PDBsum entry: 1j7g

Hydrolase

PDB id: 1j7g

Contents

Protein chain

144 a.a. *

Waters ×207

* Residue conservation analysis

PDB id:

1j7g

Name:

Hydrolase

Title:

Structure of yihz from haemophilus influenzae (hi0670), a d- tRNA(tyr) deacylase

Structure:

D-tyrosyl-tRNA(tyr) deacylase. Chain: a. Engineered: yes

Source:

Haemophilus influenzae rd kw20. Organism_taxid: 71421. Strain: kw20. Gene: hi0670. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PDB file)

Resolution:

1.64Å R-factor: 0.194 R-free: 0.220

Authors:

K.Lim,O.Herzberg,Structure 2 Function Project (S2f)

Key ref:

K.Lim et al. (2003). A catalytic mechanism for D-Tyr-tRNATyr deacylase based on the crystal structure of Hemophilus influenzae HI0670. J Biol Chem, 278, 13496-13502. PubMed id: 12571243 DOI: 10.1074/jbc.M213150200

Date:

16-May-01 Release date: 22-Apr-03

Protein chain

P44814  (DTD_HAEIN) -  D-tyrosyl-tRNA(Tyr) deacylase

Seq: 144 a.a.

Struc: 144 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: D-amino acid catabolic process (1 term)
• Biochemical function: hydrolase activity (2 terms)

DOI no: 10.1074/jbc.M213150200

J Biol Chem 278:13496-13502 (2003)

PubMed id: 12571243

A catalytic mechanism for D-Tyr-tRNATyr deacylase based on the crystal structure of Hemophilus influenzae HI0670.

K.Lim, A.Tempczyk, N.Bonander, J.Toedt, A.Howard, E.Eisenstein, O.Herzberg.

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.

Selected figure(s)

Figure 1.
Fig. 1. Stereoscopic representation of the final electron density maps at a 1.64-Å resolution together with the model. The active site region is shown. The coefficients (2F[o] F[c]) and calculated phases are used. The map is contoured at a 1 level.

Figure 5.
Fig. 5. A model of the complex between HI0670 and D-Tyr-tRNA. The molecular surfaces of the two monomers are shown in blue and yellow colors, and the tRNA molecule is shown as a green coil. The D-Tyr and four positively charged residues that interact with tRNA phosphate groups outside of the active site are shown as stick models. The molecular surface of the protein dimer was calculated with the computer program MCMS (26). The figure was generated with the computer program RASTER3D (22, 23). Note that the overall structure of the tRNA is that of tRNA^Phe, which is expected to be somewhat different from the structure of tRNA^Tyr. Thus, this is a rough model intended to demonstrate the feasibility of the proposed complex and to develop the proposed catalytic mechanism.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 13496-13502) copyright 2003.

Figures were selected by an automated process.