1J7G

Structure of YihZ from Haemophilus influenzae (HI0670), a D-Tyr-tRNA(Tyr) deacylase

Summary for 1J7G

• Entry DOI: 10.2210/pdb1j7g/pdb
• Descriptor: D-tyrosyl-tRNA(Tyr) deacylase (2 entities in total)
• Functional Keywords: d-tyr-trna(tyr) deacylase, structural genomics, hypothetical protein, structure 2 function project, s2f, hydrolase
• Biological source: Haemophilus influenzae Rd KW20
• Cellular location: Cytoplasm (Probable): P44814
• Total number of polymer chains: 1
• Total formula weight: 15879.17

Authors

Lim, K.,Herzberg, O.,Structure 2 Function Project (S2F) (deposition date: 2001-05-16, release date: 2003-04-22, Last modification date: 2024-02-07)

Primary citation

Lim, K.,Tempczyk, A.,Bonander, N.,Toedt, J.,Howard, A.,Einsenstein, E.,Herzberg, O.
A Catalytic Mechanism for D-Tyr-tRNATyr Deacylase Based on the Crystal Structure of Hemophilus influenzae HI0670
J.Biol.Chem., 278:13496-13502, 2003

PubMed Abstract: D-Tyr-tRNA(Tyr) deacylase is an editing enzyme that removes d-tyrosine and other d-amino acids from charged tRNAs, thereby preventing incorrect incorporation of d-amino acids into proteins. A model for the catalytic mechanism of this enzyme is proposed based on the crystal structure of the enzyme from Haemophilus influenzae determined at a 1.64-A resolution. Structural comparison of this dimeric enzyme with the very similar structure of the enzyme from Escherichia coli together with sequence analyses indicate that the active site is located in the dimer interface within a depression that includes an invariant threonine residue, Thr-80. The active site contains an oxyanion hole formed by the main chain nitrogen atoms of Thr-80 and Phe-79 and the side chain amide group of the invariant Gln-78. The Michaelis complex between the enzyme and D-Tyr-tRNA was modeled assuming a nucleophilic attack on the carbonyl carbon of D-Tyr by the Thr-80 O(gamma) atom and a role for the oxyanion hole in stabilizing the negatively charged tetrahedral transition states. The model is consistent with all of the available data on substrate specificity. Based on this model, we propose a substrate-assisted acylation/deacylation-catalytic mechanism in which the amino group of the D-Tyr is deprotonated and serves as the general base.

PubMed: 12571243
DOI: 10.1074/jbc.M213150200

Experimental method

X-RAY DIFFRACTION (1.64 Å)