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(-) Description

Title :  CRYSTAL STRUCTURE OF TRNA (M1A58) METHYLTRANSFERASE TRMI FROM AQUIFEX AEOLICUS
 
Authors :  T. Yanagisawa, R. Ishii, S. Yokoyama, Riken Structural Genomics/Pr Initiative (Rsgi)
Date :  13 Apr 07  (Deposition) - 01 Apr 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Trna, Methyltransferase, S-Adenosylmethionine, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Yanagisawa, R. Ishii, M. Matsuno, S. Y. Si, R. Ushikoshi-Nakayama, R. Shibata, M. Shirouzu, Y. Bessho, S. Yokoyama
Crystal Structure Of Trna (M1A58) Methyltransferase Trmi From Aquifex Aeolicus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN
    Chains: A, B, C, D
    EC Number: 2.1.1.36
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: ROSETTA(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AQ_311
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 224324
    Strain: VF5
    Synonym: TRMI PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1SAM4Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:72 , GLN A:73 , ILE A:75 , GLY A:99 , THR A:100 , GLY A:101 , SER A:102 , GLY A:103 , ALA A:104 , LEU A:105 , PHE A:119 , GLU A:120 , ALA A:121 , PHE A:125 , ASP A:148 , PHE A:149 , ASP A:165 , TYR A:172 , HOH A:625 , HOH A:711 , HOH A:723BINDING SITE FOR RESIDUE SAM A 601
2AC2SOFTWAREGLN B:73 , ILE B:75 , GLY B:99 , THR B:100 , GLY B:101 , SER B:102 , GLY B:103 , ALA B:104 , LEU B:105 , GLU B:120 , ALA B:121 , PHE B:125 , ASP B:148 , PHE B:149 , ASP B:165 , TYR B:172 , HOH B:622BINDING SITE FOR RESIDUE SAM B 602
3AC3SOFTWARETHR D:72 , GLN D:73 , ILE D:75 , GLY D:99 , THR D:100 , SER D:102 , GLY D:103 , ALA D:104 , LEU D:105 , GLU D:120 , ALA D:121 , PHE D:125 , ASP D:148 , PHE D:149 , ASP D:165 , TYR D:172 , HOH D:632BINDING SITE FOR RESIDUE SAM D 603
4AC4SOFTWARETHR C:72 , GLN C:73 , ILE C:75 , GLY C:99 , THR C:100 , SER C:102 , GLY C:103 , ALA C:104 , LEU C:105 , PHE C:119 , GLU C:120 , ALA C:121 , PHE C:125 , ASP C:148 , PHE C:149 , ASP C:165 , TYR C:172 , HOH C:659BINDING SITE FOR RESIDUE SAM C 604

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Phe A:98 -Gly A:99
2Phe B:98 -Gly B:99
3Phe C:98 -Gly C:99
4Phe D:98 -Gly D:99

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YVL)

(-) 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:247
 aligned with O66653_AQUAE | O66653 from UniProtKB/TrEMBL  Length:248

    Alignment length:247
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       
         O66653_AQUAE     2 NSFKEGEYVLIRFGEKKFLRKLLPKQSLSVKKSVLKFDEVIGKPEGVKINGFEVYRPTLEEIILLGFERKTQIIYPKDSFYIALKLNLNKEKRVLEFGTGSGALLAVLSEVAGEVWTFEAVEEFYKTAQKNLKKFNLGKNVKFFNVDFKDAEVPEGIFHAAFVDVREPWHYLEKVHKSLMEGAPVGFLLPTANQVIKLLESIENYFGNLEVVEILHRHYKTISERFRPEDQMVAHTAYLVFGRKLKT 248
               SCOP domains d2yvla_ A: automated matches                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------2yvlA02 A:60-248 Vaccinia Virus protein VP39                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee..eeeeee.....eeee..eeee.hhh......eee..eeee..hhhhhhhhh........hhhhhhhhhhhh......eeeee....hhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhh.....eeee...............eeee...hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhh...eeeeeeeeeeeeee..hhhhh....eee....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yvl A   2 NSFKEGEYVLIRFGEKKFLRKLLPKQSLSVKKSVLKFDEVIGKPEGVKINGFEVYRPTLEEIILLGFERKTQIIYPKDSFYIALKLNLNKEKRVLEFGTGSGALLAVLSEVAGEVWTFEAVEEFYKTAQKNLKKFNLGKNVKFFNVDFKDAEVPEGIFHAAFVDVREPWHYLEKVHKSLMEGAPVGFLLPTANQVIKLLESIENYFGNLEVVEILHRHYKTISERFRPEDQMVAHTAYLVFGRKLKT 248
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       


Chain B from PDB  Type:PROTEIN  Length:247
 aligned with O66653_AQUAE | O66653 from UniProtKB/TrEMBL  Length:248

    Alignment length:247
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       
         O66653_AQUAE     2 NSFKEGEYVLIRFGEKKFLRKLLPKQSLSVKKSVLKFDEVIGKPEGVKINGFEVYRPTLEEIILLGFERKTQIIYPKDSFYIALKLNLNKEKRVLEFGTGSGALLAVLSEVAGEVWTFEAVEEFYKTAQKNLKKFNLGKNVKFFNVDFKDAEVPEGIFHAAFVDVREPWHYLEKVHKSLMEGAPVGFLLPTANQVIKLLESIENYFGNLEVVEILHRHYKTISERFRPEDQMVAHTAYLVFGRKLKT 248
               SCOP domains d2yvlb_ B: automated matches                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------2yvlB02 B:60-248 Vaccinia Virus protein VP39                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee..eeeeee.....eeee..eeee.hhh......eee..eeee..hhhhhhhhhh.......hhhhhhhhhhhh......eeeee....hhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhh.....eeee...............eeee...hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhh..eeeeeeeeeeeeee..hhhhh....eee....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yvl B   2 NSFKEGEYVLIRFGEKKFLRKLLPKQSLSVKKSVLKFDEVIGKPEGVKINGFEVYRPTLEEIILLGFERKTQIIYPKDSFYIALKLNLNKEKRVLEFGTGSGALLAVLSEVAGEVWTFEAVEEFYKTAQKNLKKFNLGKNVKFFNVDFKDAEVPEGIFHAAFVDVREPWHYLEKVHKSLMEGAPVGFLLPTANQVIKLLESIENYFGNLEVVEILHRHYKTISERFRPEDQMVAHTAYLVFGRKLKT 248
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       


Chain C from PDB  Type:PROTEIN  Length:247
 aligned with O66653_AQUAE | O66653 from UniProtKB/TrEMBL  Length:248

    Alignment length:247
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       
         O66653_AQUAE     2 NSFKEGEYVLIRFGEKKFLRKLLPKQSLSVKKSVLKFDEVIGKPEGVKINGFEVYRPTLEEIILLGFERKTQIIYPKDSFYIALKLNLNKEKRVLEFGTGSGALLAVLSEVAGEVWTFEAVEEFYKTAQKNLKKFNLGKNVKFFNVDFKDAEVPEGIFHAAFVDVREPWHYLEKVHKSLMEGAPVGFLLPTANQVIKLLESIENYFGNLEVVEILHRHYKTISERFRPEDQMVAHTAYLVFGRKLKT 248
               SCOP domains d2yvlc_ C: automated matches                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------2yvlC02 C:60-248 Vaccinia Virus protein VP39                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee..eeeeee.....eeee..eeee.hhh......eee..eeee..hhhhhhhhh........hhhhhhhhhhhh......eeeee....hhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhh.....eeee..hhhhh........eeee...hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhh...eeeeeeeeeeeeee..hhhhh....eee....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yvl C   2 NSFKEGEYVLIRFGEKKFLRKLLPKQSLSVKKSVLKFDEVIGKPEGVKINGFEVYRPTLEEIILLGFERKTQIIYPKDSFYIALKLNLNKEKRVLEFGTGSGALLAVLSEVAGEVWTFEAVEEFYKTAQKNLKKFNLGKNVKFFNVDFKDAEVPEGIFHAAFVDVREPWHYLEKVHKSLMEGAPVGFLLPTANQVIKLLESIENYFGNLEVVEILHRHYKTISERFRPEDQMVAHTAYLVFGRKLKT 248
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       


Chain D from PDB  Type:PROTEIN  Length:247
 aligned with O66653_AQUAE | O66653 from UniProtKB/TrEMBL  Length:248

    Alignment length:247
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       
         O66653_AQUAE     2 NSFKEGEYVLIRFGEKKFLRKLLPKQSLSVKKSVLKFDEVIGKPEGVKINGFEVYRPTLEEIILLGFERKTQIIYPKDSFYIALKLNLNKEKRVLEFGTGSGALLAVLSEVAGEVWTFEAVEEFYKTAQKNLKKFNLGKNVKFFNVDFKDAEVPEGIFHAAFVDVREPWHYLEKVHKSLMEGAPVGFLLPTANQVIKLLESIENYFGNLEVVEILHRHYKTISERFRPEDQMVAHTAYLVFGRKLKT 248
               SCOP domains d2yvld_ D: automated matches                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------2yvlD02 D:60-248 Vaccinia Virus protein VP39                                                                                                                                                  CATH domains
           Pfam domains (1) GCD14-2yvlD01 D:2-239                                                                                                                                                                                                                         --------- Pfam domains (1)
           Pfam domains (2) GCD14-2yvlD02 D:2-239                                                                                                                                                                                                                         --------- Pfam domains (2)
           Pfam domains (3) GCD14-2yvlD03 D:2-239                                                                                                                                                                                                                         --------- Pfam domains (3)
           Pfam domains (4) GCD14-2yvlD04 D:2-239                                                                                                                                                                                                                         --------- Pfam domains (4)
         Sec.struct. author .......eeeeee..eeeeee.....eeee..eeeehhhhh.....eee..eeee..hhhhhhhhh........hhhhhhhhhhhh......eeeee....hhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhh.....eeee...............eeee...hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhh...eeeeeeeeeeeeee..hhhhh....eee....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yvl D   2 NSFKEGEYVLIRFGEKKFLRKLLPKQSLSVKKSVLKFDEVIGKPEGVKINGFEVYRPTLEEIILLGFERKTQIIYPKDSFYIALKLNLNKEKRVLEFGTGSGALLAVLSEVAGEVWTFEAVEEFYKTAQKNLKKFNLGKNVKFFNVDFKDAEVPEGIFHAAFVDVREPWHYLEKVHKSLMEGAPVGFLLPTANQVIKLLESIENYFGNLEVVEILHRHYKTISERFRPEDQMVAHTAYLVFGRKLKT 248
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241
   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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)
(-)
Family: GCD14 (7)
(-)
Aquifex aeolicus (1)
1aGCD14-2yvlD01D:2-239
1bGCD14-2yvlD02D:2-239
1cGCD14-2yvlD03D:2-239
1dGCD14-2yvlD04D:2-239

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (O66653_AQUAE | O66653)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016429    tRNA (adenine-N1-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing N1-methyladenine.
biological process
    GO:0030488    tRNA methylation    The posttranscriptional addition of methyl groups to specific residues in a tRNA molecule.
cellular component
    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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  2yvl
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 Related Entries

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