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(-) Description

Title :  CRYSTAL STRUCTURE OF A. AEOLICUS KSGA AT 1.44-ANGSTROM RESOLUTION
 
Authors :  C. Tu, X. Ji
Date :  12 Jan 09  (Deposition) - 24 Mar 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.44
Chains :  Asym./Biol. Unit :  A
Keywords :  Ksga, Rossmann-Like Fold, Rna Methyltransferase, Mtase, Antibiotic Resistance, Methyltransferase, Rna-Binding, Rrna Processing, S- Adenosyl-L-Methionine, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Tu, J. E. Tropea, B. P. Austin, D. L. Court, D. S. Waugh, X. Ji
Structural Basis For Binding Of Rna And Cofactor By A Ksga Methyltransferase.
Structure V. 17 374 2009
PubMed-ID: 19278652  |  Reference-DOI: 10.1016/J.STR.2009.01.010

(-) Compounds

Molecule 1 - DIMETHYLADENOSINE TRANSFERASE
    Chains: A
    EC Number: 2.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBA1939
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector: PDONR221
    Expression System Vector Type: PLASMID
    Gene: AQ_1816, KSGA
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 224324
    Strain: VF5
    Synonym: S-ADENOSYLMETHIONINE-6-N', N'-ADENOSYL(RRNA) DIMETHYLTRANSFERASE, 16S RRNA DIMETHYLASE, HIGH LEVEL KASUGAMYCIN RESISTANCE PROTEIN KSGA, KASUGAMYCIN DIMETHYLTRANSFERASE

 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 3FTD)

(-) Sites  (0, 0)

(no "Site" information available for 3FTD)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:90 -A:120

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val A:167 -Pro A:168

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRNA_A_DIMETHPS01131 Ribosomal RNA adenine dimethylases signature.RSMA_AQUAE34-62  1A:34-62

(-) Exons   (0, 0)

(no "Exon" information available for 3FTD)

(-) 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:240
 aligned with RSMA_AQUAE | O67680 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:240
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246
           RSMA_AQUAE     7 SFGQHLLVSEGVLKKIAEELNIEEGNTVVEVGGGTGNLTKVLLQHPLKKLYVIELDREMVENLKSIGDERLEVINEDASKFPFCSLGKELKVVGNLPYNVASLIIENTVYNKDCVPLAVFMVQKEVAEKLQGKKDTGWLSVFVRTFYDVNYVMTVPPRFFVPPPKVQSAVIKLVKNEKFPVKDLKNYKKFLTKIFQNRRKVLRKKIPEELLKEAGINPDARVEQLSLEDFFKLYRLIEDS 246
               SCOP domains d3ftda_ A: automated matches                                                                                                                                                                                                                     SCOP domains
               CATH domains 3ftdA01 A:7-183 Vaccinia Virus protein VP39                                                                                                                                      --------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eehhhhhhhhhhhh......eeeeee.hhhhhhhhhh.....eeeee..hhhhhhhhh......eeee.......hhhhh...eeeeee....hhhhhhhhhhhhhhhh.eeeeeeehhhhhhhhh....hhhhhhhhhheeeeeeeeehhh.ee......eeeeeeee.......hhhhhhhhhhhhhh....hhhhh.hhhhhhhh......hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------RRNA_A_DIMETH  PDB: A:34-62  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ftd A   7 SFGQHLLVSEGVLKKIAEELNIEEGNTVVEVGGGTGNLTKVLLQHPLKKLYVIELDREMVENLKSIGDERLEVINEDASKFPFCSLGKELKVVGNLPYNVASLIIENTVYNKDCVPLAVFMVQKEVAEKLQGKKDTGWLSVFVRTFYDVNYVMTVPPRFFVPPPKVQSAVIKLVKNEKFPVKDLKNYKKFLTKIFQNRRKVLRKKIPEELLKEAGINPDARVEQLSLEDFFKLYRLIEDS 246
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246
   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  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RSMA_AQUAE | O67680)
molecular function
    GO:0052908    16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity    Catalysis of the reaction: 4 S-adenosyl-L-methionine + adenine(1518)/adenine(1519) in 16S rRNA = 4 S-adenosyl-L-homocysteine + N(6)-dimethyladenine(1518)/N(6)-dimethyladenine(1519) in 16S rRNA.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0016433    rRNA (adenine) methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing methyladenine.
    GO:0000179    rRNA (adenine-N6,N6-)-dimethyltransferase activity    Catalysis of the dimethylation two adjacent A residues in the loop closing the 3'-terminal stem of the 18S rRNA, using S-adenosyl-L-methionine as a methyl donor.
    GO:0008649    rRNA methyltransferase activity    Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a nucleoside residue in an rRNA 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:0031167    rRNA methylation    The posttranscriptional addition of methyl groups to specific residues in an rRNA molecule.
    GO:0000154    rRNA modification    The covalent alteration of one or more nucleotides within an rRNA molecule to produce an rRNA molecule with a sequence that differs from that coded genetically.
    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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    Val A:167 - Pro A:168   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        RSMA_AQUAE | O67680: 3ftc 3fte 3ftf 3r9x

(-) Related Entries Specified in the PDB File

1g38 M.TAQI IN COMPLEX WITH DNA AND COFACTOR ANALOG NEA
1qyr LIGAND-FREE E. COLI KSGA
1zq9 H. SAPIENS DIM1 IN COMPLEX WITH SAM
3ftc LIGAND-FREE A. AEOLICUS KSGA (KSGA2)
3fte A. AEOLICUS KSGA IN COMPLEX WITH RNA (KSGA-RNA)
3ftf A. AEOLICUS KSGA IN COMPLEX WITH RNA AND SAH (KSGA-RNA-SAH)