2DLC

Crystal structure of the ternary complex of yeast tyrosyl-tRNA synthetase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis for recognition of cognate tRNA by tyrosyl-tRNA synthetase from three kingdoms.

Tsunoda, M.Kusakabe, Y.Tanaka, N.Ohno, S.Nakamura, M.Senda, T.Moriguchi, T.Asai, N.Sekine, M.Yokogawa, T.Nishikawa, K.Nakamura, K.T.

(2007) Nucleic Acids Res. 35: 4289-4300

  • DOI: 10.1093/nar/gkm417

  • PubMed Abstract: 
  • The specific aminoacylation of tRNA by tyrosyl-tRNA synthetases (TyrRSs) relies on the identity determinants in the cognate tRNA(Tyr)s. We have determined the crystal structure of Saccharomyces cerevisiae TyrRS (SceTyrRS) complexed with a Tyr-AMP ana ...

    The specific aminoacylation of tRNA by tyrosyl-tRNA synthetases (TyrRSs) relies on the identity determinants in the cognate tRNA(Tyr)s. We have determined the crystal structure of Saccharomyces cerevisiae TyrRS (SceTyrRS) complexed with a Tyr-AMP analog and the native tRNA(Tyr)(GPsiA). Structural information for TyrRS-tRNA(Tyr) complexes is now full-line for three kingdoms. Because the archaeal/eukaryotic TyrRSs-tRNA(Tyr)s pairs do not cross-react with their bacterial counterparts, the recognition modes of the identity determinants by the archaeal/eukaryotic TyrRSs were expected to be similar to each other but different from that by the bacterial TyrRSs. Interestingly, however, the tRNA(Tyr) recognition modes of SceTyrRS have both similarities and differences compared with those in the archaeal TyrRS: the recognition of the C1-G72 base pair by SceTyrRS is similar to that by the archaeal TyrRS, whereas the recognition of the A73 by SceTyrRS is different from that by the archaeal TyrRS but similar to that by the bacterial TyrRS. Thus, the lack of cross-reactivity between archaeal/eukaryotic and bacterial TyrRS-tRNA(Tyr) pairs most probably lies in the different sequence of the last base pair of the acceptor stem (C1-G72 vs G1-C72) of tRNA(Tyr). On the other hand, the recognition mode of Tyr-AMP is conserved among the TyrRSs from the three kingdoms.


    Organizational Affiliation

    School of Pharmaceutical Sciences, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142-8555, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tyrosyl-tRNA synthetase, cytoplasmic
X
394Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: TYS1 (MGM104)
EC: 6.1.1.1
Find proteins for P36421 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P36421
Entity ID: 1
MoleculeChainsLengthOrganism
T-RNA (76-MER)Y76N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
YMP
Query on YMP

Download SDF File 
Download CCD File 
X
O-(ADENOSINE-5'-O-YL)-N-(L-TYROSYL)PHOSPHORAMIDATE
TYROSYL-ADENYLATE ANALOGUE, TYR-AMP ANALOGUE
C19 H24 N7 O8 P
WJKRKCCMHCWYJU-QTOWJTHWSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
X
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  9 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
Y
RNA LINKINGC9 H13 N2 O9 PU
5MC
Query on 5MC
Y
RNA LINKINGC10 H16 N3 O8 PC
M2G
Query on M2G
Y
RNA LINKINGC12 H18 N5 O8 PG
1MA
Query on 1MA
Y
RNA LINKINGC11 H16 N5 O7 PA
2MG
Query on 2MG
Y
RNA LINKINGC11 H16 N5 O8 PG
OMG
Query on OMG
Y
RNA LINKINGC11 H16 N5 O8 PG
6IA
Query on 6IA
Y
RNA LINKINGC15 H24 N5 O7 PA
5MU
Query on 5MU
Y
RNA LINKINGC10 H15 N2 O9 PU
H2U
Query on H2U
Y
RNA LINKINGC9 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.245 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 63.854α = 90.00
b = 63.854β = 90.00
c = 330.334γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
REFMACrefinement
SHARPphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-12
    Type: Initial release
  • Version 1.1: 2008-04-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-07-12
    Type: Database references