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PDBsum entry 2ct8

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protein dna_rna ligands Protein-protein interface(s) links
Ligase/RNA PDB id
2ct8
Jmol
Contents
Protein chains
465 a.a. *
DNA/RNA
Ligands
MSP ×2
Waters ×78
* Residue conservation analysis
PDB id:
2ct8
Name: Ligase/RNA
Title: Crystal structure of aquifex aeolicus methionyl-tRNA synthetase complexed with tRNA(met) and methionyl-adenylate anologue
Structure: RNA (74-mer). Chain: c, d. Engineered: yes. Methionyl-tRNA synthetase. Chain: a, b. Synonym: methionine--tRNA ligase, metrs. Engineered: yes
Source: Synthetic: yes. Aquifex aeolicus. Organism_taxid: 63363. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.70Å     R-factor:   0.217     R-free:   0.272
Authors: K.Nakanishi,Y.Ogiso,T.Nakama,S.Fukai,O.Nureki,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref:
K.Nakanishi et al. (2005). Structural basis for anticodon recognition by methionyl-tRNA synthetase. Nat Struct Biol, 12, 931-932. PubMed id: 16155581 DOI: 10.1038/nsmb988
Date:
23-May-05     Release date:   20-Sep-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O67298  (SYM_AQUAE) -  Methionine--tRNA ligase
Seq:
Struc:
497 a.a.
465 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
Bound ligand (Het Group name = MSP)
matches with 54.00% similarity
+ 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     translation   3 terms 
  Biochemical function     nucleotide binding     6 terms  

 

 
    reference    
 
 
DOI no: 10.1038/nsmb988 Nat Struct Biol 12:931-932 (2005)
PubMed id: 16155581  
 
 
Structural basis for anticodon recognition by methionyl-tRNA synthetase.
K.Nakanishi, Y.Ogiso, T.Nakama, S.Fukai, O.Nureki.
 
  ABSTRACT  
 
In the 2.7-A resolution crystal structure of methionyl-tRNA synthetase (MetRS) in complex with tRNA(Met) and a methionyl-adenylate analog, the tRNA anticodon loop is distorted to form a triple-base stack comprising C34, A35 and A38. A tryptophan residue stacks on C34 to extend the triple-base stack. In addition, C34 forms Watson-Crick-type hydrogen bonds with Arg357. This structure resolves the longstanding question of how MetRS specifically recognizes tRNA(Met).
 
  Selected figure(s)  
 
Figure 1.
Figure 1. The A. aeolicus MetRS‚ąítRNA[m]^Met complex. Green, the Rossmann fold domain; cyan and dark blue, the CP1 and CP2 insertions, respectively; salmon, the MetRS-specific -strand insertion; red, the stem-contact-fold domain; pink, the -helix bundle domain; yellow, tRNA[m]^Met; stick model, MetSA.
Figure 2.
Figure 2. Recognition of the anticodon CAU of tRNA[m]^Met by MetRS. (a) Conformational change of A. aeolicus tRNA[m]^Met (yellow) upon binding MetRS, as compared with unbound yeast tRNA^Phe (blue). (b) Interaction between MetRS and the tRNA[m]^Met anticodon. Yellow, tRNA[m]^Met nucleotides; light purple, MetRS residues; dotted lines, hydrogen bonds; red, oxygen; blue, nitrogen.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2005, 12, 931-932) copyright 2005.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21482813 T.E.Jones, R.W.Alexander, and T.Pan (2011).
Misacylation of specific nonmethionyl tRNAs by a bacterial methionyl-tRNA synthetase.
  Proc Natl Acad Sci U S A, 108, 6933-6938.  
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
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
20954242 S.Havrylenko, R.Legouis, B.Negrutskii, and M.Mirande (2010).
Methionyl-tRNA synthetase from Caenorhabditis elegans: a specific multidomain organization for convergent functional evolution.
  Protein Sci, 19, 2475-2484.  
19837083 E.Schmitt, I.C.Tanrikulu, T.H.Yoo, M.Panvert, D.A.Tirrell, and Y.Mechulam (2009).
Switching from an induced-fit to a lock-and-key mechanism in an aminoacyl-tRNA synthetase with modified specificity.
  J Mol Biol, 394, 843-851.
PDB codes: 3h97 3h99 3h9b 3h9c
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
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
18981688 K.Yura (2008).
[Trial to predict interactions between proteins and biomolecules based on their three-dimensional structures]
  Yakugaku Zasshi, 128, 1547-1555.  
18552770 P.F.Agris (2008).
Bringing order to translation: the contributions of transfer RNA anticodon-domain modifications.
  EMBO Rep, 9, 629-635.  
17898174 A.Ghosh, and S.Vishveshwara (2007).
A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis.
  Proc Natl Acad Sci U S A, 104, 15711-15716.  
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.  
17707400 L.M.Wadley, K.S.Keating, C.M.Duarte, and A.M.Pyle (2007).
Evaluating and learning from RNA pseudotorsional space: quantitative validation of a reduced representation for RNA structure.
  J Mol Biol, 372, 942-957.  
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.  
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.