spacer
spacer

PDBsum entry 1jh3

Go to PDB code: 
protein links
Ligase PDB id
1jh3
Jmol
Contents
Protein chain
99 a.a. *
* Residue conservation analysis
PDB id:
1jh3
Name: Ligase
Title: Solution structure of tyrosyl-tRNA synthetasE C-terminal domain.
Structure: Tyrosyl-tRNA synthetase. Chain: a. Fragment: c-terminal domain (residues 321-419). Engineered: yes
Source: Geobacillus stearothermophilus. Organism_taxid: 1422. Gene: tyrs. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
NMR struc: 20 models
Authors: J.I.Guijarro,A.Pintar,A.Prochnicka-Chalufour,V.Guez, B.Gilquin,H.Bedouelle,M.Delepierre
Key ref:
J.I.Guijarro et al. (2002). Structure and dynamics of the anticodon arm binding domain of Bacillus stearothermophilus Tyrosyl-tRNA synthetase. Structure, 10, 311-317. PubMed id: 12005430 DOI: 10.1016/S0969-2126(02)00699-8
Date:
27-Jun-01     Release date:   20-Mar-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00952  (SYY_GEOSE) -  Tyrosine--tRNA ligase
Seq:
Struc:
419 a.a.
99 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
+ diphosphate
+ L-tyrosyl-tRNA(Tyr)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     RNA binding     2 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(02)00699-8 Structure 10:311-317 (2002)
PubMed id: 12005430  
 
 
Structure and dynamics of the anticodon arm binding domain of Bacillus stearothermophilus Tyrosyl-tRNA synthetase.
J.I.Guijarro, A.Pintar, A.Prochnicka-Chalufour, V.Guez, B.Gilquin, H.Bedouelle, M.Delepierre.
 
  ABSTRACT  
 
The structure of a recombinant protein, TyrRS(delta4), corresponding to the anticodon arm binding domain of Bacillus stearothermophilus tyrosyl-tRNA synthetase, has been solved, and its dynamics have been studied by nuclear magnetic resonance (NMR). It is the first structure described for such a domain of a tyrosyl-tRNA synthetase. It consists of a five-stranded beta sheet, packed against two alpha helices on one side and one alpha helix on the other side. A large part of the domain is structurally similar to other functionally unrelated RNA binding proteins. The basic residues known to be essential for tRNA binding and charging are exposed to the solvent on the same face of the molecule. The structure of TyrRS(delta4), together with previous mutagenesis data, allows one to delineate the region of interaction with tRNATyr.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Surface Representations of the Structure of TyrRS(D4)Residues 330-418. A ribbon diagram is displayed at the center of the figure to show the orientation of the molecule used in the surface representations.(A) The six basic residues identified by mutagenesis as essential for interaction with tRNA^Tyr are shown in blue, while mutated residues that are not relevant to tRNA interaction as assessed by an in vivo genetic complementation assay [7] are represented in orange. Different blues are used for clarity.(B and C) Surface electrostatic potential of TyrRS(D4) in the same orientation as in (A) and after a 180 y rotation, respectively. Positive and negative potentials are represented in blue and red, respectively. Electrostatic potentials were calculated with MOLMOL [39].(D) Analysis of the putative binding surface. The basic residues known to be important (blue) or irrelevant for tRNA binding (orange) shown in (A) are displayed without label. The remaining residues on the tRNA binding face are labeled and colored: red, negatively charged residues that most probably do not interact with tRNA; cyan, positively charged residues that could in principle interact with tRNA phosphates; dark purple and violet, polar residues (purple) and glycines (violet) with an exposed amide group that could form hydrogen bonds with tRNA bases or ribose; yellow, exposed aromatic residues that could stack with tRNA bases; purple, A[378].
 
  The above figure is reprinted by permission from Cell Press: Structure (2002, 10, 311-317) copyright 2002.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18413600 P.J.Paukstelis, and A.M.Lambowitz (2008).
Identification and evolution of fungal mitochondrial tyrosyl-tRNA synthetases with group I intron splicing activity.
  Proc Natl Acad Sci U S A, 105, 6010-6015.  
17576676 M.Tsunoda, Y.Kusakabe, N.Tanaka, S.Ohno, M.Nakamura, T.Senda, T.Moriguchi, N.Asai, M.Sekine, T.Yokogawa, K.Nishikawa, and K.T.Nakamura (2007).
Structural basis for recognition of cognate tRNA by tyrosyl-tRNA synthetase from three kingdoms.
  Nucleic Acids Res, 35, 4289-4300.
PDB code: 2dlc
15694342 P.J.Paukstelis, R.Coon, L.Madabusi, J.Nowakowski, A.Monzingo, J.Robertus, and A.M.Lambowitz (2005).
A tyrosyl-tRNA synthetase adapted to function in group I intron splicing by acquiring a new RNA binding surface.
  Mol Cell, 17, 417-428.
PDB code: 1y42
12110594 A.Yaremchuk, I.Kriklivyi, M.Tukalo, and S.Cusack (2002).
Class I tyrosyl-tRNA synthetase has a class II mode of cognate tRNA recognition.
  EMBO J, 21, 3829-3840.
PDB codes: 1h3e 1h3f
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 code is shown on the right.