Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 69328.52 
• Atom Count: 4206 
• Residue Count: 470 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

2DLC

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

• DOI: 10.2210/pdb2DLC/pdb
• NDB: PR0198

• Classification: LIGASE/tRNA
• Organism(s): Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2006-04-18 Released: 2007-06-12 
• Deposition Author(s): Tsunoda, M., Kusakabe, Y., Tanaka, N., Nakamura, K.T.

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Experimental Data Snapshot

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

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

• PubMed: 17576676 
• 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 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
Tyrosyl-tRNA synthetase, cytoplasmic	X	394	Saccharomyces 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
Molecule	Chains	Length	Organism
T-RNA (76-MER)	Y	76	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
YMP	X	O-(ADENOSINE-5'-O-YL)-N-(L-TYROSYL)PHOSPHORAMIDATE TYROSYL-ADENYLATE ANALOGUE, TYR-AMP ANALOGUE C19 H24 N7 O8 P WJKRKCCMHCWYJU-QTOWJTHWSA-N
MG	X	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  9 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PSU	Y	RNA LINKING	C9 H13 N2 O9 P		U
5MC	Y	RNA LINKING	C10 H16 N3 O8 P		C
M2G	Y	RNA LINKING	C12 H18 N5 O8 P		G
1MA	Y	RNA LINKING	C11 H16 N5 O7 P		A
2MG	Y	RNA LINKING	C11 H16 N5 O8 P		G
OMG	Y	RNA LINKING	C11 H16 N5 O8 P		G
6IA	Y	RNA LINKING	C15 H24 N5 O7 P		A
5MU	Y	RNA LINKING	C10 H15 N2 O9 P		U
H2U	Y	RNA LINKING	C9 H15 N2 O9 P		U

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 = 63.854	α = 90.00
b = 63.854	β = 90.00
c = 330.334	γ = 90.00

Software Package:

Software Name	Purpose
ADSC	data collection
REFMAC	refinement
SHARP	phasing
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-04-18 
• Released Date: 2007-06-12 
• Deposition Author(s): Tsunoda, M., Kusakabe, Y., Tanaka, N., Nakamura, K.T.

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