4YYE

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.301 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The crystal structure of yeast mitochondrial ThrRS in complex with the canonical threonine tRNA.

Holman, K.M.Wu, J.Ling, J.Simonovic, M.

(2016) Nucleic Acids Res. 44: 1428-1439

  • DOI: 10.1093/nar/gkv1501

  • PubMed Abstract: 
  • In mitochondria of Saccharomyces cerevisiae, a single aminoacyl-tRNA synthetase (aaRS), MST1, aminoacylates two isoacceptor tRNAs, tRNA1(Thr) and tRNA2(Thr), that harbor anticodon loops of different size and sequence. As a result of this promiscuity, ...

    In mitochondria of Saccharomyces cerevisiae, a single aminoacyl-tRNA synthetase (aaRS), MST1, aminoacylates two isoacceptor tRNAs, tRNA1(Thr) and tRNA2(Thr), that harbor anticodon loops of different size and sequence. As a result of this promiscuity, reassignment of the CUN codon box from leucine to threonine is facilitated. However, the mechanism by which a single aaRS binds distinct anticodon loops with high specificity is not well understood. Herein, we present the crystal structure of MST1 in complex with the canonical tRNA2(Thr) and non-hydrolyzable analog of threonyl adenylate. Our structure reveals that the dimeric arrangement of MST1 is essential for binding the 5'-phosphate, the second base pair of the acceptor stem, the first two base pairs of the anticodon stem and the first nucleotide of the variable arm. Further, in contrast to the bacterial ortholog that 'reads' the entire anticodon sequence, MST1 recognizes bases in the second and third position and the nucleotide upstream of the anticodon sequence. We speculate that a flexible loop linking strands β4 and β5 may be allosteric regulator that establishes cross-subunit communication between the aminoacylation and tRNA-binding sites. We also propose that structural features of the anticodon-binding domain in MST1 permit binding of the enlarged anticodon loop of tRNA1(Thr).


    Organizational Affiliation

    Department of Microbiology and Molecular Genetics, The University of Texas, Health Science Center at Houston, Houston, TX 77030, USA.,Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA.,Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA msimon5@uic.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Threonine--tRNA ligase, mitochondrial
A, B
460Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MST1
EC: 6.1.1.3
Find proteins for P07236 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MST1
Go to UniProtKB:  P07236
Entity ID: 2
MoleculeChainsLengthOrganism
tRNAC,D76Saccharomyces cerevisiae
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
TSB
Query on TSB

Download SDF File 
Download CCD File 
A, B
5'-O-(N-(L-THREONYL)-SULFAMOYL)ADENOSINE
C14 H21 N7 O8 S
UPVAPSGKXAAHBG-CKTDUXNWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.301 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.160 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 69.021α = 63.86
b = 77.228β = 75.04
c = 86.157γ = 89.39
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MOLREPphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM097042
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM115431
Department of Energy (DOE, United States)United StatesDE-AC02-06CH11357

Revision History 

  • Version 1.0: 2016-01-06
    Type: Initial release
  • Version 1.1: 2016-03-02
    Type: Database references
  • Version 1.2: 2016-03-16
    Type: Data collection
  • Version 1.3: 2020-01-01
    Type: Author supporting evidence, Derived calculations