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(-) Description

Title :  CRYSTAL STRUCTURE OF RNA 2'-O RIBOSE METHYLTRANSFERASE
 
Authors :  O. Nureki, M. Shirouzu, K. Hashimoto, R. Ishitani, T. Terada, M. Tamakoshi, T. Oshima, M. Chijimatsu, K. Takio, D. G. Vassylyev, T. Shibata, Y. Inoue, S. Kuramitsu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  02 May 01  (Deposition) - 10 Jul 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Deep Trefoil Knot, Rossmann Fold, El30-Like Fold, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Nureki, M. Shirouzu, K. Hashimoto, R. Ishitani, T. Terada, M. Tamakoshi, T. Oshima, M. Chijimatsu, K. Takio, D. G. Vassylyev, T. Shibata, Y. Inoue, S. Kuramitsu, S. Yokoyama
An Enzyme With A Deep Trefoil Knot For The Active-Site Architecture.
Acta Crystallogr. , Sect. D V. 58 1129 2002
PubMed-ID: 12077432  |  Reference-DOI: 10.1107/S0907444902006601
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RNA 2'-O-RIBOSE METHYLTRANSFERASE
    Chains: A
    EC Number: 2.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET16B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
    Synonym: RRMH

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1IPA)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1IPA)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1IPA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1IPA)

(-) 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:258
 aligned with Q7SID4_THETH | Q7SID4 from UniProtKB/TrEMBL  Length:274

    Alignment length:263
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260   
         Q7SID4_THETH     1 MRITSTANPRIKELARLLERKHRDSQRRFLIEGAREIERALQAGIELEQALVWEGGLNPEEQQVYAALGRVGRLALLEVSEAVLKKLSVRDNPAGLIALARMPERTLEEYRPSPDALILVAVGLEKPGNLGAVLRSADAAGAEAVLVAGGVDLYSPQVIRNSTGVVFSLRTLAASESEVLDWIKQHNLPLVATTPHAEALYWEANLRPPVAIAVGPEHEGLRAAWLEAAQTQVRIPMQGQADSLNVSVSAALLLYEALRQRLL 263
               SCOP domains d1ipaa2 A:1-105 RrmA (RrmH), N-terminal domain                                                           d1ipaa1 A:106-263 RrmA (RrmH), C-terminal domain                                                                                                               SCOP domains
               CATH domains 1ipaA01 A:1-104  [code=3.30.1330.30, no name defined]                                                   ------1ipaA02 A:111-263  [code=3.40.1280.10, no name defined]                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee....hhhhhhhhh..hhhhhhhhheeeeehhhhhhhhhhh...eeeeeee....hhhhhhhhhh.-----.eeeeehhhhhhhhh.......eeeeee...............eeeeee...hhhhhhhhhhhhhhhh..eeeee......hhhhhhhh.hhhhh..eeeehhhhhhhhhhhh...eeee.......hhhh.....eeeee.......hhhhhhhh.eee...........hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ipa A   1 MRITSTANPRIKELARLLERKHRDSQRRFLIEGAREIERALQAGIELEQALVWEGGLNPEEQQVYAAL-----LALLEVSEAVLKKLSVRDNPAGLIALARMPERTLEEYRPSPDALILVAVGLEKPGNLGAVLRSADAAGAEAVLVAGGVDLYSPQVIRNSTGVVFSLRTLAASESEVLDWIKQHNLPLVATTPHAEALYWEANLRPPVAIAVGPEHEGLRAAWLEAAQTQVRIPMQGQADSLNVSVSAALLLYEALRQRLL 263
                                    10        20        30        40        50        60       | -   |    80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260   
                                                                                              68    74
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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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IPA)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q7SID4_THETH | Q7SID4)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0008173    RNA methyltransferase activity    Catalysis of the transfer of a methyl group from a donor to a nucleoside residue in an RNA molecule.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor 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: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:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.

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