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protein dna_rna ligands metals links
Ligase/RNA PDB id
1qf6
Jmol
Contents
Protein chain
641 a.a. *
DNA/RNA
Ligands
AMP
Metals
_ZN
Waters ×244
* Residue conservation analysis
PDB id:
1qf6
Name: Ligase/RNA
Title: Structure of e. Coli threonyl-tRNA synthetase complexed with cognate tRNA
Structure: Threonine tRNA. Chain: b. Synonym: tRNA (thr). Other_details: complexed with adenosine monophosphate. Threonyl-tRNA synthetase. Chain: a. Synonym: thrrs. Ec: 6.1.1.3
Source: Escherichia coli. Organism_taxid: 562. Organism_taxid: 562
Biol. unit: Tetramer (from PQS)
Resolution:
2.90Å     R-factor:   0.195     R-free:   0.239
Authors: R.Sankaranarayanan,A.C.Dock-Bregeon,B.Rees,D.Moras
Key ref:
R.Sankaranarayanan et al. (1999). The structure of threonyl-tRNA synthetase-tRNA(Thr) complex enlightens its repressor activity and reveals an essential zinc ion in the active site. Cell, 97, 371-381. PubMed id: 10319817 DOI: 10.1016/S0092-8674(00)80746-1
Date:
06-Apr-99     Release date:   06-May-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A8M3  (SYT_ECOLI) -  Threonyl-tRNA synthetase
Seq:
Struc: 		 
Seq:
Struc: 		642 a.a.
641 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.6.1.1.3  - Threonine--tRNA ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + L-threonine + tRNA(Thr) = AMP + diphosphate + L-threonyl-tRNA(Thr)
ATP
 + L-threonine
 + tRNA(Thr)
 =
AMP
Bound ligand (Het Group name = AMP)
corresponds exactly 		+ diphosphate
 + L-threonyl-tRNA(Thr)
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     regulation of translation   6 terms 
  Biochemical function     nucleotide binding     12 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0092-8674(00)80746-1 Cell 97:371-381 (1999)
PubMed id: 10319817  
 
 
The structure of threonyl-tRNA synthetase-tRNA(Thr) complex enlightens its repressor activity and reveals an essential zinc ion in the active site.
R.Sankaranarayanan, A.C.Dock-Bregeon, P.Romby, J.Caillet, M.Springer, B.Rees, C.Ehresmann, B.Ehresmann, D.Moras.
 
  ABSTRACT  
 
E. coli threonyl-tRNA synthetase (ThrRS) is a class II enzyme that represses the translation of its own mRNA. We report the crystal structure at 2.9 A resolution of the complex between tRNA(Thr) and ThrRS, whose structural features reveal novel strategies for providing specificity in tRNA selection. These include an amino-terminal domain containing a novel protein fold that makes minor groove contacts with the tRNA acceptor stem. The enzyme induces a large deformation of the anticodon loop, resulting in an interaction between two adjacent anticodon bases, which accounts for their prominent role in tRNA identity and translational regulation. A zinc ion found in the active site is implicated in amino acid recognition/discrimination.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. The Structure of ThrRS from E. coli(A) A view along the 2-fold axis with the dimer and the tRNAs in CPK representation. The monomers are shown in green and yellow and the corresponding tRNAs in red and violet. The view highlights the CCA ends entering the catalytic core and the cross-subunit contacts.(B) Domain architecture of a monomer of ThrRS. The same color code is used throughout for the different domains. The figure was made using SETOR ([16]).
Figure 4.
Figure 4. Acceptor Arm Recognition(A) CCA interactions in the active site domain. Motifs 2 and 3 are colored in red and green, respectively. The CCA and the protein residues interacting with it are in stick representation. The AMP, the zinc, and a water molecule are represented in orange stick, pink, and cyan spheres, respectively.(B) Minor groove recognition at the acceptor stem. The base-specific interactions are indicated. The phosphate backbone of the tRNA is shown as a purple ribbon where a stick model represents the bases. The interacting residues from the N2 domain are indicated in stick representation.(C) Sequence comparison with AlaRS for the N2 domain. TRSEc represents ThrRS from Escherichia coli, and ARSEc, ARSTt, ARSSc, and ARSHs represent AlaRS from Escherichia coli, Thermus thermophilus, Saccharomyces cerevisiae, and Homo sapiens, respectively. The highly conserved residues in ThrRS and AlaRS surrounding a cleft are indicated by red spheres. (A) and (B) were made using SETOR ([16]) and (C) was made using ALSCRIPT ( [2]).
 
  The above figures are reprinted by permission from Cell Press: Cell (1999, 97, 371-381) copyright 1999.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21222438 A.Minajigi, B.Deng, and C.S.Francklyn (2011).
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PDB codes: 3hri 3hrk 3lc0
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PDB codes: 2zni 2znj
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PDB code: 3g98
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PDB codes: 2ztg 2zvf
19385727 P.Babitzke, C.S.Baker, and T.Romeo (2009).
Regulation of translation initiation by RNA binding proteins.
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19710017 R.T.Guo, Y.E.Chong, M.Guo, and X.L.Yang (2009).
Crystal structures and biochemical analyses suggest a unique mechanism and role for human glycyl-tRNA synthetase in Ap4A homeostasis.
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RNA-assisted catalysis in a protein enzyme: The 2'-hydroxyl of tRNA(Thr) A76 promotes aminoacylation by threonyl-tRNA synthetase.
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18850722 C.S.Francklyn (2008).
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  J Biol Chem, 281, 27862-27872.  
16731979 V.Jain, R.Saleem-Batcha, A.China, and D.Chatterji (2006).
Molecular dissection of the mycobacterial stringent response protein Rel.
  Protein Sci, 15, 1449-1464.  
15507440 B.Ruan, M.L.Bovee, M.Sacher, C.Stathopoulos, K.Poralla, C.S.Francklyn, and D.Söll (2005).
A unique hydrophobic cluster near the active site contributes to differences in borrelidin inhibition among threonyl-tRNA synthetases.
  J Biol Chem, 280, 571-577.  
16059752 H.L.Wu, S.Bagby, and J.M.van den Elsen (2005).
Evolution of the genetic triplet code via two types of doublet codons.
  J Mol Evol, 61, 54-64.  
16087889 M.Sokabe, A.Okada, M.Yao, T.Nakashima, and I.Tanaka (2005).
Molecular basis of alanine discrimination in editing site.
  Proc Natl Acad Sci U S A, 102, 11669-11674.
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  Proc Natl Acad Sci U S A, 101, 10260-10265.  
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Post-transfer editing in vitro and in vivo by the beta subunit of phenylalanyl-tRNA synthetase.
  EMBO J, 23, 4639-4648.  
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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.  
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The zinc-binding site of a class I aminoacyl-tRNA synthetase is a SWIM domain that modulates amino acid binding via the tRNA acceptor arm.
  Eur J Biochem, 271, 724-733.  
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Biosynthesis of nonribosomal peptides1.
  Annu Rev Microbiol, 58, 453-488.  
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Cloning, expression, purification, crystallization and preliminary X-ray crystallographic investigations of a unique editing domain from archaebacteria.
  Acta Crystallogr D Biol Crystallogr, 60, 1662-1664.  
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  J Bacteriol, 185, 4031-4037.
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The long-range electrostatic interactions control tRNA-aminoacyl-tRNA synthetase complex formation.
  Protein Sci, 12, 1247-1251.  
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Crystal structure of tRNA(m1G37)methyltransferase: insights into tRNA recognition.
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PDB codes: 1uaj 1uak 1ual 1uam
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Tools for the automatic identification and classification of RNA base pairs.
  Nucleic Acids Res, 31, 3450-3460.  
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Trans-editing of mischarged tRNAs.
  Proc Natl Acad Sci U S A, 100, 15422-15427.  
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The modular structure of Escherichia coli threonyl-tRNA synthetase as both an enzyme and a regulator of gene expression.
  Mol Microbiol, 47, 961-974.  
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  J Bacteriol, 185, 4204-4210.
PDB codes: 1o09 1p9k
14690420 M.L.Bovee, M.A.Pierce, and C.S.Francklyn (2003).
Induced fit and kinetic mechanism of adenylation catalyzed by Escherichia coli threonyl-tRNA synthetase.
  Biochemistry, 42, 15102-15113.  
12787346 P.J.Schlax, and D.J.Worhunsky (2003).
Translational repression mechanisms in prokaryotes.
  Mol Microbiol, 48, 1157-1169.  
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Bacterial translational control at atomic resolution.
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Structural basis of translational control by Escherichia coli threonyl tRNA synthetase.
  Nat Struct Biol, 9, 343-347.
PDB code: 1kog
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Aminoacyl-tRNA synthetases: versatile players in the changing theater of translation.
  RNA, 8, 1363-1372.  
12165569 F.J.Grundy, W.C.Winkler, and T.M.Henkin (2002).
tRNA-mediated transcription antitermination in vitro: codon-anticodon pairing independent of the ribosome.
  Proc Natl Acad Sci U S A, 99, 11121-11126.  
12379656 J.A.Carrodeguas, K.G.Pinz, and D.F.Bogenhagen (2002).
DNA binding properties of human pol gammaB.
  J Biol Chem, 277, 50008-50014.  
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Isothermal titration calorimetry reveals a zinc ion as an atomic switch in the diadenosine polyphosphates.
  J Biol Chem, 277, 3073-3078.  
  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
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Structure of the 16S rRNA pseudouridine synthase RsuA bound to uracil and UMP.
  Nat Struct Biol, 9, 353-358.
PDB codes: 1ksk 1ksl 1ksv
12392550 K.Ye, A.Serganov, W.Hu, M.Garber, and D.J.Patel (2002).
Ribosome-associated factor Y adopts a fold resembling a double-stranded RNA binding domain scaffold.
  Eur J Biochem, 269, 5182-5191.
PDB code: 1l4s
12022232 P.J.Beuning, M.C.Nagan, C.J.Cramer, K.Musier-Forsyth, J.L.Gelpí, and D.Bashford (2002).
Efficient aminoacylation of the tRNA(Ala) acceptor stem: dependence on the 2:71 base pair.
  RNA, 8, 659-670.  
12019264 T.Takita, and K.Inouye (2002).
Transition state stabilization by the N-terminal anticodon-binding domain of lysyl-tRNA synthetase.
  J Biol Chem, 277, 29275-29282.  
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Structural and mutational studies of the recognition of the arginine tRNA-specific major identity element, A20, by arginyl-tRNA synthetase.
  Proc Natl Acad Sci U S A, 98, 13537-13542.
PDB codes: 1iq0 1ir4
  11435117 H.A.Lewis, E.B.Furlong, B.Laubert, G.A.Eroshkina, Y.Batiyenko, J.M.Adams, M.G.Bergseid, C.D.Marsh, T.S.Peat, W.E.Sanderson, J.M.Sauder, and S.G.Buchanan (2001).
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  Structure, 9, 527-537.
PDB codes: 1inn 1j6v 1j6w 1j6x 1vje
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Crystal structure and deletion analysis show that the accessory subunit of mammalian DNA polymerase gamma, Pol gamma B, functions as a homodimer.
  Mol Cell, 7, 43-54.
PDB codes: 1g5h 1g5i
11269237 L.Ribas de Pouplana, and P.Schimmel (2001).
Two classes of tRNA synthetases suggested by sterically compatible dockings on tRNA acceptor stem.
  Cell, 104, 191-193.  
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Aminoacyl-tRNA synthetases: potential markers of genetic code development.
  Trends Biochem Sci, 26, 591-596.  
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Crystal structure of the quorum-sensing protein LuxS reveals a catalytic metal site.
  Proc Natl Acad Sci U S A, 98, 11169-11174.
PDB code: 1ie0
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Structure at 2.6 A resolution of phenylalanyl-tRNA synthetase complexed with phenylalanyl-adenylate in the presence of manganese.
  Acta Crystallogr D Biol Crystallogr, 57, 1534-1544.
PDB code: 1jjc
11329259 S.A.Hawko, and C.S.Francklyn (2001).
Covariation of a specificity-determining structural motif in an aminoacyl-tRNA synthetase and a tRNA identity element.
  Biochemistry, 40, 1930-1936.  
10679466 A.A.Antson (2000).
Single-stranded-RNA binding proteins.
  Curr Opin Struct Biol, 10, 87-94.  
10851193 A.D.Frankel (2000).
Fitting peptides into the RNA world.
  Curr Opin Struct Biol, 10, 332-340.  
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Crystal structure of a eukaryote/archaeon-like protyl-tRNA synthetase and its complex with tRNAPro(CGG).
  EMBO J, 19, 4745-4758.  
11112540 B.Burke, F.Yang, F.Chen, C.Stehlin, B.Chan, and K.Musier-Forsyth (2000).
Evolutionary coadaptation of the motif 2--acceptor stem interaction in the class II prolyl-tRNA synthetase system.
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11060012 B.Delagoutte, D.Moras, and J.Cavarelli (2000).
tRNA aminoacylation by arginyl-tRNA synthetase: induced conformations during substrates binding.
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PDB codes: 1f7u 1f7v
10675344 B.L.Staker, P.Korber, J.C.Bardwell, and M.A.Saper (2000).
Structure of Hsp15 reveals a novel RNA-binding motif.
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PDB code: 1dm9
10710420 C.S.Chiang, and G.J.Liaw (2000).
A missense mutation in the nuclear gene coding for the mitochondrial aspartyl-tRNA synthetase suppresses a mitochondrial tRNA(Asp) mutation.
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  10745012 E.Westhof, and V.Fritsch (2000).
RNA folding: beyond Watson-Crick pairs.
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10841541 G.Minasov, M.Teplova, G.C.Stewart, E.V.Koonin, W.F.Anderson, and M.Egli (2000).
Functional implications from crystal structures of the conserved Bacillus subtilis protein Maf with and without dUTP.
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PDB codes: 1ex2 1exc
10678983 G.Subramanian, E.V.Koonin, and L.Aravind (2000).
Comparative genome analysis of the pathogenic spirochetes Borrelia burgdorferi and Treponema pallidum.
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10676814 H.A.Lewis, K.Musunuru, K.B.Jensen, C.Edo, H.Chen, R.B.Darnell, and S.K.Burley (2000).
Sequence-specific RNA binding by a Nova KH domain: implications for paraneoplastic disease and the fragile X syndrome.
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PDB code: 1ec6
10813833 H.Zhang, K.Huang, Z.Li, L.Banerjei, K.E.Fisher, N.V.Grishin, E.Eisenstein, and O.Herzberg (2000).
Crystal structure of YbaK protein from Haemophilus influenzae (HI1434) at 1.8 A resolution: functional implications.
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PDB codes: 1dbu 1dbx
10889033 J.A.Pleiss, A.D.Wolfson, and O.C.Uhlenbeck (2000).
Mapping contacts between Escherichia coli alanyl tRNA synthetase and 2' hydroxyls using a complete tRNA molecule.
  Biochemistry, 39, 8250-8258.  
10966471 M.Ibba, and D.Soll (2000).
Aminoacyl-tRNA synthesis.
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11118226 M.Kaminska, M.Deniziak, P.Kerjan, J.Barciszewski, and M.Mirande (2000).
A recurrent general RNA binding domain appended to plant methionyl-tRNA synthetase acts as a cis-acting cofactor for aminoacylation.
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10592262 M.Szymanski, and J.Barciszewski (2000).
Aminoacyl-tRNA synthetases database Y2K.
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11041850 S.Onesti, G.Desogus, A.Brevet, J.Chen, P.Plateau, S.Blanquet, and P.Brick (2000).
Structural studies of lysyl-tRNA synthetase: conformational changes induced by substrate binding.
  Biochemistry, 39, 12853-12861.
PDB codes: 1bbu 1bbw
11105758 T.A.Nissan, and J.J.Perona (2000).
Alternative designs for construction of the class II transfer RNA tertiary core.
  RNA, 6, 1585-1596.  
10632708 V.Cura, D.Moras, and D.Kern (2000).
Sequence analysis and modular organization of threonyl-tRNA synthetase from Thermus thermophilus and its interrelation with threonyl-tRNA synthetases of other origins.
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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.
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10497122 J.H.Cate, M.M.Yusupov, G.Z.Yusupova, T.N.Earnest, and H.F.Noller (1999).
X-ray crystal structures of 70S ribosome functional complexes.
  Science, 285, 2095-2104.
PDB code: 486d
10518524 K.Y.Chang, G.Varani, S.Bhattacharya, H.Choi, and W.H.McClain (1999).
Correlation of deformability at a tRNA recognition site and aminoacylation specificity.
  Proc Natl Acad Sci U S A, 96, 11764-11769.  
10737860 P.J.Beuning, and K.Musier-Forsyth (1999).
Transfer RNA recognition by aminoacyl-tRNA synthetases.
  Biopolymers, 52, 1.  
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