2PID

Crystal structure of human mitochondrial tyrosyl-tRNA synthetase in complex with an adenylate analog

Summary for 2PID

• Entry DOI: 10.2210/pdb2pid/pdb
• Related: 1vbm 3ts1
• Descriptor: Tyrosyl-tRNA synthetase, 5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE (3 entities in total)
• Functional Keywords: aminoacyl-trna synthetase, protein-substrate complex, atp-binding, ligase, mitochondrion, nucleotide-binding, protein biosynthesis
• Biological source: Homo sapiens (human)
• Cellular location: Mitochondrion matrix: Q9Y2Z4
• Total number of polymer chains: 2
• Total formula weight: 80943.73

Authors

Bonnefond, L.,Frugier, M.,Touze, E.,Lorber, B.,Florentz, C.,Giege, R.,Sauter, C.,Rudinger-Thirion, J. (deposition date: 2007-04-13, release date: 2007-10-23, Last modification date: 2024-03-13)

Primary citation

Bonnefond, L.,Frugier, M.,Touze, E.,Lorber, B.,Florentz, C.,Giege, R.,Sauter, C.,Rudinger-Thirion, J.
Crystal Structure of Human Mitochondrial Tyrosyl-tRNA Synthetase Reveals Common and Idiosyncratic Features.
Structure, 15:1505-1516, 2007

PubMed Abstract: We report the structure of a strictly mitochondrial human synthetase, namely tyrosyl-tRNA synthetase (mt-TyrRS), in complex with an adenylate analog at 2.2 A resolution. The structure is that of an active enzyme deprived of the C-terminal S4-like domain and resembles eubacterial TyrRSs with a canonical tyrosine-binding pocket and adenylate-binding residues typical of class I synthetases. Two bulges at the enzyme surface, not seen in eubacterial TyrRSs, correspond to conserved sequences in mt-TyrRSs. The synthetase electrostatic surface potential differs from that of other TyrRSs, including the human cytoplasmic homolog and the mitochondrial one from Neurospora crassa. The homodimeric human mt-TyrRS shows an asymmetry propagating from the dimer interface toward the two catalytic sites and extremities of each subunit. Mutagenesis of the catalytic domain reveals functional importance of Ser200 in line with an involvement of A73 rather than N1-N72 in tyrosine identity.

PubMed: 17997975
DOI: 10.1016/j.str.2007.09.018

Experimental method

X-RAY DIFFRACTION (2.2 Å)