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protein dna_rna ligands Protein-protein interface(s) links
Ligase/RNA PDB id
1ivs
Jmol
Contents
Protein chains
862 a.a. *
DNA/RNA
Ligands
VAA ×2
Waters ×218
* Residue conservation analysis
PDB id:
1ivs
Name: Ligase/RNA
Title: Crystal structure of thermus thermophilus valyl-tRNA synthetase complexed with tRNA(val) and valyl-adenylate analogue
Structure: tRNA (val). Chain: c, d. Engineered: yes. Other_details: tRNA (val) with the cac anticodon. Valyl-tRNA synthetase. Chain: a, b. Synonym: valine-tRNA ligase, valrs. Engineered: yes
Source: Synthetic: yes. Thermus thermophilus. Organism_taxid: 274. Gene: vals. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.90Å     R-factor:   0.248     R-free:   0.282
Authors: S.Fukai,O.Nureki,S.-I.Sekine,A.Shimada,D.G.Vassylyev, S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref: S.Fukai et al. (2003). Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase. Rna, 9, 100-111. PubMed id: 12554880 DOI: 10.1261/rna.2760703
Date:
29-Mar-02     Release date:   11-Feb-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P96142  (SYV_THETH) -  Valyl-tRNA synthetase
Seq:
Struc: 		 
Seq:
Struc: 		862 a.a.
862 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.6.1.1.9  - Valine--tRNA ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + L-valine + tRNA(Val) = AMP + diphosphate + L-valyl-tRNA(Val)
ATP
 + L-valine
 + tRNA(Val)
 =
AMP
Bound ligand (Het Group name = VAA)
matches with 51.00% similarity 		+ diphosphate
 + L-valyl-tRNA(Val)
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     translation   3 terms 
  Biochemical function     nucleotide binding     6 terms  

 

 
    reference    
 
 
DOI no: 10.1261/rna.2760703 Rna 9:100-111 (2003)
PubMed id: 12554880  
 
 
Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase.
S.Fukai, O.Nureki, S.Sekine, A.Shimada, D.G.Vassylyev, S.Yokoyama.
 
  ABSTRACT  
 
The molecular interactions between valyl-tRNA synthetase (ValRS) and tRNA(Val), with the C34-A35-C36 anticodon, from Thermus thermophilus were studied by crystallographic analysis and structure-based mutagenesis. In the ValRS-bound structure of tRNA(Val), the successive A35-C36 residues (the major identity elements) of tRNA(Val) are base-stacked upon each other, and fit into a pocket on the alpha-helix bundle domain of ValRS. Hydrogen bonds are formed between ValRS and A35-C36 of tRNA(Val) in a base-specific manner. The C-terminal coiled-coil domain of ValRS interacts electrostatically with A20 and hydrophobically with the G19*C56 tertiary base pair. The loss of these interactions by the deletion of the coiled-coil domain of ValRS increased the K(M) value for tRNA(Val) 28-fold and decreased the k(cat) value 19-fold in the aminoacylation. The tRNA(Val) K(M) and k(cat) values were increased 21-fold and decreased 32-fold, respectively, by the disruption of the G18*U55 and G19*C56 tertiary base pairs, which associate the D- and T-loops for the formation of the L-shaped tRNA structure. Therefore, the coiled-coil domain of ValRS is likely to stabilize the L-shaped tRNA structure during the aminoacylation reaction.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19116923 C.Vignal, A.T.Bansal, D.J.Balding, M.H.Binks, M.C.Dickson, D.S.Montgomery, and A.G.Wilson (2009).
Genetic association of the major histocompatibility complex with rheumatoid arthritis implicates two non-DRB1 loci.
  Arthritis Rheum, 60, 53-62.  
19505149 F.Fan, and J.S.Blanchard (2009).
Toward the catalytic mechanism of a cysteine ligase (MshC) from Mycobacterium smegmatis: an enzyme involved in the biosynthetic pathway of mycothiol.
  Biochemistry, 48, 7150-7159.  
19656186 M.Konno, T.Sumida, E.Uchikawa, Y.Mori, T.Yanagisawa, S.Sekine, and S.Yokoyama (2009).
Modeling of tRNA-assisted mechanism of Arg activation based on a structure of Arg-tRNA synthetase, tRNA, and an ATP analog (ANP).
  FEBS J, 276, 4763-4779.
PDB codes: 2zue 2zuf
19749755 S.Goto-Ito, T.Ito, M.Kuratani, Y.Bessho, and S.Yokoyama (2009).
Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation.
  Nat Struct Mol Biol, 16, 1109-1115.
PDB codes: 2zzm 2zzn
18704948 S.S.Pendley, Y.B.Yu, and T.E.Cheatham (2009).
Molecular dynamics guided study of salt bridge length dependence in both fluorinated and non-fluorinated parallel dimeric coiled-coils.
  Proteins, 74, 612-629.  
19053270 L.W.Tremblay, F.Fan, M.W.Vetting, and J.S.Blanchard (2008).
The 1.6 A crystal structure of Mycobacterium smegmatis MshC: the penultimate enzyme in the mycothiol biosynthetic pathway.
  Biochemistry, 47, 13326-13335.
PDB code: 3c8z
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.  
17407263 M.T.Vu, and S.A.Martinis (2007).
A unique insert of leucyl-tRNA synthetase is required for aminoacylation and not amino acid editing.
  Biochemistry, 46, 5170-5176.  
16461956 R.Oliva, L.Cavallo, and A.Tramontano (2006).
Accurate energies of hydrogen bonded nucleic acid base pairs and triplets in tRNA tertiary interactions.
  Nucleic Acids Res, 34, 865-879.  
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.  
15856481 J.Roach, S.Sharma, M.Kapustina, and C.W.Carter (2005).
Structure alignment via Delaunay tetrahedralization.
  Proteins, 60, 66-81.  
16155581 K.Nakanishi, Y.Ogiso, T.Nakama, S.Fukai, and O.Nureki (2005).
Structural basis for anticodon recognition by methionyl-tRNA synthetase.
  Nat Struct Mol Biol, 12, 931-932.
PDB codes: 2csx 2ct8
16155584 R.Fukunaga, and S.Yokoyama (2005).
Aminoacylation complex structures of leucyl-tRNA synthetase and tRNALeu reveal two modes of discriminator-base recognition.
  Nat Struct Mol Biol, 12, 915-922.  
14970394 K.D.Tardif, and J.Horowitz (2004).
Functional group recognition at the aminoacylation and editing sites of E. coli valyl-tRNA synthetase.
  RNA, 10, 493-503.  
15489861 S.Hauenstein, C.M.Zhang, Y.M.Hou, and J.J.Perona (2004).
Shape-selective RNA recognition by cysteinyl-tRNA synthetase.
  Nat Struct Mol Biol, 11, 1134-1141.
PDB code: 1u0b
15208367 Y.G.Zheng, H.Wei, C.Ling, F.Martin, G.Eriani, and E.D.Wang (2004).
Two distinct domains of the beta subunit of Aquifex aeolicus leucyl-tRNA synthetase are involved in tRNA binding as revealed by a three-hybrid selection.
  Nucleic Acids Res, 32, 3294-3303.  
14690419 R.Geslain, G.Bey, J.Cavarelli, and G.Eriani (2003).
Limited set of amino acid residues in a class Ia aminoacyl-tRNA synthetase is crucial for tRNA binding.
  Biochemistry, 42, 15092-15101.  
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.