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(-) Description

Title :  CRYSTAL STRUCTURE OF METHYLTRANSFERASE INVOLVED IN CELL DIVISION FROM THERMOPLASMA VOLCANICUM GSS1
 
Authors :  Y. Patskovsky, S. Ozyurt, M. Dickey, S. Hu, K. Bain, S. Wasserman, J. M. Sauder, S. K. Burley, S. C. Almo, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  06 Jul 08  (Deposition) - 02 Sep 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  A
Keywords :  Methyltransferase, Cell Division, Structural Genomics, Protein Structure Initiative, Psi, New York Structural Genomix Research Consortium, Nysgxrc, Transferase, Cytoplasm, Rrna Processing, New York Sgx Research Center For Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Patskovsky, S. Ozyurt, M. Dickey, S. Hu, K. Bain, S. Wasserman, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Methyltransferase Involved In Cell Division From Thermoplasma Volcanicum
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE J
    Chains: A
    EC Number: 2.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: C TERMINAL SEGMENT, RESIDUES 17-196
    Gene: RRMJ, TV0292, TVG0303954
    Organism Scientific: THERMOPLASMA VOLCANIUM
    Organism Taxid: 50339
    Strain: GSS1
    Synonym: RRNA (URIDINE-2'-O-)-METHYLTRANSFERASE, 23S RRNA M2U2552 METHYLTRANSFERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE
2SAM1Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:22 , GLY A:46 , SER A:48 , PRO A:49 , GLY A:50 , GLY A:51 , TRP A:52 , ASP A:67 , LEU A:68 , GLN A:69 , CYS A:82 , ASP A:83 , ILE A:84 , PHE A:85 , ASP A:111 , ALA A:112 , LYS A:151 , HOH A:215 , HOH A:287 , HOH A:307 , HOH A:337BINDING SITE FOR RESIDUE SAM A 1

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser A:48 -Pro A:49

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 3DOU)

(-) 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    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:175
 aligned with RLME_THEVO | Q97C13 from UniProtKB/Swiss-Prot  Length:197

    Alignment length:181
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196 
           RLME_THEVO    17 QLRSRAAFKLEFLLDRYRVVRKGDAVIEIGSSPGGWTQVLNSLARKIISIDLQEMEEIAGVRFIRCDIFKETIFDDIDRALREEGIEKVDDVVSDAMAKVSGIPSRDHAVSYQIGQRVMEIAVRYLRNGGNVLLKQFQGDMTNDFIAIWRKNFSSYKISKPPASRGSSSEIYIMFFGFKAP 197
               SCOP domains d3doua_ A: automated matches                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh......eeeee....hhhhhhhh....eeeeee..........eeee......hhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhhhhhhhhhheeeeeeeeeeee...hhhhhhhhhh..eeeeeee..------..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dou A  17 QLRSRAAFKLEFLLDRYRVVRKGDAVIEIGSSPGGWTQVLNSLARKIISIDLQEmEEIAGVRFIRCDIFKETIFDDIDRALREEGIEKVDDVVSDAmAKVSGIPSRDHAVSYQIGQRVmEIAVRYLRNGGNVLLKQFQGDmTNDFIAIWRKNFSSYKISKP------SSEIYImFFGFKAE 197
                                    26        36        46        56        66    |   76        86        96       106      |116       126       136       146       156|      166       176|      186   |   196 
                                                                                 71-MSE                                   113-MSE               135-MSE               157-MSE             177    184     |       
                                                                                                                                                                                                       190-MSE
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  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 3DOU)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RLME_THEVO | Q97C13)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0008650    rRNA (uridine-2'-O-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing 2'-O-methyluridine.
    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:0001510    RNA methylation    Posttranscriptional addition of a methyl group to either a nucleotide or 2'-O ribose in a polyribonucleotide. Usually uses S-adenosylmethionine as a cofactor.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0031167    rRNA methylation    The posttranscriptional addition of methyl groups to specific residues in an rRNA 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.
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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