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PDBsum entry 1a8h

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Aminoacyl-tRNA synthetase PDB id
1a8h
Jmol
Contents
Protein chain
500 a.a. *
Metals
_ZN
Waters ×135
* Residue conservation analysis
PDB id:
1a8h
Name: Aminoacyl-tRNA synthetase
Title: Methionyl-tRNA synthetase from thermus thermophilus
Structure: Methionyl-tRNA synthetase. Chain: a. Synonym: metrs. Other_details: zn in zn finger
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8
Resolution:
2.00Å     R-factor:   0.205     R-free:   0.283
Authors: I.Sugiura,O.Nureki,Y.Ugaji,S.Kuwabara,B.Lober,R.Giege,D.Mora S.Yokoyama,M.Konno,Riken Structural Genomics/proteomics Ini (Rsgi)
Key ref: I.Sugiura et al. (2000). The 2.0 A crystal structure of Thermus thermophilus methionyl-tRNA synthetase reveals two RNA-binding modules. Structure, 8, 197-208. PubMed id: 10673435
Date:
26-Mar-98     Release date:   04-May-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P23395  (SYM_THET8) -  Methionine--tRNA ligase
Seq:
Struc:
 
Seq:
Struc:
618 a.a.
500 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.6.1.1.10  - Methionine--tRNA ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + L-methionine + tRNA(Met) = AMP + diphosphate + L-methionyl- tRNA(Met)
ATP
+ L-methionine
+ tRNA(Met)
= AMP
+ diphosphate
+ L-methionyl- tRNA(Met)
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     tRNA aminoacylation for protein translation   2 terms 
  Biochemical function     nucleotide binding     4 terms  

 

 
    reference    
 
 
Structure 8:197-208 (2000)
PubMed id: 10673435  
 
 
The 2.0 A crystal structure of Thermus thermophilus methionyl-tRNA synthetase reveals two RNA-binding modules.
I.Sugiura, O.Nureki, Y.Ugaji-Yoshikawa, S.Kuwabara, A.Shimada, M.Tateno, B.Lorber, R.Giegé, D.Moras, S.Yokoyama, M.Konno.
 
  ABSTRACT  
 
BACKGROUND: The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. The 10 class I synthetases are considered to have in common the catalytic domain structure based on the Rossmann fold, which is totally different from the class II catalytic domain structure. The class I synthetases are further divided into three subclasses, a, b and c, according to sequence homology. No conserved structural features for tRNA recognition by class I synthetases have been established. RESULTS: We determined the crystal structure of the class Ia methionyl-tRNA synthetase (MetRS) at 2.0 A resolution, using MetRS from an extreme thermophile, Thermus thermophilus HB8. The T. thermophilus MetRS structure is in full agreement with the biochemical and genetic data from Escherichia coli MetRS. The conserved 'anticodon-binding' residues are spatially clustered on an alpha-helix-bundle domain. The Rossmann-fold and anticodon-binding domains are connected by a beta-alpha-alpha-beta-alpha topology ('SC fold') domain that contains the class I specific KMSKS motif. CONCLUSIONS: The alpha-helix-bundle domain identified in the MetRS structure is the signature of the class Ia enzymes, as it was also identified in the class Ia structures of the isoleucyl- and arginyl-tRNA synthetases. The beta-alpha-alpha-beta-alpha topology domain, which can now be identified in all known structures of the class Ia and Ib synthetases, is likely to dock with the inner side of the L-shaped tRNA, thereby positioning the anticodon stem.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20796028 H.Ingvarsson, and T.Unge (2010).
Flexibility and communication within the structure of the Mycobacterium smegmatis methionyl-tRNA synthetase.
  FEBS J, 277, 3947-3962.
PDB codes: 2x1l 2x1m
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.  
19220918 J.A.Velázquez-Muriel, M.Rueda, I.Cuesta, A.Pascual-Montano, M.Orozco, and J.M.Carazo (2009).
Comparison of molecular dynamics and superfamily spaces of protein domain deformation.
  BMC Struct Biol, 9, 6.  
19847269 K.Nakanishi, L.Bonnefond, S.Kimura, T.Suzuki, R.Ishitani, and O.Nureki (2009).
Structural basis for translational fidelity ensured by transfer RNA lysidine synthetase.
  Nature, 461, 1144-1148.
PDB codes: 3a2k 3hj7
  19153456 T.T.Doan, S.Natarajan, H.Kim, Y.J.Ahn, J.G.Kim, B.M.Lee, and L.W.Kang (2009).
Cloning, expression, crystallization and preliminary X-ray crystallographic analysis of glutamyl-tRNA synthetase (Xoo1504) from Xanthomonas oryzae pv. oryzae.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 51-54.  
18400783 J.Rorbach, A.A.Yusoff, H.Tuppen, D.P.Abg-Kamaludin, Z.M.Chrzanowska-Lightowlers, R.W.Taylor, D.M.Turnbull, R.McFarland, and R.N.Lightowlers (2008).
Overexpression of human mitochondrial valyl tRNA synthetase can partially restore levels of cognate mt-tRNAVal carrying the pathogenic C25U mutation.
  Nucleic Acids Res, 36, 3065-3074.  
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
17510965 M.E.Budiman, M.H.Knaggs, J.S.Fetrow, and R.W.Alexander (2007).
Using molecular dynamics to map interaction networks in an aminoacyl-tRNA synthetase.
  Proteins, 68, 670-689.  
16949614 C.I.Jones, A.C.Spencer, J.L.Hsu, L.L.Spremulli, S.A.Martinis, M.DeRider, and P.F.Agris (2006).
A counterintuitive Mg2+-dependent and modification-assisted functional folding of mitochondrial tRNAs.
  J Mol Biol, 362, 771-786.  
16698554 J.H.Han, N.Kerrison, C.Chothia, and S.A.Teichmann (2006).
Divergence of interdomain geometry in two-domain proteins.
  Structure, 14, 935-945.  
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
15781491 M.Sakurai, T.Ohtsuki, and K.Watanabe (2005).
Modification at position 9 with 1-methyladenosine is crucial for structure and function of nematode mitochondrial tRNAs lacking the entire T-arm.
  Nucleic Acids Res, 33, 1653-1661.  
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.  
12581659 A.R.Ferré-D'Amaré (2003).
RNA-modifying enzymes.
  Curr Opin Struct Biol, 13, 49-55.  
12600987 B.S.Laursen, K.K.Mortensen, H.U.Sperling-Petersen, and D.W.Hoffman (2003).
A conserved structural motif at the N terminus of bacterial translation initiation factor IF2.
  J Biol Chem, 278, 16320-16328.
PDB code: 1nd9
12737824 L.D.Sherlin, and J.J.Perona (2003).
tRNA-dependent active site assembly in a class I aminoacyl-tRNA synthetase.
  Structure, 11, 591-603.
PDB code: 1nyl
12554880 S.Fukai, O.Nureki, S.Sekine, A.Shimada, D.G.Vassylyev, and S.Yokoyama (2003).
Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase.
  RNA, 9, 100-111.
PDB codes: 1ivs 1iyw
12032090 K.J.Newberry, Y.M.Hou, and J.J.Perona (2002).
Structural origins of amino acid selection without editing by cysteinyl-tRNA synthetase.
  EMBO J, 21, 2778-2787.
PDB codes: 1li5 1li7
11970956 M.Kitabatake, K.Ali, A.Demain, K.Sakamoto, S.Yokoyama, and D.Söll (2002).
Indolmycin resistance of Streptomyces coelicolor A3(2) by induced expression of one of its two tryptophanyl-tRNA synthetases.
  J Biol Chem, 277, 23882-23887.  
11887185 T.Terada, O.Nureki, R.Ishitani, A.Ambrogelly, M.Ibba, D.Söll, and S.Yokoyama (2002).
Functional convergence of two lysyl-tRNA synthetases with unrelated topologies.
  Nat Struct Biol, 9, 257-262.
PDB code: 1irx
11698642 A.Shimada, O.Nureki, M.Goto, S.Takahashi, and S.Yokoyama (2001).
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
12762019 O.Nureki, S.Fukai, S.Sekine, A.Shimada, T.Terada, T.Nakama, M.Shirouzu, D.G.Vassylyev, and S.Yokoyama (2001).
Structural basis for amino acid and tRNA recognition by class I aminoacyl-tRNA synthetases.
  Cold Spring Harb Symp Quant Biol, 66, 167-173.  
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.
  EMBO J, 19, 6908-6917.  
10811626 S.Cusack, A.Yaremchuk, and M.Tukalo (2000).
The 2 A crystal structure of leucyl-tRNA synthetase and its complex with a leucyl-adenylate analogue.
  EMBO J, 19, 2351-2361.
PDB code: 1h3n
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.