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(-) Description

Title :  METHIONYL-TRNAFMET FORMYLTRANSFERASE COMPLEXED WITH FORMYL-METHIONYL-TRNAFMET
 
Authors :  E. Schmitt, Y. Mechulam, S. Blanquet
Date :  29 Jul 98  (Deposition) - 29 Jul 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Complex (Methyltransferase/Trna), Formyltransferase, Initiation Of Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Schmitt, M. Panvert, S. Blanquet, Y. Mechulam
Crystal Structure Of Methionyl-Trnafmet Transformylase Complexed With The Initiator Formyl-Methionyl-Trnafmet.
Embo J. V. 17 6819 1998
PubMed-ID: 9843487  |  Reference-DOI: 10.1093/EMBOJ/17.23.6819
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FORMYL-METHIONYL-TRNAFMET2
    ChainsC, D
    EngineeredYES
    SynonymINITIATOR TRNA
    SyntheticYES
 
Molecule 2 - METHIONYL-TRNA FMET FORMYLTRANSFERASE
    Cellular LocationCYTOPLASM
    ChainsA, B
    EC Number2.1.2.9
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Cellular LocationCYTOPLASM
    Expression System PlasmidPUCFATG
    Expression System StrainJM101TR
    Expression System Taxid562
    Expression System VectorPUC18
    Expression System Vector TypePLASMID
    GeneFMT
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    StrainK37
    Synonym10-FORMYLTETRAHYDROFOLATE L-METHIONYL TRNAFMET FORMYLTRANSFERASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 14)

Asymmetric/Biological Unit (7, 14)
No.NameCountTypeFull Name
14SU2Mod. Nucleotide4-THIOURIDINE-5'-MONOPHOSPHATE
25MU2Mod. Nucleotide5-METHYLURIDINE 5'-MONOPHOSPHATE
3FME2Mod. ResidueN-FORMYLMETHIONINE
4H2U2Mod. Nucleotide5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
5MG2Ligand/IonMAGNESIUM ION
6OMC2Mod. NucleotideO2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
7PSU2Mod. NucleotidePSEUDOURIDINE-5'-MONOPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC3SOFTWARE4SU C:8 , G C:9BINDING SITE FOR RESIDUE MG C 584
2AC4SOFTWAREALA A:89 , TYR A:90 , ASN A:108 , GLY A:119 , ALA A:120 , A C:76BINDING SITE FOR RESIDUE FME C 585
3AC5SOFTWARE4SU D:8 , G D:9BINDING SITE FOR RESIDUE MG D 585
4AC6SOFTWAREALA B:89 , TYR B:90 , ASN B:108 , GLY B:111 , GLY B:119 , ALA B:120 , A D:76BINDING SITE FOR RESIDUE FME D 586

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2FMT)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Leu A:114 -Pro A:115
2Asn A:231 -Pro A:232
3Trp A:233 -Pro A:234
4Leu B:114 -Pro B:115
5Asn B:231 -Pro B:232
6Trp B:233 -Pro B:234

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2FMT)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GARTPS00373 Phosphoribosylglycinamide formyltransferase active site.FMT_ECOLI136-159
 
  2A:135-158
B:135-158

(-) Exons   (0, 0)

(no "Exon" information available for 2FMT)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:314
 aligned with FMT_ECOLI | P23882 from UniProtKB/Swiss-Prot  Length:315

    Alignment length:314
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311    
            FMT_ECOLI     2 SESLRIIFAGTPDFAARHLDALLSSGHNVVGVFTQPDRPAGRGKKLMPSPVKVLAEEKGLPVFQPVSLRPQENQQLVAELQADVMVVVAYGLILPKAVLEMPRLGCINVHGSLLPRWRGAAPIQRSLWAGDAETGVTIMQMDVGLDTGDMLYKLSCPITAEDTSGTLYDKLAELGPQGLITTLKQLADGTAKPEVQDETLVTYAEKLSKEEARIDWSLSAAQLERCIRAFNPWPMSWLEIEGQPVKVWKASVIDTATNAAPGTILEANKQGIQVATGDGILNLLSLQPAGKKAMSAQDLLNSRREWFVPGNRLV 315
               SCOP domains d2fmta2 A:1-206 Methionyl-tRNAfmet formyltransferase                                                                                                                                                          d2fmta1 A:207-314 Methionyl-tRNAfmet formyltransferase, C-terminal domain                                    SCOP domains
               CATH domains 2fmtA01 A:1-208  [code=3.40.50.170, no name defined]                                                                                                                                                            2fmtA02 A:209-313 Methionyl-tRNA Fmet Formyltransferase; Chain A, domain 2                               - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee..hhhhhhhhhhhh...eeeeee................hhhhhhhhh............hhhhhhhhhh...eeeee.......hhhhhh....eeeee...........hhhhhhh....eeeeeeee.........eeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhh.........hhh........hhhh.......hhhhhhhhhh.......eee....eeeeeeeeee..................eeee....eeee.eeee....eeehhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------GART  PDB: A:135-158    ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fmt A   1 SESLRIIFAGTPDFAARHLDALLSSGHNVVGVFTQPDRPAGRGKKLMPSPVKVLAEEKGLPVFQPVSLRPQENQQLVAELQADVMVVVAYGLILPKAVLEMPRLGCINVHGSLLPRWRGAAPIQRSLWAGDAETGVTIMQMDVGLDTGDMLYKLSCPITAEDTSGTLYDKLAELGPQGLITTLKQLADGTAKPEVQDETLVTYAEKLSKEEARIDWSLSAAQLERCIRAFNPWPMSWLEIEGQPVKVWKASVIDTATNAAPGTILEANKQGIQVATGDGILNLLSLQPAGKKAMSAQDLLNSRREWFVPGNRLV 314
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310    

Chain B from PDB  Type:PROTEIN  Length:314
 aligned with FMT_ECOLI | P23882 from UniProtKB/Swiss-Prot  Length:315

    Alignment length:314
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311    
            FMT_ECOLI     2 SESLRIIFAGTPDFAARHLDALLSSGHNVVGVFTQPDRPAGRGKKLMPSPVKVLAEEKGLPVFQPVSLRPQENQQLVAELQADVMVVVAYGLILPKAVLEMPRLGCINVHGSLLPRWRGAAPIQRSLWAGDAETGVTIMQMDVGLDTGDMLYKLSCPITAEDTSGTLYDKLAELGPQGLITTLKQLADGTAKPEVQDETLVTYAEKLSKEEARIDWSLSAAQLERCIRAFNPWPMSWLEIEGQPVKVWKASVIDTATNAAPGTILEANKQGIQVATGDGILNLLSLQPAGKKAMSAQDLLNSRREWFVPGNRLV 315
               SCOP domains d2fmtb2 B:1-206 Methionyl-tRNAfmet formyltransferase                                                                                                                                                          d2fmtb1 B:207-314 Methionyl-tRNAfmet formyltransferase, C-terminal domain                                    SCOP domains
               CATH domains 2fmtB01 B:1-208  [code=3.40.50.170, no name defined]                                                                                                                                                            2fmtB02 B:209-313 Methionyl-tRNA Fmet Formyltransferase; Chain A, domain 2                               - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee..hhhhhhhhhhhh...eeeeee................hhhhhhhhh............hhhhhhhhhh...eeeee.......hhhhhh....eeeee...........hhhhhhh....eeeeeeee.........eeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhh.........hhh........hhhh.......hhhhhhhhhh.......eee....eeeeeeeeee..................eeee....eeee.eeee....eeehhhhh...hhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------GART  PDB: B:135-158    ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fmt B   1 SESLRIIFAGTPDFAARHLDALLSSGHNVVGVFTQPDRPAGRGKKLMPSPVKVLAEEKGLPVFQPVSLRPQENQQLVAELQADVMVVVAYGLILPKAVLEMPRLGCINVHGSLLPRWRGAAPIQRSLWAGDAETGVTIMQMDVGLDTGDMLYKLSCPITAEDTSGTLYDKLAELGPQGLITTLKQLADGTAKPEVQDETLVTYAEKLSKEEARIDWSLSAAQLERCIRAFNPWPMSWLEIEGQPVKVWKASVIDTATNAAPGTILEANKQGIQVATGDGILNLLSLQPAGKKAMSAQDLLNSRREWFVPGNRLV 314
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310    

Chain C from PDB  Type:RNA  Length:77
                                                                                                             
                 2fmt C   1 CGCGGGGuGGAGCAGCCUGGuAGCUCGUCGGGcUCAUAACCCGAAGAUCGUCGGuuCAAAUCCGGCCCCCGCAACCA  76
                                   |10       |19|       29  |     39        49    ||  59        69       
                                   8-4SU   17A  |          32-OMC                54-5MU                  
                                               20-H2U                             55-PSU                 

Chain D from PDB  Type:RNA  Length:77
                                                                                                             
                 2fmt D   1 CGCGGGGuGGAGCAGCCUGGuAGCUCGUCGGGcUCAUAACCCGAAGAUCGUCGGuuCAAAUCCGGCCCCCGCAACCA  76
                                   |10       |19|       29  |     39        49    ||  59        69       
                                   8-4SU   17A  |          32-OMC                54-5MU                  
                                               20-H2U                             55-PSU                 

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FMT)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (FMT_ECOLI | P23882)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016742    hydroxymethyl-, formyl- and related transferase activity    Catalysis of the transfer of a hydroxymethyl- or formyl group from one compound (donor) to another (acceptor).
    GO:0004479    methionyl-tRNA formyltransferase activity    Catalysis of the reaction: 10-formyltetrahydrofolate + L-methionyl-tRNA + H2O = tetrahydrofolate + N-formylmethionyl-tRNA.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    GO:0019988    charged-tRNA amino acid modification    The covalent alteration of an amino acid charged on a tRNA before it is incorporated into a protein, as in N-formylmethionine, selenocysteine or pyrrolysine.
    GO:0071951    conversion of methionyl-tRNA to N-formyl-methionyl-tRNA    The modification process that results in the conversion of methionine charged on a tRNA(fMet) to N-formyl-methionine-tRNA(fMet).
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
    GO:0006413    translational initiation    The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        FMT_ECOLI | P238821fmt

(-) Related Entries Specified in the PDB File

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