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(-) Description

Title :  STRUCTURE OF TRM8, M7G METHYLATION ENZYME
 
Authors :  N. Leulliot, M. Chaillet, D. Durand, N. Ulryck, K. Blondeau, H. Van Tilbeurgh
Date :  11 Oct 07  (Deposition) - 18 Dec 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  E,F
Biol. Unit 1:  E  (1x)
Biol. Unit 2:  F  (1x)
Biol. Unit 3:  E,F  (1x)
Keywords :  S-Adenosyl-L-Methionine, Phosphorylation, Methyltransferase, M7G, Trna, Spout Mt, Transferase, Trna Processing (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Leulliot, M. Chaillet, D. Durand, N. Ulryck, K. Blondeau, H. Van Tilbeurgh
Structure Of The Yeast Trna M7G Methylation Complex.
Structure V. 16 52 2008
PubMed-ID: 18184583  |  Reference-DOI: 10.1016/J.STR.2007.10.025

(-) Compounds

Molecule 1 - TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE
    Chains: E, F
    EC Number: 2.1.1.33
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: GOLD (DE3)
    Expression System Taxid: 562
    Expression System Vector: PET9
    Fragment: RESIDUES 47-286
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Other Details: 46 N-TERMNIAL TRUNCATION
    Synonym: TRNA(M7G46)-METHYLTRANSFERASE, TRM8

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : EF
Biological Unit 1 (1x): E 
Biological Unit 2 (1x):  F
Biological Unit 3 (1x): EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SAM2Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SAM1Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SAM1Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1SAM2Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY E:103 , CYS E:104 , GLY E:105 , GLU E:126 , ILE E:127 , ARG E:128 , GLY E:160 , ASN E:161 , ALA E:162 , CYS E:181 , PHE E:182 , ASP E:184 , THR E:259 , GLU E:261 , HOH E:2086 , HOH E:2087BINDING SITE FOR RESIDUE SAM E1287
2AC2SOFTWAREGLY F:103 , CYS F:104 , GLU F:126 , ILE F:127 , ARG F:128 , GLY F:160 , ASN F:161 , ALA F:162 , CYS F:181 , PHE F:182 , ASP F:184 , THR F:259 , GLU F:261 , HOH F:2116 , HOH F:2117 , HOH F:2119BINDING SITE FOR RESIDUE SAM F1287

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2VDV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VDV)

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDL201W1YDL201W.1IV:99562-100422861TRMB_YEAST1-2862862E:60-286 (gaps)
F:60-286 (gaps)		228
228

(-) Sequences/Alignments

Asymmetric 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 E from PDB  Type:PROTEIN  Length:216
 aligned with TRMB_YEAST | Q12009 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:227
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       
          TRMB_YEAST     60 NPFSDHQLEYPVSPQDMDWSKLYPYYKNAENGQMTKKVTIADIGCGFGGLMIDLSPAFPEDLILGMEIRVQVTNYVEDRIIALRNNTASKHGFQNINVLRGNAMKFLPNFFEKGQLSKMFFCFPDPHFKQRKHKARIITNTLLSEYAYVLKEGGVVYTITDVKDLHEWMVKHLEEHPLFERLSKEWEENDECVKIMRNATEEGKKVERKKGDKFVACFTRLPTPAIL  286
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh..........hhhhhhhhh..----.....eeeeee....hhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhh.-.......eeeee.....hhhhh.....eeeeeee....------......hhhhhhhhhhheeeeeeeeeee.hhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: E:60-286 (gaps) UniProt: 1-286 [INCOMPLETE]                                                                                                                                                                          Transcript 1
                2vdv E   60 NPFSDHQLEYPVSPQDMDWSKLYPYYKN----QMTKKVTIADIGCGFGGLMIDLSPAFPEDLILGMEIRVQVTNYVEDRIIALRNNT-SKHGFQNINVLRGNAMKFLPNFFEKGQLSKMFFCFPDP------HKARIITNTLLSEYAYVLKEGGVVYTITDVKDLHEWMVKHLEEHPLFERLSKEWEENDECVKIMRNATEEGKKVERKKGDKFVACFTRLPTPAIL  286
                                    69        79       | -  |     99       109       119       129       139      |149       159       169       179     |   -  |    199       209       219       229       239       249       259       269       279       
                                                      87   92                                                   146 |               166B|              185    192                                                                                              
                                                                                                                  148                 168                                                                                                                      


Chain F from PDB  Type:PROTEIN  Length:216
 aligned with TRMB_YEAST | Q12009 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:227
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       
          TRMB_YEAST     60 NPFSDHQLEYPVSPQDMDWSKLYPYYKNAENGQMTKKVTIADIGCGFGGLMIDLSPAFPEDLILGMEIRVQVTNYVEDRIIALRNNTASKHGFQNINVLRGNAMKFLPNFFEKGQLSKMFFCFPDPHFKQRKHKARIITNTLLSEYAYVLKEGGVVYTITDVKDLHEWMVKHLEEHPLFERLSKEWEENDECVKIMRNATEEGKKVERKKGDKFVACFTRLPTPAIL  286
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh..........hhhhhhhhh..----.....eeeeee....hhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhh.-.......eeeee.....hhhhh.....eeeeeee....------......hhhhhhhhhhheeeeeeeeeee.hhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: F:60-286 (gaps) UniProt: 1-286 [INCOMPLETE]                                                                                                                                                                          Transcript 1
                2vdv F   60 NPFSDHQLEYPVSPQDMDWSKLYPYYKN----QMTKKVTIADIGCGFGGLMIDLSPAFPEDLILGMEIRVQVTNYVEDRIIALRNNT-SKHGFQNINVLRGNAMKFLPNFFEKGQLSKMFFCFPDP------HKARIITNTLLSEYAYVLKEGGVVYTITDVKDLHEWMVKHLEEHPLFERLSKEWEENDECVKIMRNATEEGKKVERKKGDKFVACFTRLPTPAIL  286
                                    69        79       | -  |     99       109       119       129       139      |149       159       169       179     |   -  |    199       209       219       229       239       249       259       269       279       
                                                      87   92                                                   146 |               166B|              185    192                                                                                              
                                                                                                                  148                 168
   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  (0, 0)

(no "SCOP Domain" information available for 2VDV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2VDV)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain E,F   (TRMB_YEAST | Q12009)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0008176    tRNA (guanine-N7-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing N7-methylguanine.
    GO:0000049    tRNA binding    Interacting selectively and non-covalently with transfer RNA.
    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:0036265    RNA (guanine-N7)-methylation    The addition of a methyl group to the N7 atom in the base portion of a guanine nucleotide residue in an RNA molecule.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0030488    tRNA methylation    The posttranscriptional addition of methyl groups to specific residues in a tRNA molecule.
    GO:0006400    tRNA modification    The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
cellular component
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0043527    tRNA methyltransferase complex    A multimeric protein complex involved in the methylation of specific nucleotides in tRNA.

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(-) Related Entries Specified in the PDB File

2vdu STRUCTURE OF TRM8, M7G METHYLATION ENZYME