2E1B

Crystal structure of the AlaX-M trans-editing enzyme from Pyrococcus horikoshii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 

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This is version 1.2 of the entry. See complete history


Literature

Structure of the AlaX-M trans-editing enzyme from Pyrococcus horikoshii

Fukunaga, R.Yokoyama, S.

(2007) Acta Crystallogr D Biol Crystallogr 63: 390-400

  • DOI: 10.1107/S090744490605640X
  • Primary Citation of Related Structures:  
    2E1B

  • PubMed Abstract: 
  • The editing domain of alanyl-tRNA synthetase (AlaRS) contributes to high-fidelity aminoacylation by hydrolyzing (editing) the incorrect products Ser-tRNA(Ala) and Gly-tRNA(Ala) (cis-editing). The AlaX protein shares sequence homology to the editing domain of AlaRS ...

    The editing domain of alanyl-tRNA synthetase (AlaRS) contributes to high-fidelity aminoacylation by hydrolyzing (editing) the incorrect products Ser-tRNA(Ala) and Gly-tRNA(Ala) (cis-editing). The AlaX protein shares sequence homology to the editing domain of AlaRS. There are three types of AlaX proteins, with different numbers of amino-acid residues (AlaX-S, AlaX-M and AlaX-L). In this report, AlaX-M from Pyrococcus horikoshii is shown to deacylate Ser-tRNA(Ala) and Gly-tRNA(Ala) (trans-editing). The crystal structure of P. horikoshii AlaX-M has been determined at 2.7 A resolution. AlaX-M consists of an N-terminal domain (N-domain) and a C-terminal domain (C-domain). A zinc ion is coordinated by the conserved zinc-binding cluster in the C-domain, which is expected to be the enzymatic active site. The glycine-rich motif, consisting of successive conserved glycine residues in the N-domain, forms a loop (the 'glycine-rich loop'). The glycine-rich loop is located near the active site and may be involved in substrate recognition and/or catalysis.


    Organizational Affiliation

    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
216aa long hypothetical alanyl-tRNA synthetaseA216Pyrococcus horikoshiiMutation(s): 0 
EC: 6.1.1.7 (PDB Primary Data), 3.1.1.29 (PDB Primary Data)
Find proteins for O57848 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Explore O57848 
Go to UniProtKB:  O57848
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.223α = 90
b = 80.223β = 90
c = 72.269γ = 120
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MLPHAREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-03-06
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance