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(-) Description

Title :  CRYSTAL STRUCTURE OF ATRM4
 
Authors :  M. Hirano, M. Kuratani, S. Yokoyama, Riken Structural Genomics/Pro Initiative (Rsgi)
Date :  01 Jun 10  (Deposition) - 30 Jun 10  (Release) - 01 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.27
Chains :  Asym./Biol. Unit :  A
Keywords :  Trna, M5C, Rossmann Fold, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Methyltransferase, S-Adenosyl- L-Methionine, Transferase, Nppsfa, National Project On Protein Structural And Functional Analyses (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Kuratani, M. Hirano, S. Goto-Ito, Y. Itoh, Y. Hikida, M. Nishimoto, S. Sekine, Y. Bessho, T. Ito, H. Grosjean, S. Yokoyama
Crystal Structure Of Methanocaldococcus Jannaschii Trm4 Complexed With Sinefungin.
J. Mol. Biol. V. 401 323 2010
PubMed-ID: 20600111  |  Reference-DOI: 10.1016/J.JMB.2010.06.046

(-) Compounds

Molecule 1 - PUTATIVE METHYLTRANSFERASE MJ0026
    Chains: A
    EC Number: 2.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MJ0026
    Organism Common: METHANOCOCCUS JANNASCHII
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2IPA1Ligand/IonISOPROPYL ALCOHOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:144 , ARG A:189 , GLU A:192 , HOH A:493BINDING SITE FOR RESIDUE GOL A 900
2AC2SOFTWAREGLU A:250 , GLY A:251 , ARG A:258 , PHE A:260BINDING SITE FOR RESIDUE IPA A 950

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:91 -A:186
2A:166 -A:212

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:93 -Pro A:94
2Pro A:261 -Pro A:262

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3AJD)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NOL1_NOP2_SUNPS01153 NOL1/NOP2/sun family signature.TRM4_METJA157-168  1A:157-166

(-) Exons   (0, 0)

(no "Exon" information available for 3AJD)

(-) 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:254
 aligned with TRM4_METJA | Q60343 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:266
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268      
           TRM4_METJA     9 KMQFIRVNTLKINPEVLKKRLENKGVVLEKTFLDYAFEVKKSPFSIGSTPEYLFGYYMPQSISSMIPPIVLNPREDDFILDMCAAPGGKTTHLAQLMKNKGTIVAVEISKTRTKALKSNINRMGVLNTIIINADMRKYKDYLLKNEIFFDKILLDAPCSGNIIKDKNRNVSEEDIKYCSLRQKELIDIGIDLLKKDGELVYSTCSMEVEENEEVIKYILQKRNDVELIIIKANEFKGINIKEGYIKGTLRVFPPNEPFFIAKLRKI 274
               SCOP domains d3ajda_ A: automated matches                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....hhhhhhhhhhh...eeee.....eeeeee.......hhhhhh..eee..hhhhhhhhhhh.....eeee.....hhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhh...eeeeeeee..------------hhhhhhhhhhhhhhhhhhhhhheeeeeeeeeee.......hhhhhhhhhhhh..eeee...........eee......eee......eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------NOL1_NOP2_SU---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ajd A   9 KMQFIRVNTLKINPEVLKKRLENKGVVLEKTFLDYAFEVKKSPFSIGSTPEYLFGYYMPQSISSMIPPIVLNPREDDFILDMCAAPGGKTTHLAQLMKNKGTIVAVEISKTRTKALKSNINRMGVLNTIIINADMRKYKDYLLKNEIFFDKILLDAPC------------SEEDIKYCSLRQKELIDIGIDLLKKDGELVYSTCSMEVEENEEVIKYILQKRNDVELIIIKANEFKGINIKEGYIKGTLRVFPPNEPFFIAKLRKI 274
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       | -         -|      188       198       208       218       228       238       248       258       268      
                                                                                                                                                                                       166          179
   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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3AJD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3AJD)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TRM4_METJA | Q60343)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0008757    S-adenosylmethionine-dependent methyltransferase activity    Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a substrate.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0016428    tRNA (cytosine-5-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing 5-methylcytosine.
    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:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TRM4_METJA | Q60343: 3a4t

(-) Related Entries Specified in the PDB File

3a4t RELATED ID: MJA001000026.1 RELATED DB: TARGETDB