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PDBsum entry 1c0a

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protein dna_rna ligands links
Ligase/RNA PDB id
1c0a
Jmol
Contents
Protein chain
585 a.a. *
DNA/RNA
Ligands
SO4
AMP
AMO
Waters ×514
* Residue conservation analysis
PDB id:
1c0a
Name: Ligase/RNA
Title: Crystal structure of the e. Coli aspartyl-tRNA synthetase : trnaasp : aspartyl-adenylate complex
Structure: Aspartyl tRNA. Chain: b. Engineered: yes. Aspartyl tRNA synthetase. Chain: a. Synonym: aspartate-tRNA ligase, asprs. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
Resolution:
2.40Å     R-factor:   0.208     R-free:   0.249
Authors: S.Eiler,A.-C.Dock-Bregeon,L.Moulinier,J.-C.Thierry,D.Moras
Key ref:
S.Eiler et al. (1999). Synthesis of aspartyl-tRNA(Asp) in Escherichia coli--a snapshot of the second step. EMBO J, 18, 6532-6541. PubMed id: 10562565 DOI: 10.1093/emboj/18.22.6532
Date:
15-Jul-99     Release date:   23-Nov-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P21889  (SYD_ECOLI) -  Aspartate--tRNA ligase
Seq:
Struc:
 
Seq:
Struc:
590 a.a.
585 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.6.1.1.12  - Aspartate--tRNA ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + L-aspartate + tRNA(Asp) = AMP + diphosphate + L-aspartyl-tRNA(Asp)
ATP
+ L-aspartate
+ tRNA(Asp)
=
AMP
Bound ligand (Het Group name = AMP)
corresponds exactly
+ diphosphate
+ L-aspartyl-tRNA(Asp)
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    
 
 
DOI no: 10.1093/emboj/18.22.6532 EMBO J 18:6532-6541 (1999)
PubMed id: 10562565  
 
 
Synthesis of aspartyl-tRNA(Asp) in Escherichia coli--a snapshot of the second step.
S.Eiler, A.Dock-Bregeon, L.Moulinier, J.C.Thierry, D.Moras.
 
  ABSTRACT  
 
The 2.4 A crystal structure of the Escherichia coli aspartyl-tRNA synthetase (AspRS)-tRNA(Asp)-aspartyl-adenylate complex shows the two substrates poised for the transfer of the aspartic acid moiety from the adenylate to the 3'-hydroxyl of the terminal adenosine of the tRNA. A general molecular mechanism is proposed for the second step of the aspartylation reaction that accounts for the observed conformational changes, notably in the active site pocket. The stabilization of the transition state is mediated essentially by two amino acids: the class II invariant arginine of motif 2 and the eubacterial-specific Gln231, which in eukaryotes and archaea is replaced by a structurally non-homologous serine. Two archetypal RNA-protein modes of interactions are observed: the anticodon stem-loop, including the wobble base Q, binds to the N-terminal beta-barrel domain through direct protein-RNA interactions, while the binding of the acceptor stem involves both direct and water-mediated hydrogen bonds in an original recognition scheme.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 (A) CPK representation of the dimeric E.coli AspRS -tRNA^Asp complex. The protein subunits are coloured in yellow and cyan with their cognate tRNAs in blue and orange, respectively. (B) Ribbon representation of one monomer of the complex showing the domain architecture of AspRS with: (i) the N-terminal domain (residues 1 -108) coloured in yellow; (ii) the small hinge module (residues 109 -131) in red; (iii) the catalytic domain (residues 132 -270 and 422 -585) in grey; and (iv) the insertion domain characteristic of eubacterial AspRSs (residues 271 -421) in blue. The three signature motifs characteristic of class II aaRSs are shown in green (motif 1), cyan (motif 2) and magenta (motif 3). The tRNA is shown in orange. (C) Topology diagram of E.coli AspRS. The -strands are represented as arrows and the helices as rods. Motif 1 is coloured in green, motif 2 in cyan and motif 3 in magenta. The same colour code is used for both (B) and (C). Figures 1,2,3,4 were generated using the Program SETOR (Evans, 1998).
Figure 2.
Figure 2 (A) Cloverleaf representation of E.coli tRNA^Asp. The circles indicate the positions of the identity elements according to Nameki et al. (1992). Red circles correspond to major identity elements and yellow circles to minor determinants. (B) AspRS -wobble base interaction: hydrogen bonds between the protein and Q34 are shown as yellow dotted lines. Oxygen atoms are represented in red, nitrogen atoms in blue. The N1 and N2 atoms of the purine ring interact with the carboxyl side chain of Glu93, O6 makes a salt bridge with Arg76 and the 2' OH group hydrogen-bonds to Asn82. The loop between strands S4 and S5, which is missing in archaeal AspRSs, is represented in orange. (C) AspRS -tRNA^Asp acceptor stem contacts: the interacting loops and helices from the AspRS catalytic domain and the eubacterial insertion domain are shown in red. These include the flipping loop (residues 167 -173), the motif 2 loop (residues 216 -228), the histidine loop (a eubacterial aspartic acid specific motif located on the N-terminal side of motif 3, residues 436 -449), the C-terminal extremity (residues 544 -565) and two helices belonging to the insertion domain (residues 335 -344 and 399 -409). (D) Pattern of solvation around the G -U pair. The electron density map shown results from a 2F[obs] - F[calc] synthesis and is contoured at 1.0 standard deviation.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1999, 18, 6532-6541) copyright 1999.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22002223 T.Osawa, S.Kimura, N.Terasaka, H.Inanaga, T.Suzuki, and T.Numata (2011).
Structural basis of tRNA agmatinylation essential for AUA codon decoding.
  Nat Struct Mol Biol, 18, 1275-1280.
PDB codes: 3amt 3amu 3au7
  20944219 D.Das, P.Kozbial, G.W.Han, D.Carlton, L.Jaroszewski, P.Abdubek, T.Astakhova, H.L.Axelrod, C.Bakolitsa, C.Chen, H.J.Chiu, M.Chiu, T.Clayton, M.C.Deller, L.Duan, K.Ellrott, M.A.Elsliger, D.Ernst, C.L.Farr, J.Feuerhelm, A.Grzechnik, J.C.Grant, K.K.Jin, H.A.Johnson, H.E.Klock, M.W.Knuth, S.S.Krishna, A.Kumar, D.Marciano, D.McMullan, M.D.Miller, A.T.Morse, E.Nigoghossian, A.Nopakun, L.Okach, S.Oommachen, J.Paulsen, C.Puckett, R.Reyes, C.L.Rife, N.Sefcovic, H.J.Tien, C.B.Trame, H.van den Bedem, D.Weekes, T.Wooten, Q.Xu, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2010).
The structure of KPN03535 (gi|152972051), a novel putative lipoprotein from Klebsiella pneumoniae, reveals an OB-fold.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 1254-1260.
PDB code: 3f1z
19874856 E.A.Merritt, T.L.Arakaki, E.T.Larson, A.Kelley, N.Mueller, A.J.Napuli, L.Zhang, G.Deditta, J.Luft, C.L.Verlinde, E.Fan, F.Zucker, F.S.Buckner, W.C.Van Voorhis, and W.G.Hol (2010).
Crystal structure of the aspartyl-tRNA synthetase from Entamoeba histolytica.
  Mol Biochem Parasitol, 169, 95.
PDB code: 3i7f
20729861 T.Yanagisawa, T.Sumida, R.Ishii, C.Takemoto, and S.Yokoyama (2010).
A paralog of lysyl-tRNA synthetase aminoacylates a conserved lysine residue in translation elongation factor P.
  Nat Struct Mol Biol, 17, 1136-1143.
PDB codes: 3a5y 3a5z
19168611 A.Metlitskaya, T.Kazakov, G.H.Vondenhoff, M.Novikova, A.Shashkov, T.Zatsepin, E.Semenova, N.Zaitseva, V.Ramensky, A.Van Aerschot, and K.Severinov (2009).
Maturation of the translation inhibitor microcin C.
  J Bacteriol, 191, 2380-2387.  
19118381 K.Nozawa, P.O'Donoghue, S.Gundllapalli, Y.Araiso, R.Ishitani, T.Umehara, D.Söll, and O.Nureki (2009).
Pyrrolysyl-tRNA synthetase-tRNA(Pyl) structure reveals the molecular basis of orthogonality.
  Nature, 457, 1163-1167.
PDB codes: 2zni 2znj
19767615 M.Messmer, J.Pütz, T.Suzuki, T.Suzuki, C.Sauter, M.Sissler, and F.Catherine (2009).
Tertiary network in mammalian mitochondrial tRNAAsp revealed by solution probing and phylogeny.
  Nucleic Acids Res, 37, 6881-6895.  
18452949 A.Shulman-Peleg, M.Shatsky, R.Nussinov, and H.J.Wolfson (2008).
Prediction of interacting single-stranded RNA bases by protein-binding patterns.
  J Mol Biol, 379, 299-316.  
18076053 D.Thompson, C.Lazennec, P.Plateau, and T.Simonson (2008).
Probing electrostatic interactions and ligand binding in aspartyl-tRNA synthetase through site-directed mutagenesis and computer simulations.
  Proteins, 71, 1450-1460.  
18211890 P.Aliprandi, C.Sizun, J.Perez, F.Mareuil, S.Caputo, J.L.Leroy, B.Odaert, S.Laalami, M.Uzan, and F.Bontems (2008).
S1 ribosomal protein functions in translation initiation and ribonuclease RegB activation are mediated by similar RNA-protein interactions: an NMR and SAXS analysis.
  J Biol Chem, 283, 13289-13301.  
18384044 S.Goto-Ito, T.Ito, R.Ishii, Y.Muto, Y.Bessho, and S.Yokoyama (2008).
Crystal structure of archaeal tRNA(m(1)G37)methyltransferase aTrm5.
  Proteins, 72, 1274-1289.
PDB code: 2yx1
17172343 C.Wang, B.W.Sobral, and K.P.Williams (2007).
Loss of a universal tRNA feature.
  J Bacteriol, 189, 1954-1962.  
17690095 D.Thompson, C.Lazennec, P.Plateau, and T.Simonson (2007).
Ammonium scanning in an enzyme active site. The chiral specificity of aspartyl-tRNA synthetase.
  J Biol Chem, 282, 30856-30868.  
17317626 E.C.Guth, and C.S.Francklyn (2007).
Kinetic discrimination of tRNA identity by the conserved motif 2 loop of a class II aminoacyl-tRNA synthetase.
  Mol Cell, 25, 531-542.  
17384640 G.C.Scheper, T.van der Klok, R.J.van Andel, C.G.van Berkel, M.Sissler, J.Smet, T.I.Muravina, S.V.Serkov, G.Uziel, M.Bugiani, R.Schiffmann, I.Krägeloh-Mann, J.A.Smeitink, C.Florentz, R.Van Coster, J.C.Pronk, and M.S.van der Knaap (2007).
Mitochondrial aspartyl-tRNA synthetase deficiency causes leukoencephalopathy with brain stem and spinal cord involvement and lactate elevation.
  Nat Genet, 39, 534-539.  
17447878 I.A.Vasil'eva, and N.A.Moor (2007).
Interaction of aminoacyl-tRNA synthetases with tRNA: general principles and distinguishing characteristics of the high-molecular-weight substrate recognition.
  Biochemistry (Mosc), 72, 247-263.  
  17620724 K.Suzuki, Y.Sato, Y.Maeda, S.Shimizu, M.T.Hossain, S.Ubukata, T.Sekiguchi, and A.Takénaka (2007).
Crystallization and preliminary X-ray crystallographic study of a putative aspartyl-tRNA synthetase from the crenarchaeon Sulfolobus tokodaii strain 7.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 608-612.  
17507661 R.Tyagi, and D.H.Mathews (2007).
Predicting helical coaxial stacking in RNA multibranch loops.
  RNA, 13, 939-951.  
17932062 R.Villet, M.Fonvielle, P.Busca, M.Chemama, A.P.Maillard, J.E.Hugonnet, L.Dubost, A.Marie, N.Josseaume, S.Mesnage, C.Mayer, J.M.Valéry, M.Ethève-Quelquejeu, and M.Arthur (2007).
Idiosyncratic features in tRNAs participating in bacterial cell wall synthesis.
  Nucleic Acids Res, 35, 6870-6883.  
17488812 Y.Bessho, R.Shibata, S.Sekine, K.Murayama, K.Higashijima, C.Hori-Takemoto, M.Shirouzu, S.Kuramitsu, and S.Yokoyama (2007).
Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA.
  Proc Natl Acad Sci U S A, 104, 8293-8298.
PDB codes: 1wjx 2czj
17698001 Y.Hirano, M.M.Hossain, K.Takeda, H.Tokuda, and K.Miki (2007).
Structural studies of the Cpx pathway activator NlpE on the outer membrane of Escherichia coli.
  Structure, 15, 963-976.
PDB codes: 2z4h 2z4i
16597625 A.Fender, C.Sauter, M.Messmer, J.Pütz, R.Giegé, C.Florentz, and M.Sissler (2006).
Loss of a primordial identity element for a mammalian mitochondrial aminoacylation system.
  J Biol Chem, 281, 15980-15986.  
16408313 D.Thompson, P.Plateau, and T.Simonson (2006).
Free-energy simulations and experiments reveal long-range electrostatic interactions and substrate-assisted specificity in an aminoacyl-tRNA synthetase.
  Chembiochem, 7, 337-344.  
16774919 D.Thompson, and T.Simonson (2006).
Molecular dynamics simulations show that bound Mg2+ contributes to amino acid and aminoacyl adenylate binding specificity in aspartyl-tRNA synthetase through long range electrostatic interactions.
  J Biol Chem, 281, 23792-23803.  
16809540 H.Oshikane, K.Sheppard, S.Fukai, Y.Nakamura, R.Ishitani, T.Numata, R.L.Sherrer, L.Feng, E.Schmitt, M.Panvert, S.Blanquet, Y.Mechulam, D.Söll, and O.Nureki (2006).
Structural basis of RNA-dependent recruitment of glutamine to the genetic code.
  Science, 312, 1950-1954.
PDB code: 2d6f
16923806 J.Mercante, K.Suzuki, X.Cheng, P.Babitzke, and T.Romeo (2006).
Comprehensive alanine-scanning mutagenesis of Escherichia coli CsrA defines two subdomains of critical functional importance.
  J Biol Chem, 281, 31832-31842.  
16681365 J.S.Weinger, and S.A.Strobel (2006).
Participation of the tRNA A76 hydroxyl groups throughout translation.
  Biochemistry, 45, 5939-5948.  
16734422 N.T.Uter, and J.J.Perona (2006).
Active-site assembly in glutaminyl-tRNA synthetase by tRNA-mediated induced fit.
  Biochemistry, 45, 6858-6865.  
16800632 P.Chuawong, and T.L.Hendrickson (2006).
The nondiscriminating aspartyl-tRNA synthetase from Helicobacter pylori: anticodon-binding domain mutations that impact tRNA specificity and heterologous toxicity.
  Biochemistry, 45, 8079-8087.  
16216574 E.Schmitt, M.Panvert, S.Blanquet, and Y.Mechulam (2005).
Structural basis for tRNA-dependent amidotransferase function.
  Structure, 13, 1421-1433.
PDB code: 1zq1
15719017 I.Leiros, J.Timmins, D.R.Hall, and S.McSweeney (2005).
Crystal structure and DNA-binding analysis of RecO from Deinococcus radiodurans.
  EMBO J, 24, 906-918.
PDB code: 1w3s
15665334 T.Spreter, M.Pech, and B.Beatrix (2005).
The crystal structure of archaeal nascent polypeptide-associated complex (NAC) reveals a unique fold and the presence of a ubiquitin-associated domain.
  J Biol Chem, 280, 15849-15854.
PDB code: 1tr8
15766524 T.T.Lee, S.Agarwalla, and R.M.Stroud (2005).
A unique RNA Fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function.
  Cell, 120, 599-611.
PDB code: 2bh2
15289581 F.Martin, S.Barends, and G.Eriani (2004).
Single amino acid changes in AspRS reveal alternative routes for expanding its tRNA repertoire in vivo.
  Nucleic Acids Res, 32, 4081-4089.  
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
15016354 P.Auffinger, L.Bielecki, and E.Westhof (2004).
Anion binding to nucleic acids.
  Structure, 12, 379-388.  
15121895 P.S.Klosterman, D.K.Hendrix, M.Tamura, S.R.Holbrook, and S.E.Brenner (2004).
Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns.
  Nucleic Acids Res, 32, 2342-2352.  
12766171 A.Brevet, J.Chen, S.Commans, C.Lazennec, S.Blanquet, and P.Plateau (2003).
Anticodon recognition in evolution: switching tRNA specificity of an aminoacyl-tRNA synthetase by site-directed peptide transplantation.
  J Biol Chem, 278, 30927-30935.  
14627743 B.Wu, A.Yee, A.Pineda-Lucena, A.Semesi, T.A.Ramelot, J.R.Cort, J.W.Jung, A.Edwards, W.Lee, M.Kennedy, and C.H.Arrowsmith (2003).
Solution structure of ribosomal protein S28E from Methanobacterium thermoautotrophicum.
  Protein Sci, 12, 2831-2837.
PDB code: 1ne3
12660169 C.Charron, H.Roy, M.Blaise, R.Giegé, and D.Kern (2003).
Non-discriminating and discriminating aspartyl-tRNA synthetases differ in the anticodon-binding domain.
  EMBO J, 22, 1632-1643.
PDB code: 1n9w
12598368 D.L.Theobald, R.M.Mitton-Fry, and D.S.Wuttke (2003).
Nucleic acid recognition by OB-fold proteins.
  Annu Rev Biophys Biomol Struct, 32, 115-133.  
12649491 H.Choi, K.Gabriel, J.Schneider, S.Otten, and W.H.McClain (2003).
Recognition of acceptor-stem structure of tRNA(Asp) by Escherichia coli aspartyl-tRNA synthetase.
  RNA, 9, 386-393.  
12824344 H.Yang, F.Jossinet, N.Leontis, L.Chen, J.Westbrook, H.Berman, and E.Westhof (2003).
Tools for the automatic identification and classification of RNA base pairs.
  Nucleic Acids Res, 31, 3450-3460.  
12730374 L.Feng, D.Tumbula-Hansen, H.Toogood, and D.Soll (2003).
Expanding tRNA recognition of a tRNA synthetase by a single amino acid change.
  Proc Natl Acad Sci U S A, 100, 5676-5681.  
11907568 A.B.Simonson, and J.A.Lake (2002).
The transorientation hypothesis for codon recognition during protein synthesis.
  Nature, 416, 281-285.
PDB codes: 1ks1 1l1u
12149259 D.Tumbula-Hansen, L.Feng, H.Toogood, K.O.Stetter, and D.Söll (2002).
Evolutionary divergence of the archaeal aspartyl-tRNA synthetases into discriminating and nondiscriminating forms.
  J Biol Chem, 277, 37184-37190.  
12429096 E.Enggist, L.Thöny-Meyer, P.Güntert, and K.Pervushin (2002).
NMR structure of the heme chaperone CcmE reveals a novel functional motif.
  Structure, 10, 1551-1557.
PDB codes: 1liz 1sr3
11468411 C.Charron, H.Roy, B.Lorber, D.Kern, and R.Giegé (2001).
Crystallization and preliminary X-ray diffraction data of the second and archaebacterial-type aspartyl-tRNA synthetase from Thermus thermophilus.
  Acta Crystallogr D Biol Crystallogr, 57, 1177-1179.  
11250908 H.Qiu, J.Dong, C.Hu, C.S.Francklyn, and A.G.Hinnebusch (2001).
The tRNA-binding moiety in GCN2 contains a dimerization domain that interacts with the kinase domain and is required for tRNA binding and kinase activation.
  EMBO J, 20, 1425-1438.  
11726494 J.Moser, W.D.Schubert, V.Beier, I.Bringemeier, D.Jahn, and D.W.Heinz (2001).
V-shaped structure of glutamyl-tRNA reductase, the first enzyme of tRNA-dependent tetrapyrrole biosynthesis.
  EMBO J, 20, 6583-6590.
PDB code: 1gpj
11566892 L.Moulinier, S.Eiler, G.Eriani, J.Gangloff, J.C.Thierry, K.Gabriel, W.H.McClain, and D.Moras (2001).
The structure of an AspRS-tRNA(Asp) complex reveals a tRNA-dependent control mechanism.
  EMBO J, 20, 5290-5301.
PDB code: 1il2
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.  
  11680848 S.T.Nonekowski, and G.A.Garcia (2001).
tRNA recognition by tRNA-guanine transglycosylase from Escherichia coli: the role of U33 in U-G-U sequence recognition.
  RNA, 7, 1432-1441.  
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.
  Biochemistry, 39, 15540-15547.  
11060012 B.Delagoutte, D.Moras, and J.Cavarelli (2000).
tRNA aminoacylation by arginyl-tRNA synthetase: induced conformations during substrates binding.
  EMBO J, 19, 5599-5610.
PDB codes: 1f7u 1f7v
11101501 M.A.Swairjo, A.J.Morales, C.C.Wang, A.R.Ortiz, and P.Schimmel (2000).
Crystal structure of trbp111: a structure-specific tRNA-binding protein.
  EMBO J, 19, 6287-6298.
PDB codes: 1pxf 1pyb 3ers
10966471 M.Ibba, and D.Soll (2000).
Aminoacyl-tRNA synthesis.
  Annu Rev Biochem, 69, 617-650.  
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.