2CYB

Crystal structure of Tyrosyl-tRNA Synthetase complexed with L-tyrosine from Archaeoglobus fulgidus

Summary for 2CYB

• Entry DOI: 10.2210/pdb2cyb/pdb
• Descriptor: Tyrosyl-tRNA synthetase, TYROSINE (3 entities in total)
• Functional Keywords: rossmann-fold, structural genomics, nppsfa, national project on protein structural and functional analyses, riken structural genomics/proteomics initiative, rsgi, ligase
• Biological source: Archaeoglobus fulgidus
• Cellular location: Cytoplasm: O29482
• Total number of polymer chains: 2
• Total formula weight: 73699.10

Authors

Kuratani, M.,Sakai, H.,Takahashi, M.,Yanagisawa, T.,Kobayashi, T.,Terada, T.,Shirouzu, M.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2005-07-06, release date: 2005-11-22, Last modification date: 2024-03-13)

Primary citation

Kuratani, M.,Sakai, H.,Takahashi, M.,Yanagisawa, T.,Kobayashi, T.,Murayama, K.,Chen, L.,Liu, Z.J.,Wang, B.C.,Kuroishi, C.,Kuramitsu, S.,Terada, T.,Bessho, Y.,Shirouzu, M.,Sekine, S.,Yokoyama, S.
Crystal Structures of Tyrosyl-tRNA Synthetases from Archaea
J.Mol.Biol., 355:395-408, 2006

PubMed Abstract: Tyrosyl-tRNA synthetase (TyrRS) catalyzes the tyrosylation of tRNA(Tyr) in a two-step reaction. TyrRS has the "HIGH" and "KMSKS" motifs, which play essential roles in the formation of the tyrosyl-adenylate from tyrosine and ATP. Here, we determined the crystal structures of Archaeoglobus fulgidus and Pyrococcus horikoshii TyrRSs in the l-tyrosine-bound form at 1.8A and 2.2A resolutions, respectively, and that of Aeropyrum pernix TyrRS in the substrate-free form at 2.2 A. The conformation of the KMSKS motif differs among the three TyrRSs. In the A.pernix TyrRS, the KMSKS loop conformation corresponds to the ATP-bound "closed" form. In contrast, the KMSKS loop of the P.horikoshii TyrRS forms a novel 3(10) helix, which appears to correspond to the "semi-closed" form. This conformation enlarges the entrance to the tyrosine-binding pocket, which facilitates the pyrophosphate ion release after the tyrosyl-adenylate formation, and probably is involved in the initial tRNA binding. The KMSSS loop of the A.fulgidus TyrRS is somewhat farther from the active site and is stabilized by hydrogen bonds. Based on the three structures, possible structural changes of the KMSKS motif during the tyrosine activation reaction are discussed. We suggest that the insertion sequence just before the KMSKS motif, which exists in some archaeal species, enhances the binding affinity of the TyrRS for its cognate tRNA. In addition, a non-proline cis peptide bond, which is involved in the tRNA binding, is conserved among the archaeal TyrRSs.

PubMed: 16325203
DOI: 10.1016/j.jmb.2005.10.073

Experimental method

X-RAY DIFFRACTION (1.8 Å)