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(-) Description

Title :  2.1 ANGSTROM CRYSTAL STRUCTURE OF KSGA: A UNIVERSALLY CONSERVED ADENOSINE DIMETHYLTRANSFERASE
 
Authors :  H. C. O'Farrell, J. N. Scarsdale, H. T. Wright, J. P. Rife
Date :  11 Sep 03  (Deposition) - 29 Jun 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Kasugamycin Resistance; Adenosine Dimethyltransferase; Rrna Modification, Transferase, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. C. O'Farrell, J. N. Scarsdale, J. P. Rife
Crystal Structure Of Ksga, A Universally Conserved Rrna Adenine Dimethyltransferase In Escherichia Coli
J. Mol. Biol. V. 339 337 2004
PubMed-ID: 15136037  |  Reference-DOI: 10.1016/J.JMB.2004.02.068

(-) Compounds

Molecule 1 - HIGH LEVEL KASUGAMYCIN RESISTANCE PROTEIN
    ChainsA, B
    EC Number2.1.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainHMS174
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneKSGA
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymKSGA

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1QYR)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Thr A:182 -Pro A:183
2Thr B:182 -Pro B:183

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRNA_A_DIMETHPS01131 Ribosomal RNA adenine dimethylases signature.RSMA_ECOLI41-68
 
  2A:41-68
B:41-68
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRNA_A_DIMETHPS01131 Ribosomal RNA adenine dimethylases signature.RSMA_ECOLI41-68
 
  1A:41-68
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRNA_A_DIMETHPS01131 Ribosomal RNA adenine dimethylases signature.RSMA_ECOLI41-68
 
  1-
B:41-68

(-) Exons   (0, 0)

(no "Exon" information available for 1QYR)

(-) 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 A from PDB  Type:PROTEIN  Length:252
 aligned with RSMA_ECOLI | P06992 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:252
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266  
           RSMA_ECOLI    17 QNFLNDQFVIDSIVSAINPQKGQAMVEIGPGLAALTEPVGERLDQLTVIELDRDLAARLQTHPFLGPKLTIYQQDAMTFNFGELAEKMGQPLRVFGNLPYNISTPLMFHLFSYTDAIADMHFMLQKEVVNRLVAGPNSKAYGRLSVMAQYYCNVIPVLEVPPSAFTPPPKVDSAVVRLVPHATMPHPVKDVRVLSRITTEAFNQRRKTIRNSLGNLFSVEVLTGMGIDPAMRAENISVAQYCQMANYLAENA 268
               SCOP domains d1qyra_ A: High level kasugamycin resistance protein KsgA                                                                                                                                                                                                    SCOP domains
               CATH domains 1qyrA01 A:17-200 Vaccinia Virus protein VP39                                                                                                                                            1qyrA02 A:201-268  [code=1.10.8.100, no name defined]                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee.hhhhhhhhhhhhh......eeee......hhhhhhh....eeee..hhhhhhhhhh...hhh.eeee..hhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhh.eeeeeeeeehhhhhhhhh.......hhhhhhhhhheeeeeeeeehhh.ee......eeeeeeee.........hhhhhhhhhhhhhhh...hhhhhh....hhhhhhhh......hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------RRNA_A_DIMETH  PDB: A:41-68 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qyr A  17 QNFLNDQFVIDSIVSAINPQKGQAMVEIGPGLAALTEPVGERLDQLTVIELDRDLAARLQTHPFLGPKLTIYQQDAMTFNFGELAEKMGQPLRVFGNLPYNISTPLMFHLFSYTDAIADMHFMLQKEVVNRLVAGPNSKAYGRLSVMAQYYCNVIPVLEVPPSAFTPPPKVDSAVVRLVPHATMPHPVKDVRVLSRITTEAFNQRRKTIRNSLGNLFSVEVLTGMGIDPAMRAENISVAQYCQMANYLAENA 268
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266  

Chain B from PDB  Type:PROTEIN  Length:252
 aligned with RSMA_ECOLI | P06992 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:252
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266  
           RSMA_ECOLI    17 QNFLNDQFVIDSIVSAINPQKGQAMVEIGPGLAALTEPVGERLDQLTVIELDRDLAARLQTHPFLGPKLTIYQQDAMTFNFGELAEKMGQPLRVFGNLPYNISTPLMFHLFSYTDAIADMHFMLQKEVVNRLVAGPNSKAYGRLSVMAQYYCNVIPVLEVPPSAFTPPPKVDSAVVRLVPHATMPHPVKDVRVLSRITTEAFNQRRKTIRNSLGNLFSVEVLTGMGIDPAMRAENISVAQYCQMANYLAENA 268
               SCOP domains d1qyrb_ B: High level kasugamycin resistance protein KsgA                                                                                                                                                                                                    SCOP domains
               CATH domains 1qyrB01 B:17-200 Vaccinia Virus protein VP39                                                                                                                                            1qyrB02 B:201-268  [code=1.10.8.100, no name defined]                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee.hhhhhhhhhhhhh.....eeeee......hhhhhhh....eeee..hhhhhhhhhh...hhh.eeee.......hhhhhhhhhh..eeeeee....hhhhhhhhhhhh...eeeeeeeeehhhhhhhhh.......hhhhhhhhhheeeeeeeeehhh.ee......eeeeeeee.........hhhhhhhhhhhhhhh...hhhhhh....hhhhhhhh......hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------RRNA_A_DIMETH  PDB: B:41-68 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qyr B  17 QNFLNDQFVIDSIVSAINPQKGQAMVEIGPGLAALTEPVGERLDQLTVIELDRDLAARLQTHPFLGPKLTIYQQDAMTFNFGELAEKMGQPLRVFGNLPYNISTPLMFHLFSYTDAIADMHFMLQKEVVNRLVAGPNSKAYGRLSVMAQYYCNVIPVLEVPPSAFTPPPKVDSAVVRLVPHATMPHPVKDVRVLSRITTEAFNQRRKTIRNSLGNLFSVEVLTGMGIDPAMRAENISVAQYCQMANYLAENA 268
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266  

   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, 2)

Asymmetric Unit

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RSMA_ECOLI | P06992)
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:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    GO:0003729    mRNA binding    Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
    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:0019843    rRNA binding    Interacting selectively and non-covalently with ribosomal RNA.
    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:0070475    rRNA base methylation    The addition of a methyl group to an atom in the nucleoside base portion of a nucleotide residue 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.
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
    GO:0000028    ribosomal small subunit assembly    The aggregation, arrangement and bonding together of constituent RNAs and proteins to form the small ribosomal subunit.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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        RSMA_ECOLI | P069923tpz 4adv

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