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PDBsum entry 4ts1

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protein ligands Protein-protein interface(s) links
Ligase (synthetase) PDB id
4ts1
Jmol
Contents
Protein chains
317 a.a. *
Ligands
TYR ×2
Waters ×144
* Residue conservation analysis
PDB id:
4ts1
Name: Ligase (synthetase)
Title: Crystal structure of a deletion mutant of a tyrosyl-t/RNA synthetase complexed with tyrosine
Structure: Tyrosyl-tRNA synthetase. Chain: a, b. Engineered: yes
Source: Geobacillus stearothermophilus. Organism_taxid: 1422.
Biol. unit: Dimer (from PQS)
Resolution:
2.50Å     R-factor:   0.187    
Authors: P.Brick,D.M.Blow
Key ref: P.Brick and D.M.Blow (1987). Crystal structure of a deletion mutant of a tyrosyl-tRNA synthetase complexed with tyrosine. J Mol Biol, 194, 287-297. PubMed id: 3612807
Date:
29-Jun-89     Release date:   15-Oct-89    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00952  (SYY_GEOSE) -  Tyrosine--tRNA ligase
Seq:
Struc:
419 a.a.
317 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 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
Bound ligand (Het Group name = TYR)
corresponds exactly
+ 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!
  Cellular component     cytoplasm   1 term 
  Biological process     tRNA aminoacylation for protein translation   2 terms 
  Biochemical function     nucleotide binding     4 terms  

 

 
    reference    
 
 
J Mol Biol 194:287-297 (1987)
PubMed id: 3612807  
 
 
Crystal structure of a deletion mutant of a tyrosyl-tRNA synthetase complexed with tyrosine.
P.Brick, D.M.Blow.
 
  ABSTRACT  
 
The crystal structure of a deletion mutant of tyrosyl-tRNA synthetase from Bacillus stearothermophilus has been determined at 2.5 A resolution using molecular replacement techniques. The genetically engineered molecule catalyses the activation of tyrosine with kinetic properties similar to those of the wild-type enzyme but no longer binds tRNATyr. It contains 319 residues corresponding to the region of the polypeptide chain for which interpretable electron density is present in crystals of the wild-type enzyme. The partly refined model of the wild-type enzyme was used as a starting point in determining the structure of the truncated mutant. The new crystals are of space group P2(1) and contain the molecular dimer within the asymmetric unit. The refined model has a crystallographic R-factor of 18.7% for all reflections between 8 and 2.5 A. Each subunit contains two structural domains: the alpha/beta domain (residues 1 to 220) containing a six-stranded beta-sheet and the alpha-helical domain (residues 248 to 319) containing five helices. The alpha/beta domains are related by a non-crystallographic dyad while the alpha-helical domains are in slightly different orientations in the two subunits. The tyrosine substrate binds in a slot at the bottom of a deep active site cleft in the middle of the alpha/beta domain. It is surrounded by polar side-chains and water molecules that are involved in an intricate hydrogen bonding network. Both the alpha-amino and hydroxyl groups of the substrate make good hydrogen bonds with the protein. The amino group forms hydrogen bonds with Tyr169-OH, Asp78-OD1 and Gln173-OE1. The phenolic hydroxyl group forms hydrogen bonds with Asp76-OD1 and Tyr34-OH. In contrast, the substrate carboxyl group makes no direct interactions with the enzyme. The results of both substrate inhibition studies and site-directed mutagenesis experiments have been examined in the light of the refined structure.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
18319247 A.Sheoran, G.Sharma, and E.A.First (2008).
Activation of D-tyrosine by Bacillus stearothermophilus tyrosyl-tRNA synthetase: 1. Pre-steady-state kinetic analysis reveals the mechanistic basis for the recognition of D-tyrosine.
  J Biol Chem, 283, 12960-12970.  
18180246 N.Shen, M.Zhou, B.Yang, Y.Yu, X.Dong, and J.Ding (2008).
Catalytic mechanism of the tryptophan activation reaction revealed by crystal structures of human tryptophanyl-tRNA synthetase in different enzymatic states.
  Nucleic Acids Res, 36, 1288-1299.
PDB codes: 2quh 2qui 2quj 2quk
18559342 S.I.Hauenstein, Y.M.Hou, and J.J.Perona (2008).
The homotetrameric phosphoseryl-tRNA synthetase from Methanosarcina mazei exhibits half-of-the-sites activity.
  J Biol Chem, 283, 21997-22006.  
18560823 T.Li, M.Froeyen, and P.Herdewijn (2008).
Comparative structural dynamics of Tyrosyl-tRNA synthetase complexed with different substrates explored by molecular dynamics.
  Eur Biophys J, 38, 25-35.  
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
15671170 T.Kobayashi, K.Sakamoto, T.Takimura, R.Sekine, V.P.Kelly, K.Vincent, K.Kamata, S.Nishimura, and S.Yokoyama (2005).
Structural basis of nonnatural amino acid recognition by an engineered aminoacyl-tRNA synthetase for genetic code expansion.
  Proc Natl Acad Sci U S A, 102, 1366-1371.
PDB codes: 1vbn 1wq3 1wq4
14997565 K.W.Lee, and J.M.Briggs (2004).
Molecular modeling study of the editing active site of Escherichia coli leucyl-tRNA synthetase: two amino acid binding sites in the editing domain.
  Proteins, 54, 693-704.  
12787471 S.J.Hughes, J.A.Tanner, A.D.Hindley, A.D.Miller, and I.R.Gould (2003).
Functional asymmetry in the lysyl-tRNA synthetase explored by molecular dynamics, free energy calculations and experiment.
  BMC Struct Biol, 3, 5.  
12754495 T.Kobayashi, O.Nureki, R.Ishitani, A.Yaremchuk, M.Tukalo, S.Cusack, K.Sakamoto, and S.Yokoyama (2003).
Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion.
  Nat Struct Biol, 10, 425-432.
PDB code: 1j1u
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
12011422 D.Zhang, N.Vaidehi, W.A.Goddard, J.F.Danzer, and D.Debe (2002).
Structure-based design of mutant Methanococcus jannaschii tyrosyl-tRNA synthetase for incorporation of O-methyl-L-tyrosine.
  Proc Natl Acad Sci U S A, 99, 6579-6584.  
12016229 J.Austin, and E.A.First (2002).
Comparison of the catalytic roles played by the KMSKS motif in the human and Bacillus stearothermophilus trosyl-tRNA synthetases.
  J Biol Chem, 277, 28394-28399.  
12005430 J.I.Guijarro, A.Pintar, A.Prochnicka-Chalufour, V.Guez, B.Gilquin, H.Bedouelle, and M.Delepierre (2002).
Structure and dynamics of the anticodon arm binding domain of Bacillus stearothermophilus Tyrosyl-tRNA synthetase.
  Structure, 10, 311-317.
PDB code: 1jh3
11567092 X.Qiu, C.A.Janson, W.W.Smith, S.M.Green, P.McDevitt, K.Johanson, P.Carter, M.Hibbs, C.Lewis, A.Chalker, A.Fosberry, J.Lalonde, J.Berge, P.Brown, C.S.Houge-Frydrych, and R.L.Jarvest (2001).
Crystal structure of Staphylococcus aureus tyrosyl-tRNA synthetase in complex with a class of potent and specific inhibitors.
  Protein Sci, 10, 2008-2016.
PDB codes: 1jii 1jij 1jik 1jil
10966471 M.Ibba, and D.Soll (2000).
Aminoacyl-tRNA synthesis.
  Annu Rev Biochem, 69, 617-650.  
10677223 V.Guez, S.Nair, A.Chaffotte, and H.Bedouelle (2000).
The anticodon-binding domain of tyrosyl-tRNA synthetase: state of folding and origin of the crystallographic disorder.
  Biochemistry, 39, 1739-1747.  
10570126 B.A.Steer, and P.Schimmel (1999).
Domain-domain communication in a miniature archaebacterial tRNA synthetase.
  Proc Natl Acad Sci U S A, 96, 13644-13649.  
10385005 L.Jermutus, V.Guez, and H.Bedouelle (1999).
Disordered C-terminal domain of tyrosyl-tRNA synthetase: secondary structure prediction.
  Biochimie, 81, 235-244.  
9660761 Y.C.Park, and H.Bedouelle (1998).
Dimeric tyrosyl-tRNA synthetase from Bacillus stearothermophilus unfolds through a monomeric intermediate. A quantitative analysis under equilibrium conditions.
  J Biol Chem, 273, 18052-18059.  
9050827 C.M.Joyce (1997).
Choosing the right sugar: how polymerases select a nucleotide substrate.
  Proc Natl Acad Sci U S A, 94, 1619-1622.  
7773747 M.Delarue (1995).
Aminoacyl-tRNA synthetases.
  Curr Opin Struct Biol, 5, 48-55.  
7479698 P.Bork, L.Holm, E.V.Koonin, and C.Sander (1995).
The cytidylyltransferase superfamily: identification of the nucleotide-binding site and fold prediction.
  Proteins, 22, 259-266.  
7743129 S.Doublié, G.Bricogne, C.Gilmore, and C.W.Carter (1995).
Tryptophanyl-tRNA synthetase crystal structure reveals an unexpected homology to tyrosyl-tRNA synthetase.
  Structure, 3, 17-31.  
  8468307 B.V.Taylor, J.Toy, T.L.Sit, and A.L.Bognar (1993).
Cloning and sequence determination of the valS gene, encoding valyl-tRNA synthetase in Lactobacillus casei.
  J Bacteriol, 175, 2475-2478.  
  7691478 D.D.Buechter, and P.Schimmel (1993).
Aminoacylation of RNA minihelices: implications for tRNA synthetase structural design and evolution.
  Crit Rev Biochem Mol Biol, 28, 309-322.  
8274143 M.Delarue, and D.Moras (1993).
The aminoacyl-tRNA synthetase family: modules at work.
  Bioessays, 15, 675-687.  
1581544 J.Edelman (1992).
The low-temperature heat capacity of solid proteins.
  Biopolymers, 32, 209-218.  
2183216 J.J.Burbaum, R.M.Starzyk, and P.Schimmel (1990).
Understanding structural relationships in proteins of unsolved three-dimensional structure.
  Proteins, 7, 99.  
3607872 R.A.Akins, and A.M.Lambowitz (1987).
A protein required for splicing group I introns in Neurospora mitochondria is mitochondrial tyrosyl-tRNA synthetase or a derivative thereof.
  Cell, 50, 331-345.  
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.