1WYD

Crystal Structure of Aspartyl-tRNA synthetase from Sulfolobus tokodaii

PDB DOI: https://doi.org/10.2210/pdb1WYD/pdb

Classification: LIGASE
Organism(s): Sulfurisphaera tokodaii str. 7
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2005-02-12 Released: 2006-07-04
Deposition Author(s): Maeda, Y., Hossain, M.T., Ubukata, S., Suzuki, K., Sekiguchi, T., Takenaka, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.279
R-Value Work: 0.232
R-Value Observed: 0.237

wwPDB Validation 3D Report Full Report

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

Literature

Structure of the nondiscriminating aspartyl-tRNA synthetase from the crenarchaeon Sulfolobus tokodaii strain 7 reveals the recognition mechanism for two different tRNA anticodons

Sato, Y., Maeda, Y., Shimizu, S., Hossain, M.T., Ubukata, S., Suzuki, K., Sekiguchi, T., Takenaka, A.

(2007) Acta Crystallogr D Biol Crystallogr 63: 1042-1047

PubMed: 17881821 Search on PubMed
DOI: https://doi.org/10.1107/S0907444907038292
Primary Citation of Related Structures:
1WYD

PubMed Abstract:
In protein synthesis, 20 types of aminoacyl-tRNA synthetase (aaRS) are generally required in order to distinguish between the 20 types of amino acid so that each achieves strict recognition of the cognate amino acid and the cognate tRNA. In the crenarchaeon Sulfolobus tokodaii strain 7 (St), however, asparaginyl-tRNA synthetase (AsnRS) is missing. It is believed that AspRS instead produces Asp-tRNA(Asn) in addition to Asp-tRNA(Asp). In order to reveal the recognition mechanism for the two anticodons, GUC for aspartate and GUU for asparagine, the crystal structure of St-AspRS (nondiscriminating type) has been determined at 2.3 A resolution as the first example of the nondiscriminating type of AspRS from crenarchaea. A structural comparison with structures of discriminating AspRSs indicates that the structures are similar to each other overall and that the catalytic domain is highly conserved as expected. In the N-terminal domain, however, the binding site for the third anticodon nucleotide is modified to accept two pyrimidine bases, C and U, but not purine bases. The C base can bind to form a hydrogen bond to the surrounding main-chain amide group in the discriminating AspRS, while in the nondiscriminating AspRS the corresponding amino-acid residue is replaced by proline, which has no amide H atom for hydrogen-bond formation, thus allowing the U base to be accommodated in this site. In addition, the residues that cover the base plane are missing in the nondiscriminating AspRS. These amino-acid changes make it possible for both C and U to be accepted by the nondiscriminating AspRS. It is speculated that this type of nondiscriminating AspRS has been introduced into Thermus thermophilus through horizontal gene transfer.

Organizational Affiliation

Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama 226-8501, Japan.

Macromolecule Content

Total Structure Weight: 99.03 kDa
Atom Count: 7,093
Modelled Residue Count: 857
Deposited Residue Count: 858
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical aspartyl-tRNA synthetase	A, B	429	Sulfurisphaera tokodaii str. 7	Mutation(s): 0
UniProt
Find proteins for Q976I3 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore Q976I3 Go to UniProtKB: Q976I3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q976I3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B]	E [auth A], H [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B]	D [auth A], G [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B]	C [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.279
R-Value Work: 0.232
R-Value Observed: 0.237
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.3	α = 90
b = 139.25	β = 90
c = 75.3	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling
AMoRE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2006-07-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-07-04
Type: Initial release
Version 1.1: 2007-09-14
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Source and taxonomy, Version format compliance
Version 1.3: 2024-03-13
Changes: Data collection, Database references, Derived calculations