spacer
spacer

PDBsum entry 1b8a

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Ligase PDB id
1b8a
Jmol
Contents
Protein chains
438 a.a. *
Ligands
ATP ×2
Metals
_MN ×6
Waters ×1230
* Residue conservation analysis
PDB id:
1b8a
Name: Ligase
Title: Aspartyl-tRNA synthetase
Structure: Protein (aspartyl-tRNA synthetase). Chain: a, b. Synonym: aspartyl tRNA ligase. Engineered: yes
Source: Thermococcus kodakarensis. Organism_taxid: 69014. Strain: kod1. Cellular_location: cytoplasm. Gene: asps. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
1.90Å     R-factor:   0.168     R-free:   0.202
Authors: E.Schmitt,L.Moulinier,J.-C.Thierry,D.Moras
Key ref:
E.Schmitt et al. (1998). Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation. EMBO J, 17, 5227-5237. PubMed id: 9724658 DOI: 10.1093/emboj/17.17.5227
Date:
27-Jan-99     Release date:   02-Feb-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q52428  (SYD_PYRKO) -  Aspartate--tRNA(Asp) ligase
Seq:
Struc:
438 a.a.
438 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     translation   3 terms 
  Biochemical function     nucleotide binding     8 terms  

 

 
DOI no: 10.1093/emboj/17.17.5227 EMBO J 17:5227-5237 (1998)
PubMed id: 9724658  
 
 
Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation.
E.Schmitt, L.Moulinier, S.Fujiwara, T.Imanaka, J.C.Thierry, D.Moras.
 
  ABSTRACT  
 
The crystal structure of aspartyl-tRNA synthetase (AspRS) from Pyrococcus kodakaraensis was solved at 1.9 A resolution. The sequence and three-dimensional structure of the catalytic domain are highly homologous to those of eukaryotic AspRSs. In contrast, the N-terminal domain, whose function is to bind the tRNA anticodon, is more similar to that of eubacterial enzymes. Its structure explains the unique property of archaeal AspRSs of accommodating both tRNAAsp and tRNAAsn. Soaking the apo-enzyme crystals with ATP and aspartic acid both separately and together allows the adenylate formation to be followed. Due to the asymmetry of the dimeric enzyme in the crystalline state, different steps of the reaction could be visualized within the same crystal. Four different states of the aspartic acid activation reaction could thus be characterized, revealing the functional correlation of the observed conformational changes. The binding of the amino acid substrate induces movement of two invariant loops which secure the position of the peptidyl moiety for adenylate formation. An unambiguous spatial and functional assignment of three magnesium ion cofactors can be made. This study shows the important role of residues present in both archaeal and eukaryotic AspRSs, but absent from the eubacterial enzymes.
 
  Selected figure(s)  
 
Figure 3.
Figure 3 Fragment of the 1.9 resolution 2F[o]-F[c] map contoured at 1.5 . (A) Aspartyl adenylate within the active site of monomer 1 of pkAspRS. (B) The ATP-Mg2+ molecule in monomer 2 of pkAspRS, the three magnesium ions are in yellow and the liganded water molecules are in red. In this drawing, the Ser364 side chain is oriented towards interaction with a phosphate group of ATP-Mg2+. For the sake of clarity, the alternative conformation was omitted but is clearly suggested by the electron density. (C) The aspartic acid within the active site of monomer 1 of pkAspRS. The figure was drawn using the program 'O' (Jones et al., 1991).
Figure 6.
Figure 6 Relative position of the substrates. The structures of pkAspRS complexed with ATP-Mg2+, aspartic acid and aspartyl adenylate, respectively, were superimposed by fitting the C[ ]atoms of the catalytic domain. (A) Relative location of aspartic acid and ATP-Mg2+ resulting from the superimposition. (B) Stick representation of the aspartyl adenylate molecule. (C) Superimposition of the three substrates. (D) Putative transition state leading to the adenylate formation according to the superimpositon described above. The side chains of key residues as well as the putative trigonal bipyramid of the pentacovalent intermediate (dashed blue lines) are shown.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1998, 17, 5227-5237) copyright 1998.  
  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
19927322 A.Kahraman, R.J.Morris, R.A.Laskowski, A.D.Favia, and J.M.Thornton (2010).
On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins.
  Proteins, 78, 1120-1136.  
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
20717102 M.Blaise, M.Bailly, M.Frechin, M.A.Behrens, F.Fischer, C.L.Oliveira, H.D.Becker, J.S.Pedersen, S.Thirup, and D.Kern (2010).
Crystal structure of a transfer-ribonucleoprotein particle that promotes asparagine formation.
  EMBO J, 29, 3118-3129.
PDB code: 3kfu
19703275 A.Y.Mulkidjanian, and M.Y.Galperin (2009).
On the origin of life in the Zinc world. 2. Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth.
  Biol Direct, 4, 27.  
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.  
18422966 S.Bilokapic, J.Rokov Plavec, N.Ban, and I.Weygand-Durasevic (2008).
Structural flexibility of the methanogenic-type seryl-tRNA synthetase active site and its implication for specific substrate recognition.
  FEBS J, 275, 2831-2844.  
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.  
  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.  
17881821 Y.Sato, Y.Maeda, S.Shimizu, M.T.Hossain, S.Ubukata, K.Suzuki, T.Sekiguchi, and A.Takénaka (2007).
Structure of the nondiscriminating aspartyl-tRNA synthetase from the crenarchaeon Sulfolobus tokodaii strain 7 reveals the recognition mechanism for two different tRNA anticodons.
  Acta Crystallogr D Biol Crystallogr, 63, 1042-1047.
PDB code: 1wyd
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.  
16317719 S.J.Hughes, J.A.Tanner, A.D.Miller, and I.R.Gould (2006).
Molecular dynamics simulations of LysRS: an asymmetric state.
  Proteins, 62, 649-662.  
16595681 Z.Tokgöz, R.N.Bohnsack, and A.L.Haas (2006).
Pleiotropic effects of ATP.Mg2+ binding in the catalytic cycle of ubiquitin-activating enzyme.
  J Biol Chem, 281, 14729-14737.  
15039580 C.Charron, H.Roy, M.Blaise, R.Giegé, and D.Kern (2004).
Crystallization and preliminary X-ray diffraction data of an archaeal asparagine synthetase related to asparaginyl-tRNA synthetase.
  Acta Crystallogr D Biol Crystallogr, 60, 767-769.  
15133161 C.Venclovas, K.Ginalski, and C.Kang (2004).
Sequence-structure mapping errors in the PDB: OB-fold domains.
  Protein Sci, 13, 1594-1602.
PDB code: 1s3o
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
12874385 H.Roy, H.D.Becker, J.Reinbolt, and D.Kern (2003).
When contemporary aminoacyl-tRNA synthetases invent their cognate amino acid metabolism.
  Proc Natl Acad Sci U S A, 100, 9837-9842.  
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.  
14646067 L.Moulinier, D.A.Case, and T.Simonson (2003).
Reintroducing electrostatics into protein X-ray structure refinement: bulk solvent treated as a dielectric continuum.
  Acta Crystallogr D Biol Crystallogr, 59, 2094-2103.  
12684518 M.Goto, R.Omi, I.Miyahara, M.Sugahara, and K.Hirotsu (2003).
Structures of argininosuccinate synthetase in enzyme-ATP substrates and enzyme-AMP product forms: stereochemistry of the catalytic reaction.
  J Biol Chem, 278, 22964-22971.
PDB codes: 1j1z 1j20 1j21 1kh3
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.  
14579361 R.P.Bahadur, P.Chakrabarti, F.Rodier, and J.Janin (2003).
Dissecting subunit interfaces in homodimeric proteins.
  Proteins, 53, 708-719.  
11880622 B.Min, J.T.Pelaschier, D.E.Graham, D.Tumbula-Hansen, and D.Söll (2002).
Transfer RNA-dependent amino acid biosynthesis: an essential route to asparagine formation.
  Proc Natl Acad Sci U S A, 99, 2678-2683.  
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.  
12112867 T.Imanaka, and H.Atomi (2002).
Catalyzing "hot" reactions: enzymes from hyperthermophilic Archaea.
  Chem Rec, 2, 149-163.  
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.  
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
11679717 R.Fishman, V.Ankilova, N.Moor, and M.Safro (2001).
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
10913247 G.Desogus, F.Todone, P.Brick, and S.Onesti (2000).
Active site of lysyl-tRNA synthetase: structural studies of the adenylation reaction.
  Biochemistry, 39, 8418-8425.
PDB codes: 1e1o 1e1t 1e22 1e24
10944102 G.Martin, W.Keller, and S.Doublié (2000).
Crystal structure of mammalian poly(A) polymerase in complex with an analog of ATP.
  EMBO J, 19, 4193-4203.
PDB code: 1f5a
10727213 H.D.Becker, H.Roy, L.Moulinier, M.H.Mazauric, G.Keith, and D.Kern (2000).
Thermus thermophilus contains an eubacterial and an archaebacterial aspartyl-tRNA synthetase.
  Biochemistry, 39, 3216-3230.  
10713991 K.A.Denessiouk, and M.S.Johnson (2000).
When fold is not important: a common structural framework for adenine and AMP binding in 12 unrelated protein families.
  Proteins, 38, 310-326.  
10966471 M.Ibba, and D.Soll (2000).
Aminoacyl-tRNA synthesis.
  Annu Rev Biochem, 69, 617-650.  
11053387 M.Nakatani, S.Ezaki, H.Atomi, and T.Imanaka (2000).
A DNA ligase from a hyperthermophilic archaeon with unique cofactor specificity.
  J Bacteriol, 182, 6424-6433.  
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
10408894 A.Danchin (1999).
From protein sequence to function.
  Curr Opin Struct Biol, 9, 363-367.  
  10430557 D.Tumbula, U.C.Vothknecht, H.S.Kim, M.Ibba, B.Min, T.Li, J.Pelaschier, C.Stathopoulos, H.Becker, and D.Söll (1999).
Archaeal aminoacyl-tRNA synthesis: diversity replaces dogma.
  Genetics, 152, 1269-1276.  
10562565 S.Eiler, A.Dock-Bregeon, L.Moulinier, J.C.Thierry, and D.Moras (1999).
Synthesis of aspartyl-tRNA(Asp) in Escherichia coli--a snapshot of the second step.
  EMBO J, 18, 6532-6541.
PDB code: 1c0a
10430027 W.Freist, J.F.Verhey, A.Rühlmann, D.H.Gauss, and J.G.Arnez (1999).
Histidyl-tRNA synthetase.
  Biol Chem, 380, 623-646.  
9789001 A.W.Curnow, D.L.Tumbula, J.T.Pelaschier, B.Min, and D.Söll (1998).
Glutamyl-tRNA(Gln) amidotransferase in Deinococcus radiodurans may be confined to asparagine biosynthesis.
  Proc Natl Acad Sci U S A, 95, 12838-12843.  
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.