1IQ8

Crystal Structure of archaeosine tRNA-guanine transglycosylase from Pyrococcus horikoshii

Summary for 1IQ8

• Entry DOI: 10.2210/pdb1iq8/pdb
• Descriptor: ARCHAEOSINE TRNA-GUANINE TRANSGLYCOSYLASE, ZINC ION, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: (alpha/beta)8 barrel, riken structural genomics/proteomics initiative, rsgi, structural genomics, transferase
• Biological source: Pyrococcus horikoshii
• Total number of polymer chains: 2
• Total formula weight: 133579.71

Authors

Ishitani, R.,Nureki, O.,Fukai, S.,Kijimoto, T.,Nameki, N.,Watanabe, M.,Kondo, H.,Sekine, M.,Okada, N.,Nishimura, S.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2001-07-09, release date: 2002-05-22, Last modification date: 2023-12-27)

Primary citation

Ishitani, R.,Nureki, O.,Fukai, S.,Kijimoto, T.,Nameki, N.,Watanabe, M.,Kondo, H.,Sekine, M.,Okada, N.,Nishimura, S.,Yokoyama, S.
Crystal structure of archaeosine tRNA-guanine transglycosylase.
J.Mol.Biol., 318:665-677, 2002

PubMed Abstract: Archaeosine tRNA-guanine transglycosylase (ArcTGT) catalyzes the exchange of guanine at position 15 in the D-loop of archaeal tRNAs with a free 7-cyano-7-deazaguanine (preQ(0)) base, as the first step in the biosynthesis of an archaea-specific modified base, archaeosine (7-formamidino-7-deazaguanosine). We determined the crystal structures of ArcTGT from Pyrococcus horikoshii at 2.2 A resolution and its complexes with guanine and preQ(0), at 2.3 and 2.5 A resolutions, respectively. The N-terminal catalytic domain folds into an (alpha/beta)(8) barrel with a characteristic zinc-binding site, showing structural similarity with that of the bacterial queuosine TGT (QueTGT), which is involved in queuosine (7-[[(4,5-cis-dihydroxy-2-cyclopenten-1-yl)-amino]methyl]-7-deazaguanosine) biosynthesis and targets the tRNA anticodon. ArcTGT forms a dimer, involving the zinc-binding site and the ArcTGT-specific C-terminal domain. The C-terminal domains have novel folds, including an OB fold-like "PUA domain", whose sequence is widely conserved in eukaryotic and archaeal RNA modification enzymes. Therefore, the C-terminal domains may be involved in tRNA recognition. In the free-form structure of ArcTGT, an alpha-helix located at the rim of the (alpha/beta)(8) barrel structure is completely disordered, while it is ordered in the guanine-bound and preQ(0)-bound forms. Structural comparison of the ArcTGT.preQ(0), ArcTGT.guanine, and QueTGT.preQ(1) complexes provides novel insights into the substrate recognition mechanisms of ArcTGT.

PubMed: 12054814
DOI: 10.1016/S0022-2836(02)00090-6

Experimental method

X-RAY DIFFRACTION (2.2 Å)