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(-) Description

Title :  THE STRUCTURE OF THE RIBOSOMAL RNA SMALL SUBUNIT METHYLTRANSFERASE A FROM BURKHOLDERIA PSEUDOMALLEI
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  07 Dec 11  (Deposition) - 14 Dec 11  (Release) - 14 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Rna, Ssgcid, Seattle Structural Genomics Center For Infectious Disease, Methyltransferase A, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. C. Clifton, J. Abendroth, B. Sankaran, Seattle Structural Genomics Center For Infectious Disease (Ssgcid)
The Structure Of The Ribosomal Rna Small Subunit Methyltransferase A From Burkholderia Pseudomallei
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RIBOSOMAL RNA SMALL SUBUNIT METHYLTRANSFERASE A
    Chains: A
    EC Number: 2.1.1.182
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: RSMA, KSGA, BURPS1710B_0874
    Organism Scientific: BURKHOLDERIA PSEUDOMALLEI
    Organism Taxid: 28450
    Synonym: 16S RRNA (ADENINE(1518)-N(6)/ADENINE(1519)-N(6))- DIMETHYLTRANSFERASE, 16S RRNA DIMETHYLADENOSINE TRANSFERASE, 16S RRNA DIMETHYLASE, S-ADENOSYLMETHIONINE-6-N', N'-ADENOSYL(RRNA) DIMETHYLTRANSFERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:89 , LEU A:90 , ARG A:226 , LYS A:227 , SER A:274 , GLY A:275 , HOH A:335BINDING SITE FOR RESIDUE EDO A 276
2AC2SOFTWAREGLY A:93 , ASP A:94 , THR A:97 , PHE A:98 , HOH A:321BINDING SITE FOR RESIDUE EDO A 277

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gln A:186 -Pro A:187

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3UZU)

(-) 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:262
 aligned with RSMA_BURP1 | Q3JVW6 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:262
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273  
           RSMA_BURP1    14 KRFGQNFLVDHGVIDAIVAAIRPERGERMVEIGPGLGALTGPVIARLATPGSPLHAVELDRDLIGRLEQRFGELLELHAGDALTFDFGSIARPGDEPSLRIIGNLPYNISSPLLFHLMSFAPVVIDQHFMLQNEVVERMVAEPGTKAFSRLSVMLQYRYVMDKLIDVPPESFQPPPKVDSAIVRMIPHAPHELPAVDPAVLGEVVTAAFSQRRKMLRNTLGGYRDLVDFDALGFDLARRAEDIGVDEYVRVAQAVASARASG 275
               SCOP domains d3uzua_ A: automated matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee.hhhhhhhhhhhhh.....eeeee......hhhhhhhhhh.....eeeee.hhhhhhhhhhhhh..eeeee.hhhhhhhhhhh.......eeeeee.hhhhhhhhhhhhhhhhh.eeeeeeeeehhhhhhhh........hhhhhhhhhheeeeeeeeehhh.ee......eeeeeeee.hhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3uzu A  14 KRFGQNFLVDHGVIDAIVAAIRPERGERMVEIGPGLGALTGPVIARLATPGSPLHAVELDRDLIGRLEQRFGELLELHAGDALTFDFGSIARPGDEPSLRIIGNLPYNISSPLLFHLMSFAPVVIDQHFMLQNEVVERMVAEPGTKAFSRLSVMLQYRYVMDKLIDVPPESFQPPPKVDSAIVRMIPHAPHELPAVDPAVLGEVVTAAFSQRRKMLRNTLGGYRDLVDFDALGFDLARRAEDIGVDEYVRVAQAVASARASG 275
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273  


Chain A from PDB  Type:PROTEIN  Length:262
 aligned with RSMA_BURPS | Q63X76 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:262
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273  
           RSMA_BURPS    14 KRFGQNFLVDHGVIDAIVAAIRPERGERMVEIGPGLGALTGPVIARLATPGSPLHAVELDRDLIGRLEQRFGELLELHAGDALTFDFGSIARPGDEPSLRIIGNLPYNISSPLLFHLMSFAPVVIDQHFMLQNEVVERMVAEPGTKAFSRLSVMLQYRYVMDKLIDVPPESFQPPPKVDSAIVRMIPHAPHELPAVDPAVLGEVVTAAFSQRRKMLRNTLGGYRDLVDFDALGFDLARRAEDIGVDEYVRVAQAVASARASG 275
               SCOP domains d3uzua_ A: automated matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee.hhhhhhhhhhhhh.....eeeee......hhhhhhhhhh.....eeeee.hhhhhhhhhhhhh..eeeee.hhhhhhhhhhh.......eeeeee.hhhhhhhhhhhhhhhhh.eeeeeeeeehhhhhhhh........hhhhhhhhhheeeeeeeeehhh.ee......eeeeeeee.hhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3uzu A  14 KRFGQNFLVDHGVIDAIVAAIRPERGERMVEIGPGLGALTGPVIARLATPGSPLHAVELDRDLIGRLEQRFGELLELHAGDALTFDFGSIARPGDEPSLRIIGNLPYNISSPLLFHLMSFAPVVIDQHFMLQNEVVERMVAEPGTKAFSRLSVMLQYRYVMDKLIDVPPESFQPPPKVDSAIVRMIPHAPHELPAVDPAVLGEVVTAAFSQRRKMLRNTLGGYRDLVDFDALGFDLARRAEDIGVDEYVRVAQAVASARASG 275
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273
   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  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RSMA_BURP1 | Q3JVW6)
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.

Chain A   (RSMA_BURPS | Q63X76)
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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