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(-) Description

Title :  CRYSTAL STRUCTURE OF TRNA (M1G37) METHYLTRANSFERASE FROM AQUIFEX AEOLICUS
 
Authors :  J. Liu, W. Wang, D. H. Shin, H. Yokota, R. Kim, S. H. Kim, Berkeley Struct Genomics Center (Bsgc)
Date :  03 Apr 03  (Deposition) - 11 Nov 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B  (2x)
Keywords :  Structural Genomics, Trmd, Trna (M1G37) Methyltransferase, Bsgc Structure Funded By Nih, Protein Structure Initiative, Psi, Berkeley Structural Genomics Center, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Liu, W. Wang, D. H. Shin, H. Yokota, R. Kim, S. H. Kim
Crystal Structure Of Trna (M1G37) Methyltransferase From Aquifex Aeolicus At 2. 6 A Resolution: A Novel Methyltransferase Fold.
Proteins V. 53 326 2003
PubMed-ID: 14517984  |  Reference-DOI: 10.1002/PROT.10479

(-) Compounds

Molecule 1 - TRNA (GUANINE-N(1)-)-METHYLTRANSFERASE
    Chains: A, B, C
    EC Number: 2.1.1.31
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)/PSJ1244
    Expression System Taxid: 562
    Gene: TRMD OR AQ_1489
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363
    Synonym: M1G-METHYLTRANSFERASE, TRNA [GM37] METHYLTRANSFERASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A C
Biological Unit 2 (2x):  B 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1OY5)

(-) Sites  (0, 0)

(no "Site" information available for 1OY5)

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1B:320 -B:320

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asn A:4 -Pro A:5

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OY5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1OY5)

(-) Exons   (0, 0)

(no "Exon" information available for 1OY5)

(-) 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:218
 aligned with TRMD_AQUAE | O67463 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:232
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233  
           TRMD_AQUAE     4 NPLRFFVLTIFPHIISCYSEYGIVKQAIKKGKVEVYPIDLREFAPKGQVDDVPYGGLPGMVLKPEPIYEAYDYVVENYGKPFVLITEPWGEKLNQKLVNELSKKERIMIICGRYEGVDERVKKIVDMEISLGDFILSGGEIVALAVIDAVSRVLPGVLSEPQSIQEDSFQNRWLGYPVYTRPREYRGMKVPEELLSGHHKLIELWKLWHRIENTVKKRPDLIPKDLTELEKD 235
               SCOP domains d1oy5a_ A: tRNA(m1G37)-methyltransferase TrmD                                                                                                                                                                                            SCOP domains
               CATH domains 1oy5A01 A:4-164  [code=3.40.1280.10, no name defined]                                                                                                            ----------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.hhhhhhhhh.hhhhhhhhhh..eeeeeee.hhhh.....ee.........eehhhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhh..eeeeee......hhhhhhhh.ee..........hhhhhhhhhhhhhhh........--------------........ee..ee.hhhhh.......hhhhhhhhh.hhhhh......hhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oy5 A   4 NPLRFFVLTIFPHIISCYSEYGIVKQAIKKGKVEVYPIDLREFAPKGQVDDVPYGGLPGMVLKPEPIYEAYDYVVENYGKPFVLITEPWGEKLNQKLVNELSKKERIMIICGRYEGVDERVKKIVDMEISLGDFILSGGEIVALAVIDAVSRVLPGVLSEP--------------YPVYTRPREYRGMKVPEELLSGHHKLIELWKLWHRIENTVKKRPDLIPKDLTELEKD 235
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163|        -     | 183       193       203       213       223       233  
                                                                                                                                                                                          164            179                                                        


Chain B from PDB  Type:PROTEIN  Length:218
 aligned with TRMD_AQUAE | O67463 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:232
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233  
           TRMD_AQUAE     4 NPLRFFVLTIFPHIISCYSEYGIVKQAIKKGKVEVYPIDLREFAPKGQVDDVPYGGLPGMVLKPEPIYEAYDYVVENYGKPFVLITEPWGEKLNQKLVNELSKKERIMIICGRYEGVDERVKKIVDMEISLGDFILSGGEIVALAVIDAVSRVLPGVLSEPQSIQEDSFQNRWLGYPVYTRPREYRGMKVPEELLSGHHKLIELWKLWHRIENTVKKRPDLIPKDLTELEKD 235
               SCOP domains d1oy5b_ B: tRNA(m1G37)-methyltransferase TrmD                                                                                                                                                                                            SCOP domains
               CATH domains 1oy5B01 B:304-479  [code=3.40.1280.10, no name defined]                                                                                                                         -------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.hhhhhhhhh.hhhhhhhhhh..eeeeeee.hhhh.....ee.........eehhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhh..eeeeee......hhhhhhhh.ee..........hhhhhhhhhhhhhhhh.......--------------........ee..ee.hhhhh....hhhhhhhhhhhh.hhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oy5 B 304 NPLRFFVLTIFPHIISCYSEYGIVKQAIKKGKVEVYPIDLREFAPKGQVDDVPYGGLPGMVLKPEPIYEAYDYVVENYGKPFVLITEPWGEKLNQKLVNELSKKERIMIICGRYEGVDERVKKIVDMEISLGDFILSGGEIVALAVIDAVSRVLPGVLSEP--------------YPVYTRPREYRGMKVPEELLSGHHKLIELWKLWHRIENTVKKRPDLIPKDLTELEKD 535
                                   313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463|        -     | 483       493       503       513       523       533  
                                                                                                                                                                                          464            479                                                        


Chain C from PDB  Type:PROTEIN  Length:218
 aligned with TRMD_AQUAE | O67463 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:232
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233  
           TRMD_AQUAE     4 NPLRFFVLTIFPHIISCYSEYGIVKQAIKKGKVEVYPIDLREFAPKGQVDDVPYGGLPGMVLKPEPIYEAYDYVVENYGKPFVLITEPWGEKLNQKLVNELSKKERIMIICGRYEGVDERVKKIVDMEISLGDFILSGGEIVALAVIDAVSRVLPGVLSEPQSIQEDSFQNRWLGYPVYTRPREYRGMKVPEELLSGHHKLIELWKLWHRIENTVKKRPDLIPKDLTELEKD 235
               SCOP domains d1oy5c_ C: tRNA(m1G37)-methyltransferase TrmD                                                                                                                                                                                            SCOP domains
               CATH domains 1oy5C01 C:604-764  [code=3.40.1280.10, no name defined]                                                                                                          ----------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------tRNA_m1G_MT-1oy5C01 C:627-822                                                                                                                                                                       ------------- Pfam domains (1)
           Pfam domains (2) -----------------------tRNA_m1G_MT-1oy5C02 C:627-822                                                                                                                                                                       ------------- Pfam domains (2)
           Pfam domains (3) -----------------------tRNA_m1G_MT-1oy5C03 C:627-822                                                                                                                                                                       ------------- Pfam domains (3)
         Sec.struct. author ..eeeeeee.hhhhhhhhh.hhhhhhhhhh..eeeeeee.hhhh.....ee.........eehhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhh..eeeeee......hhhhhhhh.ee..........hhhhhhhhhhhhhhh........--------------........ee..ee.hhhhhhhhhhh.hhhhhhhhh............hhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oy5 C 604 NPLRFFVLTIFPHIISCYSEYGIVKQAIKKGKVEVYPIDLREFAPKGQVDDVPYGGLPGMVLKPEPIYEAYDYVVENYGKPFVLITEPWGEKLNQKLVNELSKKERIMIICGRYEGVDERVKKIVDMEISLGDFILSGGEIVALAVIDAVSRVLPGVLSEP--------------YPVYTRPREYRGMKVPEELLSGHHKLIELWKLWHRIENTVKKRPDLIPKDLTELEKD 835
                                   613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763|        -     | 783       793       803       813       823       833  
                                                                                                                                                                                          764            779
   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, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: SPOUT (28)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (TRMD_AQUAE | O67463)
molecular function
    GO:0008685    2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity    Catalysis of the reaction: 4-CDP-2-C-methyl-D-erythritol 2-phosphate = 2-C-methyl-D-erythritol 2,4-cyclic diphosphate + CMP.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0052906    tRNA (guanine(37)-N(1))-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + guanine(37) in tRNA = N(1)-methylguanine(37) in tRNA + S-adenosyl-L-homocysteine.
    GO:0009019    tRNA (guanine-N1-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing N1-methylguanine.
    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: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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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