4EO4 | pdb_00004eo4

Crystal structure of the yeast mitochondrial threonyl-tRNA synthetase (MST1) in complex with seryl sulfamoyl adenylate

PDB DOI: https://doi.org/10.2210/pdb4EO4/pdb

Classification: LIGASE
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-04-13 Released: 2012-07-11
Deposition Author(s): Peterson, K.M., Ling, J., Simonovic, I., Soll, D., Simonovic, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.87 Å
R-Value Free:
0.229 (Depositor), 0.221 (DCC)
R-Value Work:
0.175 (Depositor), 0.170 (DCC)
R-Value Observed:
0.178 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

The mechanism of pre-transfer editing in yeast mitochondrial threonyl-tRNA synthetase.

Ling, J., Peterson, K.M., Simonovic, I., Soll, D., Simonovic, M.

(2012) J Biological Chem 287: 28518-28525

PubMed: 22773845 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1074/jbc.M112.372920
Primary Citation Related Structures:
4EO4

PubMed Abstract:
Accurate translation of mRNA into protein is a fundamental biological process critical for maintaining normal cellular functions. To ensure translational fidelity, aminoacyl-tRNA synthetases (aaRSs) employ pre-transfer and post-transfer editing activities to hydrolyze misactivated and mischarged amino acids, respectively. Whereas post-transfer editing, which requires either a specialized domain in aaRS or a trans-protein factor, is well described, the mechanism of pre-transfer editing is less understood. Here, we show that yeast mitochondrial threonyl-tRNA synthetase (MST1), which lacks an editing domain, utilizes pre-transfer editing to discriminate against serine. MST1 misactivates serine and edits seryl adenylate (Ser-AMP) in a tRNA-independent manner. MST1 hydrolyzes 80% of misactivated Ser-AMP at a rate 4-fold higher than that for the cognate threonyl adenylate (Thr-AMP) while releasing 20% of Ser-AMP into the solution. To understand the mechanism of pre-transfer editing, we solved the crystal structure of MST1 complexed with an analog of Ser-AMP. The binding of the Ser-AMP analog to MST1 induces conformational changes in the aminoacylation active site, and it positions a potential hydrolytic water molecule more favorably for nucleophilic attack. In addition, inhibition results reveal that the Ser-AMP analog binds the active site 100-fold less tightly than the Thr-AMP analog. In conclusion, we propose that the plasticity of the aminoacylation site in MST1 allows binding of Ser-AMP and the appropriate positioning of the hydrolytic water molecule.

Organizational Affiliation

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.

Macromolecule Content

Total Structure Weight: 217.62 kDa
Atom Count: 14,113
Modeled Residue Count: 1,660
Deposited Residue Count: 1,840
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Threonine--tRNA ligase, mitochondrial	A, B, C, D	460	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: MST1, YKL194C EC: 6.1.1.3
UniProt
Find proteins for P07236 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P07236 Go to UniProtKB: P07236
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07236
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SSA Query on SSA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain N [auth D] SDF format, chain O [auth D] SDF format, chain L [auth C] SDF format, chain K [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain N [auth D] mmCIF format, chain O [auth D] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C]	E [auth A] F [auth A] H [auth B] I [auth B] K [auth C] E [auth A], F [auth A], H [auth B], I [auth B], K [auth C], L [auth C], N [auth D], O [auth D]	5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE C₁₃ H₁₉ N₇ O₈ S HQXFJGONGJPTLZ-YTMOPEAISA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain N [auth D] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain N [auth D] Focus chain O [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain P [auth D] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D]	G [auth A], J [auth B], M [auth C], P [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.87 Å
R-Value Free: 0.229 (Depositor), 0.221 (DCC)
R-Value Work: 0.175 (Depositor), 0.170 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 213.233	α = 90
b = 107.498	β = 130.05
c = 153.391	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-07-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-07-11
Type: Initial release
Version 1.1: 2013-01-02
Changes: Database references
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations