1J7G

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Catalytic Mechanism for D-Tyr-tRNATyr Deacylase Based on the Crystal Structure of Hemophilus influenzae HI0670

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

(2003) J.Biol.Chem. 278: 13496-13502

  • DOI: 10.1074/jbc.M213150200

  • 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 propos ...

    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.


    Related Citations: 
    • Functional Characterization of the D-Tyr-tRNA(Tyr) Deacylase from Escherichia coli
      Soutourina, J.,Plateau, P.,Delort, F.,Peirotes, A.,Blanquet, S.
      (1999) J.Biol.Chem. 274: 19109


    Organizational Affiliation

    Center for Advanced Research In Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-tyrosyl-tRNA(Tyr) deacylase
A
144Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)Mutation(s): 0 
Gene Names: dtd
EC: 3.1.1.96
Find proteins for P44814 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd))
Go to UniProtKB:  P44814
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.194 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 55.470α = 90.00
b = 55.470β = 90.00
c = 128.750γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SOLVEphasing
DMmodel building
SCALEPACKdata scaling
MLPHAREphasing
DMphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-04-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance