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PDBsum entry 2fmt
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protein dna_rna ligands metals Protein-protein interface(s) links
Complex (methyltransferase/tRNA) PDB id
2fmt

 

 

 

 

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Contents
Protein chains
314 a.a. *
DNA/RNA
Ligands
FME ×2
Metals
_MG ×2
Waters ×83
* Residue conservation analysis
PDB id:
2fmt
Name: Complex (methyltransferase/tRNA)
Title: Methionyl-trnafmet formyltransferase complexed with formyl-methionyl- trnafmet
Structure: Formyl-methionyl-trnafmet2. Chain: c, d. Synonym: initiator tRNA. Engineered: yes. Methionyl-tRNA fmet formyltransferase. Chain: a, b. Synonym: 10-formyltetrahydrofolate l-methionyl trnafmet formyltransferase. Engineered: yes
Source: Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Escherichia coli. Organism_taxid: 562. Strain: k37. Cellular_location: cytoplasm. Gene: fmt. Expressed in: escherichia coli.
Biol. unit: Monomer (from PDB file)
Resolution:
2.80Å     R-factor:   0.247     R-free:   0.292
Authors: E.Schmitt,Y.Mechulam,S.Blanquet
Key ref: E.Schmitt et al. (1998). Crystal structure of methionyl-tRNAfMet transformylase complexed with the initiator formyl-methionyl-tRNAfMet. Embo J, 17, 6819-6826. PubMed id: 9843487
Date:
29-Jul-98     Release date:   29-Jul-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P23882  (FMT_ECOLI) -  Methionyl-tRNA formyltransferase from Escherichia coli (strain K12)
Seq:
Struc: 		315 a.a.
314 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

DNA/RNA chains
  C-G-C-G-G-G-G-4SU-G-G-A-G-C-A-G-C-C-U-G-G-H2U-A-G-C-U-C-G-U-C-G-G-G-OMC-U-C-A- 77 bases
  C-G-C-G-G-G-G-4SU-G-G-A-G-C-A-G-C-C-U-G-G-H2U-A-G-C-U-C-G-U-C-G-G-G-OMC-U-C-A- 77 bases

 Enzyme reactions 
   Enzyme class: E.C.2.1.2.9  - methionyl-tRNA formyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway: 		Folate Coenzymes
      Reaction: L-methionyl-tRNA(fMet) + (6R)-10-formyltetrahydrofolate = N-formyl-L- methionyl-tRNA(fMet) + (6S)-5,6,7,8-tetrahydrofolate + H+
10-formyltetrahydrofolate
 + L-methionyl-tRNA(fMet)
 = tetrahydrofolate
 + N-formylmethionyl-tRNA(fMet)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
Embo J 17:6819-6826 (1998)
PubMed id: 9843487  
 
 
Crystal structure of methionyl-tRNAfMet transformylase complexed with the initiator formyl-methionyl-tRNAfMet.
E.Schmitt, M.Panvert, S.Blanquet, Y.Mechulam.
 
  ABSTRACT  
 
The crystal structure of Escherichia coli methionyl-tRNAfMet transformylase complexed with formyl-methionyl-tRNAfMet was solved at 2.8 A resolution. The formylation reaction catalyzed by this enzyme irreversibly commits methionyl-tRNAfMet to initiation of translation in eubacteria. In the three-dimensional model, the methionyl-tRNAfMet formyltransferase fills in the inside of the L-shaped tRNA molecule on the D-stem side. The anticodon stem and loop are away from the protein. An enzyme loop is wedged in the major groove of the acceptor helix. As a result, the C1-A72 mismatch characteristic of the initiator tRNA is split and the 3' arm bends inside the active centre. This recognition mechanism is markedly distinct from that of elongation factor Tu, which binds the acceptor arm of aminoacylated elongator tRNAs on the T-stem side.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22447243 E.Schmitt, M.Panvert, C.Lazennec-Schurdevin, P.D.Coureux, J.Perez, A.Thompson, and Y.Mechulam (2012).
Structure of the ternary initiation complex aIF2-GDPNP-methionylated initiator tRNA.
  Nat Struct Mol Biol, 19, 450-454.
PDB code: 3v11
19716793 M.Tsuboi, H.Morita, Y.Nozaki, K.Akama, T.Ueda, K.Ito, K.H.Nierhaus, and N.Takeuchi (2009).
EF-G2mt is an exclusive recycling factor in mammalian mitochondrial protein synthesis.
  Mol Cell, 35, 502-510.  
18848533 S.A.Krupenko (2009).
FDH: an aldehyde dehydrogenase fusion enzyme in folate metabolism.
  Chem Biol Interact, 178, 84-93.  
18098265 A.Wang, N.Winblade Nairn, R.S.Johnson, D.A.Tirrell, and K.Grabstein (2008).
Processing of N-terminal unnatural amino acids in recombinant human interferon-beta in Escherichia coli.
  Chembiochem, 9, 324-330.  
18653533 P.Barraud, E.Schmitt, Y.Mechulam, F.Dardel, and C.Tisné (2008).
A unique conformation of the anticodon stem-loop is associated with the capacity of tRNAfMet to initiate protein synthesis.
  Nucleic Acids Res, 36, 4894-4901.
PDB codes: 3cw5 3cw6
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.  
17660830 A.Weixlbaumer, S.Petry, C.M.Dunham, M.Selmer, A.C.Kelley, and V.Ramakrishnan (2007).
Crystal structure of the ribosome recycling factor bound to the ribosome.
  Nat Struct Mol Biol, 14, 733-737.
PDB codes: 2v46 2v47 2v48 2v49
17507661 R.Tyagi, and D.H.Mathews (2007).
Predicting helical coaxial stacking in RNA multibranch loops.
  RNA, 13, 939-951.  
17110926 K.Suto, Y.Shimizu, K.Watanabe, T.Ueda, S.Fukai, O.Nureki, and K.Tomita (2006).
Crystal structures of leucyl/phenylalanyl-tRNA-protein transferase and its complex with an aminoacyl-tRNA analog.
  EMBO J, 25, 5942-5950.
PDB codes: 2dps 2dpt
16959973 M.Selmer, C.M.Dunham, F.V.Murphy, A.Weixlbaumer, S.Petry, A.C.Kelley, J.R.Weir, and V.Ramakrishnan (2006).
Structure of the 70S ribosome complexed with mRNA and tRNA.
  Science, 313, 1935-1942.
PDB codes: 2j00 2j01 2j02 2j03
15755955 B.S.Laursen, H.P.Sørensen, K.K.Mortensen, and H.U.Sperling-Petersen (2005).
Initiation of protein synthesis in bacteria.
  Microbiol Mol Biol Rev, 69, 101-123.  
15809294 G.J.Williams, S.D.Breazeale, C.R.Raetz, and J.H.Naismith (2005).
Structure and function of both domains of ArnA, a dual function decarboxylase and a formyltransferase, involved in 4-amino-4-deoxy-L-arabinose biosynthesis.
  J Biol Chem, 280, 23000-23008.
PDB codes: 2bll 2bln
15807526 P.Z.Gatzeva-Topalova, A.P.May, and M.C.Sousa (2005).
Crystal structure and mechanism of the Escherichia coli ArnA (PmrI) transformylase domain. An enzyme for lipid A modification with 4-amino-4-deoxy-L-arabinose and polymyxin resistance.
  Biochemistry, 44, 5328-5338.
PDB code: 1yrw
15695810 S.D.Breazeale, A.A.Ribeiro, A.L.McClerren, and C.R.Raetz (2005).
A formyltransferase required for polymyxin resistance in Escherichia coli and the modification of lipid A with 4-Amino-4-deoxy-L-arabinose. Identification and function oF UDP-4-deoxy-4-formamido-L-arabinose.
  J Biol Chem, 280, 14154-14167.  
14729668 A.A.Chumanevich, S.A.Krupenko, and C.Davies (2004).
The crystal structure of the hydrolase domain of 10-formyltetrahydrofolate dehydrogenase: mechanism of hydrolysis and its interplay with the dehydrogenase domain.
  J Biol Chem, 279, 14355-14364.
PDB code: 1s3i
15194701 L.Randau, S.Schauer, A.Ambrogelly, J.C.Salazar, J.Moser, S.Sekine, S.Yokoyama, D.Söll, and D.Jahn (2004).
tRNA recognition by glutamyl-tRNA reductase.
  J Biol Chem, 279, 34931-34937.  
15121895 P.S.Klosterman, D.K.Hendrix, M.Tamura, S.R.Holbrook, and S.E.Brenner (2004).
Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns.
  Nucleic Acids Res, 32, 2342-2352.  
14962386 S.Biarrotte-Sorin, A.P.Maillard, J.Delettré, W.Sougakoff, M.Arthur, and C.Mayer (2004).
Crystal structures of Weissella viridescens FemX and its complex with UDP-MurNAc-pentapeptide: insights into FemABX family substrates recognition.
  Structure, 12, 257-267.
PDB codes: 1ne9 1p4n
12639964 A.Stortchevoi, U.Varshney, and U.L.RajBhandary (2003).
Common location of determinants in initiator transfer RNAs for initiator-elongator discrimination in bacteria and in eukaryotes.
  J Biol Chem, 278, 17672-17679.  
12824344 H.Yang, F.Jossinet, N.Leontis, L.Chen, J.Westbrook, H.Berman, and E.Westhof (2003).
Tools for the automatic identification and classification of RNA base pairs.
  Nucleic Acids Res, 31, 3450-3460.  
11983895 A.D.Wolfson, and O.C.Uhlenbeck (2002).
Modulation of tRNAAla identity by inorganic pyrophosphatase.
  Proc Natl Acad Sci U S A, 99, 5965-5970.  
12087168 C.Mayer, and U.L.RajBhandary (2002).
Conformational change of Escherichia coli initiator methionyl-tRNA(fMet) upon binding to methionyl-tRNA formyl transferase.
  Nucleic Acids Res, 30, 2844-2850.  
11847292 J.Pei, and N.V.Grishin (2002).
Breaking the singleton of germination protease.
  Protein Sci, 11, 691-697.  
11792845 T.H.Tan, N.Bochud-Allemann, E.K.Horn, and A.Schneider (2002).
Eukaryotic-type elongator tRNAMet of Trypanosoma brucei becomes formylated after import into mitochondria.
  Proc Natl Acad Sci U S A, 99, 1152-1157.  
12101237 V.Ramesh, C.Köhrer, and U.L.RajBhandary (2002).
Expression of Escherichia coli methionyl-tRNA formyltransferase in Saccharomyces cerevisiae leads to formylation of the cytoplasmic initiator tRNA and possibly to initiation of protein synthesis with formylmethionine.
  Mol Cell Biol, 22, 5434-5442.  
12762022 C.Mayer, A.Stortchevoi, C.Köhrer, U.Varshney, and U.L.RajBhandary (2001).
Initiator tRNA and its role in initiation of protein synthesis.
  Cold Spring Harb Symp Quant Biol, 66, 195-206.  
11726494 J.Moser, W.D.Schubert, V.Beier, I.Bringemeier, D.Jahn, and D.W.Heinz (2001).
V-shaped structure of glutamyl-tRNA reductase, the first enzyme of tRNA-dependent tetrapyrrole biosynthesis.
  EMBO J, 20, 6583-6590.
PDB code: 1gpj
10851193 A.D.Frankel (2000).
Fitting peptides into the RNA world.
  Curr Opin Struct Biol, 10, 332-340.  
11106763 G.R.Andersen, L.Pedersen, L.Valente, I.Chatterjee, T.G.Kinzy, M.Kjeldgaard, and J.Nyborg (2000).
Structural basis for nucleotide exchange and competition with tRNA in the yeast elongation factor complex eEF1A:eEF1Balpha.
  Mol Cell, 6, 1261-1266.
PDB code: 1f60
10721991 I.S.Gabashvili, R.K.Agrawal, C.M.Spahn, R.A.Grassucci, D.I.Svergun, J.Frank, and P.Penczek (2000).
Solution structure of the E. coli 70S ribosome at 11.5 A resolution.
  Cell, 100, 537-549.
PDB code: 1eg0
10966471 M.Ibba, and D.Soll (2000).
Aminoacyl-tRNA synthesis.
  Annu Rev Biochem, 69, 617-650.  
10679458 S.Blanquet, Y.Mechulam, and E.Schmitt (2000).
The many routes of bacterial transfer RNAs after aminoacylation.
  Curr Opin Struct Biol, 10, 95.  
10694387 S.Gite, Y.Li, V.Ramesh, and U.L.RajBhandary (2000).
Escherichia coli methionyl-tRNA formyltransferase: role of amino acids conserved in the linker region and in the C-terminal domain on the specific recognition of the initiator tRNA.
  Biochemistry, 39, 2218-2226.  
10781559 Y.Li, W.B.Holmes, D.R.Appling, and U.L.RajBhandary (2000).
Initiation of protein synthesis in Saccharomyces cerevisiae mitochondria without formylation of the initiator tRNA.
  J Bacteriol, 182, 2886-2892.  
10508782 C.H.Weber, Y.S.Park, S.Sanker, C.Kent, and M.L.Ludwig (1999).
A prototypical cytidylyltransferase: CTP:glycerol-3-phosphate cytidylyltransferase from bacillus subtilis.
  Structure, 7, 1113-1124.
PDB code: 1coz
10499278 D.T.Newton, M.Niemkiewicz, R.Y.Lo, and D.Mangroo (1999).
Recognition of the initiator tRNA by the Pseudomonas aeruginosa methionyl-tRNA formyltransferase: importance of the base-base mismatch at the end of the acceptor stem.
  FEMS Microbiol Lett, 178, 289-298.  
10583945 M.Ibba, and D.Söll (1999).
Quality control mechanisms during translation.
  Science, 286, 1893-1897.  
10737860 P.J.Beuning, and K.Musier-Forsyth (1999).
Transfer RNA recognition by aminoacyl-tRNA synthetases.
  Biopolymers, 52, 1.  
10400475 S.Cusack (1999).
RNA-protein complexes.
  Curr Opin Struct Biol, 9, 66-73.  
9927661 V.Ramesh, C.Mayer, M.R.Dyson, S.Gite, and U.L.RajBhandary (1999).
Induced fit of a peptide loop of methionyl-tRNA formyltransferase triggered by the initiator tRNA substrate.
  Proc Natl Acad Sci U S A, 96, 875-880.  
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 code is shown on the right.

 

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