1Y2Q

Crystal structure of the editing domain of threonyl-tRNA synthetase from Pyrococcus abyssi

PDB DOI: https://doi.org/10.2210/pdb1Y2Q/pdb

Classification: LIGASE
Organism(s): Pyrococcus abyssi
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2004-11-23 Released: 2005-06-14
Deposition Author(s): Dwivedi, S., Kruparani, S.P., Sankaranarayanan, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.272
R-Value Work: 0.205
R-Value Observed: 0.209

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

A D-amino acid editing module coupled to the translational apparatus in archaea

Dwivedi, S., Kruparani, S.P., Sankaranarayanan, R.

(2005) Nat Struct Mol Biol 12: 556-557

PubMed: 15908961 Search on PubMed
DOI: https://doi.org/10.1038/nsmb943
Primary Citation of Related Structures:
1Y2Q

PubMed Abstract:
We report the crystal structure of an archaea-specific editing domain of threonyl-tRNA synthetase that reveals a marked structural similarity to D-amino acid deacylases found in eubacteria and eukaryotes. The domain can bind D-amino acids despite a low sequence identity to other D-amino acid deacylases. These results together indicate the presence of these deacylases in all three kingdoms of life. This underlines an important role they may have played in enforcing homochirality during translation.

Organizational Affiliation

Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India.

Macromolecule Content

Total Structure Weight: 16.28 kDa
Atom Count: 1,316
Modelled Residue Count: 143
Deposited Residue Count: 143
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Threonyl-tRNA synthetase	A	143	Pyrococcus abyssi	Mutation(s): 0 Gene Names: thrS EC: 6.1.1.3
UniProt
Find proteins for Q9UZ14 (Pyrococcus abyssi (strain GE5 / Orsay)) Explore Q9UZ14 Go to UniProtKB: Q9UZ14
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UZ14
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.272
R-Value Work: 0.205
R-Value Observed: 0.209
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.752	α = 90
b = 61.752	β = 90
c = 64.894	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2005-06-14

Deposition Author(s):

Kruparani, S.P.

Sankaranarayanan, R.

Revision History (Full details and data files)

Version 1.0: 2005-06-14
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-03-13
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.