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PDBsum entry 1pfw

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protein ligands metals links
Ligase PDB id
1pfw
Jmol
Contents
Protein chain
546 a.a. *
Ligands
MF3
Metals
_ZN
Waters ×489
* Residue conservation analysis
PDB id:
1pfw
Name: Ligase
Title: Methionyl-tRNA synthetase from escherichia coli complexed with trifluoromethionine
Structure: Methionyl-tRNA synthetase. Chain: a. Fragment: residues 1-551. Synonym: methionine--tRNA ligase, metrs. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: metg. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.78Å     R-factor:   0.184     R-free:   0.209
Authors: T.Crepin,E.Schmitt,Y.Mechulam,P.B.Sampson,M.D.Vaughan, J.F.Honek,S.Blanquet
Key ref:
T.Crepin et al. (2003). Use of analogues of methionine and methionyl adenylate to sample conformational changes during catalysis in Escherichia coli methionyl-tRNA synthetase. J Mol Biol, 332, 59-72. PubMed id: 12946347 DOI: 10.1016/S0022-2836(03)00917-3
Date:
27-May-03     Release date:   17-Feb-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00959  (SYM_ECOLI) -  Methionine--tRNA ligase
Seq:
Struc:
 
Seq:
Struc:
677 a.a.
546 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
Bound ligand (Het Group name = MF3)
matches with 75.00% similarity
+ 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    
 
 
DOI no: 10.1016/S0022-2836(03)00917-3 J Mol Biol 332:59-72 (2003)
PubMed id: 12946347  
 
 
Use of analogues of methionine and methionyl adenylate to sample conformational changes during catalysis in Escherichia coli methionyl-tRNA synthetase.
T.Crepin, E.Schmitt, Y.Mechulam, P.B.Sampson, M.D.Vaughan, J.F.Honek, S.Blanquet.
 
  ABSTRACT  
 
Binding of methionine to methionyl-tRNA synthetase (MetRS) is known to promote conformational changes within the active site. However, the contribution of these rearrangements to enzyme catalysis is not fully understood. In this study, several methionine and methionyl adenylate analogues were diffused into crystals of the monomeric form of Escherichia coli methionyl-tRNA synthetase. The structures of the corresponding complexes were solved at resolutions below 1.9A and compared to those of the enzyme free or complexed with methionine. Residues Y15 and W253 play key roles in the strength of the binding of the amino acid and of its analogues. Indeed, full motions of these residues are required to recover the maximum in free energy of binding. Residue Y15 also controls the size of the hydrophobic pocket where the amino acid side-chain interacts. H301 appears to participate to the specific recognition of the sulphur atom of methionine. Complexes with methionyl adenylate analogues illustrate the shielding by MetRS of the region joining the methionine and adenosine moieties. Finally, the structure of MetRS complexed to a methionine analogue mimicking the tetrahedral carbon of the transition state in the aminoacylation reaction was solved. On the basis of this model, we propose that, in response to the binding of the 3'-end of tRNA, Y15 moves again in order to deshield the anhydride bond in the natural adenylate.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Electronic densities associated with Y15 and W253. A and B show the positions of W253 and Y15 in the free enzyme[23.] (A) and in the MetRS:Met complex [16.] (B). C-F, The final 2F[o] -F[c] electron density maps are represented. Each map is contoured at 1s. C, MetRS:DFM complex; D, MetRS:TFM complex; E, MetRS:MetI complex; F, MetRS:MetP complex. E, The two alternative conformations of Y15 in the MetRS:MetI complex are shown.
Figure 4.
Figure 4. Binding of MetSA in the active site of MetRS. A, Schematic representation of the main electrostatic interactions between the enzyme and MetSA. Bottom: stereo views of active site-bound MetSA (B), Metol-AMP (C) and methionine plus adenosine (D). Only the enzyme residues relevant to the discussion in the text are drawn.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 332, 59-72) copyright 2003.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22683997 A.Palencia, T.Crépin, M.T.Vu, T.L.Lincecum, S.A.Martinis, and S.Cusack (2012).
Structural dynamics of the aminoacylation and proofreading functional cycle of bacterial leucyl-tRNA synthetase.
  Nat Struct Mol Biol, 19, 677-684.
PDB codes: 4aq7 4arc 4ari 4as1
21117131 C.Dalvit, and A.Vulpetti (2011).
Fluorine-protein interactions and ¹⁹F NMR isotropic chemical shifts: An empirical correlation with implications for drug design.
  ChemMedChem, 6, 104-114.  
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
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
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.  
19706454 I.C.Tanrikulu, E.Schmitt, Y.Mechulam, W.A.Goddard, and D.A.Tirrell (2009).
Discovery of Escherichia coli methionyl-tRNA synthetase mutants for efficient labeling of proteins with azidonorleucine in vivo.
  Proc Natl Acad Sci U S A, 106, 15285-15290.  
19015366 L.S.Green, J.M.Bullard, W.Ribble, F.Dean, D.F.Ayers, U.A.Ochsner, N.Janjic, and T.C.Jarvis (2009).
Inhibition of methionyl-tRNA synthetase by REP8839 and effects of resistance mutations on enzyme activity.
  Antimicrob Agents Chemother, 53, 86-94.  
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
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
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.  
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.  
16801548 A.J.Link, M.K.Vink, N.J.Agard, J.A.Prescher, C.R.Bertozzi, and D.A.Tirrell (2006).
Discovery of aminoacyl-tRNA synthetase activity through cell-surface display of noncanonical amino acids.
  Proc Natl Acad Sci U S A, 103, 10180-10185.  
16251366 R.Powers, N.Mirkovic, S.Goldsmith-Fischman, T.B.Acton, Y.Chiang, Y.J.Huang, L.Ma, P.K.Rajan, J.R.Cort, M.A.Kennedy, J.Liu, B.Rost, B.Honig, D.Murray, and G.T.Montelione (2005).
Solution structure of Archaeglobus fulgidis peptidyl-tRNA hydrolase (Pth2) provides evidence for an extensive conserved family of Pth2 enzymes in archea, bacteria, and eukaryotes.
  Protein Sci, 14, 2849-2861.
PDB code: 1rzw
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.