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PDBsum entry 1pys
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Aminoacyl-tRNA synthetase PDB id
1pys

 

 

 

 

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Contents
Protein chains
266 a.a. *
785 a.a. *
Metals
_MG
Waters ×996
* Residue conservation analysis
PDB id:
1pys
Name: Aminoacyl-tRNA synthetase
Title: Phenylalanyl-tRNA synthetase from thermus thermophilus
Structure: Phenylalanyl-tRNA synthetase. Chain: a. Phenylalanyl-tRNA synthetase. Chain: b. Ec: 6.1.1.20
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Strain: hb8
Biol. unit: Tetramer (from PDB file)
Resolution:
2.90Å     R-factor:   0.177     R-free:   0.236
Authors: M.Safro,L.Mosyak,Y.Goldgur,L.Reshetnikova,M.Delarue
Key ref: L.Mosyak et al. (1995). Structure of phenylalanyl-tRNA synthetase from Thermus thermophilus. Nat Struct Biol, 2, 537-547. PubMed id: 7664121
Date:
14-Nov-96     Release date:   19-Nov-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q5SGX2  (SYFA_THET8) -  Phenylalanine--tRNA ligase alpha subunit from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		350 a.a.
266 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SGX1  (SYFB_THET8) -  Phenylalanine--tRNA ligase beta subunit from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		 
Seq:
Struc: 		785 a.a.
785 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.6.1.1.20  - phenylalanine--tRNA ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: tRNA(Phe) + L-phenylalanine + ATP = L-phenylalanyl-tRNA(Phe) + AMP + diphosphate + H+
tRNA(Phe)
 + L-phenylalanine
 + ATP
 = L-phenylalanyl-tRNA(Phe)
 + AMP
 + diphosphate
 + H(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
Nat Struct Biol 2:537-547 (1995)
PubMed id: 7664121  
 
 
Structure of phenylalanyl-tRNA synthetase from Thermus thermophilus.
L.Mosyak, L.Reshetnikova, Y.Goldgur, M.Delarue, M.G.Safro.
 
  ABSTRACT  
 
The crystal structure of phenylalanyl-tRNA synthetase from Thermus thermophilus, solved at 2.9 A resolution, displays (alpha beta)2 subunit organization. Unexpectedly, both the catalytic alpha- and the non-catalytic beta-subunits comprise the characteristic fold of the class II active-site domains. The alpha beta heterodimer contains most of the building blocks so far identified in the class II synthetases. The presence of an RNA-binding domain, similar to that of the U1A spliceosomal protein, in the beta-subunit is indicative of structural relationships among different families of RNA-binding proteins. The structure suggests a plausible catalytic mechanism which explains why the primary site of tRNA aminoacylation is different from that of the other class II enzymes.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21222438 A.Minajigi, B.Deng, and C.S.Francklyn (2011).
Fidelity escape by the unnatural amino acid β-hydroxynorvaline: an efficient substrate for Escherichia coli threonyl-tRNA synthetase with toxic effects on growth.
  Biochemistry, 50, 1101-1109.  
21082706 I.Mermershtain, I.Finarov, L.Klipcan, N.Kessler, H.Rozenberg, and M.G.Safro (2011).
Idiosyncrasy and identity in the prokaryotic phe-system: crystal structure of E. coli phenylalanyl-tRNA synthetase complexed with phenylalanine and AMP.
  Protein Sci, 20, 160-167.
PDB code: 3pco
20194428 G.P.Fournier, and J.P.Gogarten (2010).
Rooting the ribosomal tree of life.
  Mol Biol Evol, 27, 1792-1801.  
20223217 I.Finarov, N.Moor, N.Kessler, L.Klipcan, and M.G.Safro (2010).
Structure of human cytosolic phenylalanyl-tRNA synthetase: evidence for kingdom-specific design of the active sites and tRNA binding patterns.
  Structure, 18, 343-353.
PDB code: 3l4g
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.  
  19193993 I.Finarov, N.Moor, N.Kessler, and M.Safro (2009).
Crystallization and X-ray analysis of human cytoplasmic phenylalanyl-tRNA synthetase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 93-97.  
19549855 L.Klipcan, N.Moor, N.Kessler, and M.G.Safro (2009).
Eukaryotic cytosolic and mitochondrial phenylalanyl-tRNA synthetases catalyze the charging of tRNA with the meta-tyrosine.
  Proc Natl Acad Sci U S A, 106, 11045-11048.
PDB codes: 3hfv 3hfz
19423669 M.Naganuma, S.Sekine, R.Fukunaga, and S.Yokoyama (2009).
Unique protein architecture of alanyl-tRNA synthetase for aminoacylation, editing, and dimerization.
  Proc Natl Acad Sci U S A, 106, 8489-8494.
PDB codes: 2ztg 2zvf
19228694 S.Bilokapic, N.Ivic, V.Godinic-Mikulcic, I.Piantanida, N.Ban, and I.Weygand-Durasevic (2009).
Idiosyncratic Helix-Turn-Helix Motif in Methanosarcina barkeri Seryl-tRNA Synthetase Has a Critical Architectural Role.
  J Biol Chem, 284, 10706-10713.  
18765802 K.Oki, K.Sakamoto, T.Kobayashi, H.M.Sasaki, and S.Yokoyama (2008).
Transplantation of a tyrosine editing domain into a tyrosyl-tRNA synthetase variant enhances its specificity for a tyrosine analog.
  Proc Natl Acad Sci U S A, 105, 13298-13303.  
18611382 L.Klipcan, I.Levin, N.Kessler, N.Moor, I.Finarov, and M.Safro (2008).
The tRNA-induced conformational activation of human mitochondrial phenylalanyl-tRNA synthetase.
  Structure, 16, 1095-1104.
PDB code: 3cmq
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.  
18186487 Y.G.Gao, M.Yao, and I.Tanaka (2008).
Structure of protein PH0536 from Pyrococcus horikoshii at 1.7 A resolution reveals a novel assembly of an oligonucleotide/oligosaccharide-binding fold and an alpha-helical bundle.
  Proteins, 71, 503-508.
PDB code: 2e8g
17595300 G.Lerman, and B.E.Shakhnovich (2007).
Defining functional distance using manifold embeddings of gene ontology annotations.
  Proc Natl Acad Sci U S A, 104, 11334-11339.  
  17768348 I.Levin, N.Kessler, N.Moor, L.Klipcan, E.Koc, P.Templeton, L.Spremulli, and M.Safro (2007).
Purification, crystallization and preliminary X-ray characterization of a human mitochondrial phenylalanyl-tRNA synthetase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 761-764.  
17185419 J.Ling, H.Roy, and M.Ibba (2007).
Mechanism of tRNA-dependent editing in translational quality control.
  Proc Natl Acad Sci U S A, 104, 72-77.  
17351629 R.Fukunaga, and S.Yokoyama (2007).
Structural insights into the first step of RNA-dependent cysteine biosynthesis in archaea.
  Nat Struct Mol Biol, 14, 272-279.
PDB codes: 2du3 2du4 2du5 2du6 2du7
17301225 S.Kamtekar, M.J.Hohn, H.S.Park, M.Schnitzbauer, A.Sauerwald, D.Söll, and T.A.Steitz (2007).
Toward understanding phosphoseryl-tRNACys formation: the crystal structure of Methanococcus maripaludis phosphoseryl-tRNA synthetase.
  Proc Natl Acad Sci U S A, 104, 2620-2625.
PDB code: 2odr
17003130 H.M.Sasaki, S.Sekine, T.Sengoku, R.Fukunaga, M.Hattori, Y.Utsunomiya, C.Kuroishi, S.Kuramitsu, M.Shirouzu, and S.Yokoyama (2006).
Structural and mutational studies of the amino acid-editing domain from archaeal/eukaryal phenylalanyl-tRNA synthetase.
  Proc Natl Acad Sci U S A, 103, 14744-14749.
PDB code: 2cxi
16338408 O.Kotik-Kogan, N.Moor, D.Tworowski, and M.Safro (2005).
Structural basis for discrimination of L-phenylalanine from L-tyrosine by phenylalanyl-tRNA synthetase.
  Structure, 13, 1799-1807.
PDB codes: 2akw 2aly 2amc
16380427 P.O'Donoghue, A.Sethi, C.R.Woese, and Z.A.Luthey-Schulten (2005).
The evolutionary history of Cys-tRNACys formation.
  Proc Natl Acad Sci U S A, 102, 19003-19008.  
15333634 A.Martins, and S.Shuman (2004).
An RNA ligase from Deinococcus radiodurans.
  J Biol Chem, 279, 50654-50661.  
14742205 D.Beyer, H.P.Kroll, R.Endermann, G.Schiffer, S.Siegel, M.Bauser, J.Pohlmann, M.Brands, K.Ziegelbauer, D.Haebich, C.Eymann, and H.Brötz-Oesterhelt (2004).
New class of bacterial phenylalanyl-tRNA synthetase inhibitors with high potency and broad-spectrum activity.
  Antimicrob Agents Chemother, 48, 525-532.  
15526031 H.Roy, J.Ling, M.Irnov, and M.Ibba (2004).
Post-transfer editing in vitro and in vivo by the beta subunit of phenylalanyl-tRNA synthetase.
  EMBO J, 23, 4639-4648.  
15053876 M.A.Swairjo, F.J.Otero, X.L.Yang, M.A.Lovato, R.J.Skene, D.E.McRee, L.Ribas de Pouplana, and P.Schimmel (2004).
Alanyl-tRNA synthetase crystal structure and design for acceptor-stem recognition.
  Mol Cell, 13, 829-841.
PDB code: 1riq
14579367 A.Seto, M.Shirouzu, T.Terada, K.Murayama, S.Kuramitsu, and S.Yokoyama (2003).
Crystal structure of a hypothetical protein, TT1725, from Thermus thermophilus HB8 at 1.7 A resolution.
  Proteins, 53, 768-771.
PDB code: 1j27
12591875 S.W.Jordan, and J.E.Cronan (2003).
The Escherichia coli lipB gene encodes lipoyl (octanoyl)-acyl carrier protein:protein transferase.
  J Bacteriol, 185, 1582-1589.  
12377129 A.E.Todd, C.A.Orengo, and J.M.Thornton (2002).
Sequence and structural differences between enzyme and nonenzyme homologs.
  Structure, 10, 1435-1451.  
12382236 I.A.Vasil'eva, V.N.Ankilova, O.I.Lavrik, and N.A.Moor (2002).
tRNA discrimination by T. thermophilus phenylalanyl-tRNA synthetase at the binding step.
  J Mol Recognit, 15, 188-196.  
11157763 L.Renault, P.Kerjan, S.Pasqualato, J.Ménétrey, J.C.Robinson, S.Kawaguchi, D.G.Vassylyev, S.Yokoyama, M.Mirande, and J.Cherfils (2001).
Structure of the EMAPII domain of human aminoacyl-tRNA synthetase complex reveals evolutionary dimer mimicry.
  EMBO J, 20, 570-578.
PDB codes: 1e7z 1fl0
11157762 S.Kawaguchi, J.Müller, D.Linde, S.Kuramitsu, T.Shibata, Y.Inoue, D.G.Vassylyev, and S.Yokoyama (2001).
The crystal structure of the ttCsaA protein: an export-related chaperone from Thermus thermophilus.
  EMBO J, 20, 562-569.
PDB code: 1gd7
10931945 C.D.Wolfgang, M.Essand, J.J.Vincent, B.Lee, and I.Pastan (2000).
TARP: a nuclear protein expressed in prostate and breast cancer cells derived from an alternate reading frame of the T cell receptor gamma chain locus.
  Proc Natl Acad Sci U S A, 97, 9437-9442.  
10966471 M.Ibba, and D.Soll (2000).
Aminoacyl-tRNA synthesis.
  Annu Rev Biochem, 69, 617-650.  
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
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.  
10562563 M.Stoldt, J.Wöhnert, O.Ohlenschläger, M.Görlach, and L.R.Brown (1999).
The NMR structure of the 5S rRNA E-domain-protein L25 complex shows preformed and induced recognition.
  EMBO J, 18, 6508-6521.
PDB code: 1d6k
9659920 G.Simos, A.Sauer, F.Fasiolo, and E.C.Hurt (1998).
A conserved domain within Arc1p delivers tRNA to aminoacyl-tRNA synthetases.
  Mol Cell, 1, 235-242.  
9736622 L.Ribas de Pouplana, D.Buechter, N.Y.Sardesai, and P.Schimmel (1998).
Functional analysis of peptide motif for RNA microhelix binding suggests new family of RNA-binding domains.
  EMBO J, 17, 5449-5457.  
9799245 M.Stoldt, J.Wöhnert, M.Görlach, and L.R.Brown (1998).
The NMR structure of Escherichia coli ribosomal protein L25 shows homology to general stress proteins and glutaminyl-tRNA synthetases.
  EMBO J, 17, 6377-6384.
PDB code: 1b75
  9521119 R.Furter (1998).
Expansion of the genetic code: site-directed p-fluoro-phenylalanine incorporation in Escherichia coli.
  Protein Sci, 7, 419-426.  
9115984 A.Aberg, A.Yaremchuk, M.Tukalo, B.Rasmussen, and S.Cusack (1997).
Crystal structure analysis of the activation of histidine by Thermus thermophilus histidyl-tRNA synthetase.
  Biochemistry, 36, 3084-3094.
PDB codes: 1adj 1ady
9207019 A.Lechler, A.Martin, T.Zuleeg, S.Limmer, and R.Kreutzer (1997).
A biologically active 53 kDa fragment of overproduced alanyl-tRNA synthetase from Thermus thermophilus HB8 specifically interacts with tRNA Ala acceptor helix.
  Nucleic Acids Res, 25, 2737-2744.  
9032056 B.F.Clark, and J.Nyborg (1997).
The ternary complex of EF-Tu and its role in protein biosynthesis.
  Curr Opin Struct Biol, 7, 110-116.  
9008164 M.Bycroft, T.J.Hubbard, M.Proctor, S.M.Freund, and A.G.Murzin (1997).
The solution structure of the S1 RNA binding domain: a member of an ancient nucleic acid-binding fold.
  Cell, 88, 235-242.
PDB code: 1sro
9434910 S.Cusack (1997).
Aminoacyl-tRNA synthetases.
  Curr Opin Struct Biol, 7, 881-889.  
9405472 S.Quevillon, F.Agou, J.C.Robinson, and M.Mirande (1997).
The p43 component of the mammalian multi-synthetase complex is likely to be the precursor of the endothelial monocyte-activating polypeptide II cytokine.
  J Biol Chem, 272, 32573-32579.  
9083113 S.Rowsell, R.A.Pauptit, A.D.Tucker, R.G.Melton, D.M.Blow, and P.Brick (1997).
Crystal structure of carboxypeptidase G2, a bacterial enzyme with applications in cancer therapy.
  Structure, 5, 337-347.
PDB code: 1cg2
9177188 S.Sen, H.Zhou, T.Ripmaster, W.N.Hittelman, P.Schimmel, and R.A.White (1997).
Expression of a gene encoding a tRNA synthetase-like protein is enhanced in tumorigenic human myeloid leukemia cells and is cell cycle stage- and differentiation-dependent.
  Proc Natl Acad Sci U S A, 94, 6164-6169.  
9016717 Y.Goldgur, L.Mosyak, L.Reshetnikova, V.Ankilova, O.Lavrik, S.Khodyreva, and M.Safro (1997).
The crystal structure of phenylalanyl-tRNA synthetase from thermus thermophilus complexed with cognate tRNAPhe.
  Structure, 5, 59-68.
PDB code: 1eiy
8910590 F.Agou, J.P.Waller, and M.Mirande (1996).
Expression of rat aspartyl-tRNA synthetase in Saccharomyces cerevisiae. Role of the NH2-terminal polypeptide extension on enzyme activity and stability.
  J Biol Chem, 271, 29295-29303.  
8610114 S.P.Hale, and P.Schimmel (1996).
Protein synthesis editing by a DNA aptamer.
  Proc Natl Acad Sci U S A, 93, 2755-2758.  
8856050 W.Freist, H.Sternbach, and F.Cramer (1996).
Phenylalanyl-tRNA synthetase from yeast and its discrimination of 19 amino acids in aminoacylation of tRNA(Phe)-C-C-A and tRNA(Phe)-C-C-A(3'NH2).
  Eur J Biochem, 240, 526-531.  
  8563641 M.Safro, and L.Mosyak (1995).
Structural similarities in the noncatalytic domains of phenylalanyl-tRNA and biotin synthetases.
  Protein Sci, 4, 2429-2432.  
8524648 R.Kreutzer, D.Kern, R.Giegé, and J.Rudinger (1995).
Footprinting of tRNA(Phe) transcripts from Thermus thermophilus HB8 with the homologous phenylalanyl-tRNA synthetase reveals a novel mode of interaction.
  Nucleic Acids Res, 23, 4598-4602.  
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.

 

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