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(-) Description

Title :  CRYSTAL STRUCTURE OF DUF358 PROTEIN REVEALS A PUTATIVE SPOUT-CLASS RRNA METHYLTRANSFERASE
 
Authors :  Y. A. Yuan, H. Y. Chen
Date :  11 May 10  (Deposition) - 30 Mar 11  (Release) - 30 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  X
Biol. Unit 1:  X  (2x)
Keywords :  Mjduf358, Rrna Methyltransferase, Spout-Class Fold, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Y. Chen, Y. A. Yuan
Crystal Structure Of Mj1640/Duf358 Protein Reveals A Putative Spout-Class Rna Methyltransferase
J Mol Cell Biol V. 2 366 2010
PubMed-ID: 21098051  |  Reference-DOI: 10.1093/JMCB/MJQ034

(-) Compounds

Molecule 1 - UPF0217 PROTEIN MJ1640
    Chains: X
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MJ1640
    Mutation: YES
    Organism Common: METHANOCOCCUS JANNASCHII
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : X
Biological Unit 1 (2x): X

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2MSE6Mod. Amino AcidSELENOMETHIONINE
3SAM1Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 1 (2, 14)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2MSE12Mod. Amino AcidSELENOMETHIONINE
3SAM2Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER X:43 , LEU X:136 , HIS X:137 , MSE X:138 , GLY X:156 , ASP X:157 , HIS X:158 , LEU X:179 , SER X:180 , LEU X:182 , GLU X:183 , LEU X:184 , ALA X:186 , CYS X:189BINDING SITE FOR RESIDUE SAM X 501
2AC2SOFTWARESER X:1A , ARG X:201BINDING SITE FOR RESIDUE MG X 502
3AC3SOFTWARETYR X:53 , TRP X:105 , GLU X:125 , GLU X:129BINDING SITE FOR RESIDUE MG X 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3AI9)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gln X:59 -Pro X:60
2Pro X:62 -Pro X:63

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3AI9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3AI9)

(-) Exons   (0, 0)

(no "Exon" information available for 3AI9)

(-) 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 X from PDB  Type:PROTEIN  Length:211
 aligned with TRMY_METJA | Q59034 from UniProtKB/Swiss-Prot  Length:205

    Alignment length:211
                                  1                                                                                                                                                                                                            
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204 
           TRMY_METJA     - ------MREFIFKANKTITSSDINLKDLPGSCGRLDLLCRCVSDAFFLSHDIRRDVVFYAVLYGQPNPPVCIKFVGSELKKVSPDERNIAIFIKKALKKFEELDEEQRKDWNQSTPGIYVRRLGFRNLVLEKLEEGKNIYYLHMNGEDVENVDIENPVFIIGDHIGIGEEDERFLDEIKAKRISLSPLELHANHCITIIHNVLDKKRICEI 205
               SCOP domains d3ai9x_ X: automated matches                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeee.........hhhhh.....hhhhhhhhhhhhhee..ee...eeeeeee.......eeeeee.........hhhhhhhhhhhhhhhhhhh..hhhhh.eeee..eeee..hhhhhhhhhhhh..eeeee....ee.hhh....eeeee.....hhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ai9 X  1F GSHmASmREFIFKANKTITSSDINLKDLPGSCGRLDLLCRCVSDAFFLSHDIRRDVVFYAVLYGQPNPPVCIKFVGSELKKVSPDERNIAIFIKKALKKFEELDEEQRKDWNQSTPGIYVRRLGFRNLVLEKLEEGKNIYYLHmNGEDVENVDIENPVFIIGDHIGIGEEDERFLDEIKAKRISLSPLELHANHCmTmmHNVLDKKRICEI 205
                            |||||||  4        14        24        34        44        54        64        74        84        94       104       114       124       134   |   144       154       164       174       184     | 194       204 
                            |||||||                                                                                                                                      138-MSE                                             190-MSE           
                           1F||||||                                                                                                                                                                                            192-MSE         
                            1E|||||                                                                                                                                                                                             193-MSE        
                             1D||||                                                                                                                                                                                                            
                              1C-MSE                                                                                                                                                                                                           
                               1B||                                                                                                                                                                                                            
                                1A|                                                                                                                                                                                                            
                                  1-MSE
   Legend:   → Mismatch (orange background)
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  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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3AI9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3AI9)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain X   (TRMY_METJA | Q59034)
molecular function
    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:0008175    tRNA methyltransferase activity    Catalysis of the transfer of a methyl group from a donor to a nucleoside residue in a tRNA molecule.
    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: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
        TRMY_METJA | Q59034: 3aia

(-) Related Entries Specified in the PDB File

3aia