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PDBsum entry 2dlc

Go to PDB code: 
protein dna_rna ligands metals links
Ligase/tRNA PDB id
2dlc
Jmol
Contents
Protein chain
339 a.a. *
DNA/RNA
Ligands
YMP
Metals
_MG
Waters ×57
* Residue conservation analysis
PDB id:
2dlc
Name: Ligase/tRNA
Title: Crystal structure of the ternary complex of yeast tyrosyl-tr synthetase
Structure: Tyrosyl-tRNA synthetase, cytoplasmic. Chain: x. Synonym: tyrosyl-tRNA ligase, tyrrs. Engineered: yes. T-RNA (76-mer). Chain: y. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes
Resolution:
2.40Å     R-factor:   0.247     R-free:   0.289
Authors: M.Tsunoda,Y.Kusakabe,N.Tanaka,K.T.Nakamura
Key ref: M.Tsunoda et al. (2007). Structural basis for recognition of cognate tRNA by tyrosyl-tRNA synthetase from three kingdoms. Nucleic Acids Res, 35, 4289-4300. PubMed id: 17576676
Date:
18-Apr-06     Release date:   12-Jun-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P36421  (SYYC_YEAST) -  Tyrosine--tRNA ligase, cytoplasmic
Seq:
Struc:
394 a.a.
339 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.6.1.1.1  - Tyrosine--tRNA ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + L-tyrosyl-tRNA(Tyr)
ATP
+ L-tyrosine
+ tRNA(Tyr)
=
AMP
Bound ligand (Het Group name = YMP)
matches with 61.11% similarity
+ diphosphate
+ L-tyrosyl-tRNA(Tyr)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   2 terms 
  Biological process     translation   3 terms 
  Biochemical function     nucleotide binding     6 terms  

 

 
    reference    
 
 
Nucleic Acids Res 35:4289-4300 (2007)
PubMed id: 17576676  
 
 
Structural basis for recognition of cognate tRNA by tyrosyl-tRNA synthetase from three kingdoms.
M.Tsunoda, Y.Kusakabe, N.Tanaka, S.Ohno, M.Nakamura, T.Senda, T.Moriguchi, N.Asai, M.Sekine, T.Yokogawa, K.Nishikawa, K.T.Nakamura.
 
  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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21325056 L.Bonnefond, T.Arai, Y.Sakaguchi, T.Suzuki, R.Ishitani, and O.Nureki (2011).
Structural basis for nonribosomal peptide synthesis by an aminoacyl-tRNA synthetase paralog.
  Proc Natl Acad Sci U S A, 108, 3912-3917.
PDB codes: 3oqh 3oqi 3oqj 3s7t
20582317 G.N.Thibodeaux, X.Liang, K.Moncivais, A.Umeda, O.Singer, L.Alfonta, and Z.J.Zhang (2010).
Transforming a pair of orthogonal tRNA-aminoacyl-tRNA synthetase from Archaea to function in mammalian cells.
  PLoS One, 5, e11263.  
19098308 G.Sharma, and E.A.First (2009).
Thermodynamic analysis reveals a temperature-dependent change in the catalytic mechanism of bacillus stearothermophilus tyrosyl-tRNA synthetase.
  J Biol Chem, 284, 4179-4190.  
19668857 J.K.Takimoto, K.L.Adams, Z.Xiang, and L.Wang (2009).
Improving orthogonal tRNA-synthetase recognition for efficient unnatural amino acid incorporation and application in mammalian cells.
  Mol Biosyst, 5, 931-934.  
18268021 L.Bonnefond, C.Florentz, R.Giegé, and J.Rudinger-Thirion (2008).
Decreased aminoacylation in pathology-related mutants of mitochondrial tRNATyr is associated with structural perturbations in tRNA architecture.
  RNA, 14, 641-648.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.