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(-) Description

Title :  CRYSTAL STRUCTURE OF A M1A58 TRNA METHYLTRANSFERASE
 
Authors :  P. Barraud, B. Golinelli-Pimpaneau, C. Tisne
Date :  14 May 07  (Deposition) - 26 Feb 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Mtase, Adomet, Trmi, Trna-M1A58, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Barraud, B. Golinelli-Pimpaneau, C. Atmanene, S. Sanglier, A. Van Dorsselaer, L. Droogmans, F. Dardel, C. Tisne
Crystal Structure Of Thermus Thermophilus Trna M(1)A(58) Methyltransferase And Biophysical Characterization Of Its Interaction With Trna.
J. Mol. Biol. V. 377 535 2008
PubMed-ID: 18262540  |  Reference-DOI: 10.1016/J.JMB.2008.01.041

(-) Compounds

Molecule 1 - TRNA (ADENINE-N(1)-)-METHYLTRANSFERASE
    Chains: A, B
    EC Number: 2.1.1.36
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: ROSETTA(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TRMI
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 262724
    Strain: HB27
    Synonym: TRNA(M1A58)-METHYLTRANSFERASE, TRNA(M1A58)MTASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
2SO43Ligand/IonSULFATE ION
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1SAH4Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
2SO46Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:51 , LEU A:52 , PHE A:213 , ARG A:214 , LEU A:215 , HOH A:532 , HOH A:655 , HOH A:747BINDING SITE FOR RESIDUE SO4 A 503
2AC2SOFTWAREHIS B:51 , ARG B:251 , GLY B:254 , HOH B:546BINDING SITE FOR RESIDUE SO4 B 504
3AC3SOFTWAREARG A:49 , ARG A:214 , GLU A:216 , ARG A:250 , LYS B:10 , SER B:57 , HIS B:59BINDING SITE FOR RESIDUE SO4 A 505
4AC4SOFTWARETHR A:75 , PRO A:76 , THR A:77 , GLY A:101 , THR A:102 , GLY A:103 , SER A:104 , GLY A:105 , GLY A:106 , LEU A:107 , GLU A:125 , ALA A:126 , ARG A:127 , HIS A:130 , GLY A:152 , LYS A:153 , LEU A:154 , GLU A:155 , ASP A:170 , LEU A:171 , HOH A:509 , HOH A:552 , HOH A:630 , HOH A:647BINDING SITE FOR RESIDUE SAH A 501
5AC5SOFTWAREALA B:74 , THR B:75 , PRO B:76 , THR B:77 , GLY B:101 , THR B:102 , GLY B:103 , SER B:104 , GLY B:105 , GLY B:106 , LEU B:107 , GLU B:125 , ALA B:126 , ARG B:127 , HIS B:130 , GLY B:152 , LYS B:153 , LEU B:154 , GLU B:155 , ASP B:170 , LEU B:171 , HOH B:505 , HOH B:506 , HOH B:527BINDING SITE FOR RESIDUE SAH A 502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ala A:100 -Gly A:101
2Leu A:230 -Pro A:231
3Ala B:100 -Gly B:101
4Leu B:230 -Pro B:231

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2PWY)

(-) 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 A from PDB  Type:PROTEIN  Length:251
 aligned with TRMI_THET2 | Q8GBB2 from UniProtKB/Swiss-Prot  Length:255

    Alignment length:251
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254 
           TRMI_THET2     5 GPLLLKDRKGRAYLVFPKEGGVFHHHKGSVPHEALLEAGPGGVVRTHLGEELSVHRPTLEEYLLHMKRSATPTYPKDASAMVTLLDLAPGMRVLEAGTGSGGLTLFLARAVGEKGLVESYEARPHHLAQAERNVRAFWQVENVRFHLGKLEEAELEEAAYDGVALDLMEPWKVLEKAALALKPDRFLVAYLPNITQVLELVRAAEAHPFRLERVLEVGWREWEVRLPVAHPRFQQVGHTAFLVALRRWKAS 255
               SCOP domains d2pwya_ A: automated matches                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.....eeee......ee......eehhhhhhhh...eee.....eeeee..hhhhhhhhh.......hhhhhhhhhhhh......eeeee....hhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh....eeeee.hhhhh......eeeeeee..hhhhhhhhhhhheeeeeeeeeee.hhhhhhhhhhhhh...eeeeeeeeeeeeeeeee..eeee.........eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pwy A   5 GPLLLKDRKGRAYLVFPKEGGVFHHHKGSVPHEALLEAGPGGVVRTHLGEELSVHRPTLEEYLLHMKRSATPTYPKDASAMVTLLDLAPGMRVLEAGTGSGGLTLFLARAVGEKGLVESYEARPHHLAQAERNVRAFWQVENVRFHLGKLEEAELEEAAYDGVALDLMEPWKVLEKAALALKPDRFLVAYLPNITQVLELVRAAEAHPFRLERVLEVGWREWEVRLPVAHPRFQQVGHTAFLVALRRWKGS 255
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254 


Chain B from PDB  Type:PROTEIN  Length:250
 aligned with TRMI_THET2 | Q8GBB2 from UniProtKB/Swiss-Prot  Length:255

    Alignment length:250
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254
           TRMI_THET2     5 GPLLLKDRKGRAYLVFPKEGGVFHHHKGSVPHEALLEAGPGGVVRTHLGEELSVHRPTLEEYLLHMKRSATPTYPKDASAMVTLLDLAPGMRVLEAGTGSGGLTLFLARAVGEKGLVESYEARPHHLAQAERNVRAFWQVENVRFHLGKLEEAELEEAAYDGVALDLMEPWKVLEKAALALKPDRFLVAYLPNITQVLELVRAAEAHPFRLERVLEVGWREWEVRLPVAHPRFQQVGHTAFLVALRRWKA 254
               SCOP domains d2pwyb_ B: automated matches                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------GCD14-2pwyB01 B:11-244                                                                                                                                                                                                                    ---------- Pfam domains (1)
           Pfam domains (2) ------GCD14-2pwyB02 B:11-244                                                                                                                                                                                                                    ---------- Pfam domains (2)
         Sec.struct. author ..eeee.....eeee......eeee..eeeehhhhhhhh...eee.....eeeee..hhhhhhhhh.......hhhhhhhhhhhh......eeeee....hhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh....eeeee.hhhhh......eeeeeee..hhhhhhhhhhhheeeeeeeeeee.hhhhhhhhhhhhhhh.eeeeeeeeeeeeeeeee..eeee.........eeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pwy B   5 GPLLLKDRKGRAYLVFPKEGGVFHHHKGSVPHEALLEAGPGGVVRTHLGEELSVHRPTLEEYLLHMKRSATPTYPKDASAMVTLLDLAPGMRVLEAGTGSGGLTLFLARAVGEKGLVESYEARPHHLAQAERNVRAFWQVENVRFHLGKLEEAELEEAAYDGVALDLMEPWKVLEKAALALKPDRFLVAYLPNITQVLELVRAAEAHPFRLERVLEVGWREWEVRLPVAHPRFQQVGHTAFLVALRRWKG 254
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (TRMI_THET2 | Q8GBB2)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0016429    tRNA (adenine-N1-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing N1-methyladenine.
    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: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: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:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    GO:0031515    tRNA (m1A) methyltransferase complex    A protein complex involved in the catalysis of the formation of the modified nucleotide 1-methyladenosine (m1A) in tRNA. In yeast, it is a heterotetramer of two subunits, Gcd10p and Gcd14p, while in bacteria and archaea it is a homotetramer.

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 Related Entries

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        TRMI_THET2 | Q8GBB2: 5c0o 5c1i

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