B

• Entry DOI: 10.2210/pdb1j2b/pdb
• Related: 1IQ8
• Descriptor: tRNA(Val), Archaeosine tRNA-guanine transglycosylase, MAGNESIUM ION, ... (5 entities in total)
• Functional Keywords: transferase, riken structural genomics/proteomics initiative, rsgi, structural genomics, transferase-rna complex, transferase/rna
• Biological source: Pyrococcus horikoshii; More
• Total number of polymer chains: 4
• Total formula weight: 183283.81

Authors

Ishitani, R.,Nureki, O.,Nameki, N.,Okada, N.,Nishimura, S.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2002-12-29, release date: 2003-05-27, Last modification date: 2023-10-25)

Primary citation

Ishitani, R.,Nureki, O.,Nameki, N.,Okada, N.,Nishimura, S.,Yokoyama, S.
Alternative Tertiary Structure of tRNA for Recognition by a Posttranscriptional Modification Enzyme
Cell(Cambridge,Mass.), 113:383-394, 2003

PubMed 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.

PubMed: 12732145
DOI: 10.1016/S0092-8674(03)00280-0

Experimental method

X-RAY DIFFRACTION (3.3 Å)