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(-) Description

Title :  T. THERMOPHILUS 16S RRNA A1518 AND A1519 METHYLTRANSFERASE (KSGA) IN COMPLEX WITH 5'-METHYLTHIOADENOSINE IN SPACE GROUP P212121
 
Authors :  H. Demirci, R. Belardinelli, E. Seri, S. T. Gregory, C. Gualerzi, A. E. D G. Jogl
Date :  14 Jan 09  (Deposition) - 31 Mar 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.56
Chains :  Asym./Biol. Unit :  A
Keywords :  Methyltransferase, Dimethyltransferase, Dual-Specific Methyltransferase, 16S Rrna Methyltransferase, Translation, Antibiotic Resistance, Rna-Binding, Rrna Processing, S-Adenosyl-L- Methionine, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Demirci, R. Belardinelli, E. Seri, S. T. Gregory, C. Gualerzi, A. E. Dahlberg, G. Jogl
Structural Rearrangements In The Active Site Of The Thermus Thermophilus 16S Rrna Methyltransferase Ksga In A Binary Complex With 5'-Methylthioadenosine.
J. Mol. Biol. V. 388 271 2009
PubMed-ID: 19285505  |  Reference-DOI: 10.1016/J.JMB.2009.02.066

(-) Compounds

Molecule 1 - DIMETHYLADENOSINE TRANSFERASE
    Chains: A
    EC Number: 2.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET26B
    Expression System Strain: BL21 (DE3)STAR
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: KSGA, TTHA0083
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8
    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  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1MTA1Ligand/Ion5'-DEOXY-5'-METHYLTHIOADENOSINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:25 , GLY A:26 , GLN A:27 , ASN A:28 , GLY A:54 , GLY A:56 , ILE A:74 , GLU A:75 , LYS A:76 , ASP A:99 , ALA A:100 , ASN A:117 , PRO A:119 , HIS A:121 , HOH A:296BINDING SITE FOR RESIDUE MTA A 272

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg A:44 -Pro A:45
2Phe A:185 -Pro A:186

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_RNA_A_N6_MTPS51689 rRNA adenine N(6)-methyltransferase family profile.RSMA_THET821-271  1A:21-268
2RRNA_A_DIMETHPS01131 Ribosomal RNA adenine dimethylases signature.RSMA_THET850-77  1A:50-77

(-) Exons   (0, 0)

(no "Exon" information available for 3FUW)

(-) 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:263
 aligned with RSMA_THET8 | Q5SM60 from UniProtKB/Swiss-Prot  Length:271

    Alignment length:263
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265   
           RSMA_THET8     6 SPQSVRALLERHGLFADKRFGQNFLVSEAHLRRIVEAARPFTGPVFEVGPGLGALTRALLEAGAEVTAIEKDLRLRPVLEETLSGLPVRLVFQDALLYPWEEVPQGSLLVANLPYHIATPLVTRLLKTGRFARLVFLVQKEVAERMTARPKTPAYGVLTLRVAHHAVAERLFDLPPGAFFPPPKVWSSLVRLTPTGALDDPGLFRLVEAAFGKRRKTLLNALAAAGYPKARVEEALRALGLPPRVRAEELDLEAFRRLREGLE 268
               SCOP domains d3fuwa_ A: automated matches                                                                                                                                                                                                                                            SCOP domains
               CATH domains 3fuwA01 A:6-203 Vaccinia Virus protein VP39                                                                                                                                                           ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh....hhhhh..ee.hhhhhhhhhhhhh.....eeee....hhhhhhhhhh...eeeee.hhhhhhhhhhhh....eeeee.hhhhhhhhhh...eeeeee....hhhhhhhhhhhhh.eeeeeeeeehhhhhhhh........hhhhhhhhhheeeeeeeeehhh.ee......eeeeeeee.....hhhhhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------SAM_RNA_A_N6_MT  PDB: A:21-268 UniProt: 21-271                                                                                                                                                                                                           PROSITE (1)
                PROSITE (2) --------------------------------------------RRNA_A_DIMETH  PDB: A:50-77 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fuw A   6 SPQSVRALLERHGLFADKRFGQNFLVSEAHLRRIVEAARPFTGPVFEVGPGLGALTRALLEAGAEVTAIEKDLRLRPVLEETLSGLPVRLVFQDALLYPWEEVPQGSLLVANLPYHIATPLVTRLLKTGRFARLVFLVQKEVAERMTARPKTPAYGVLTLRVAHHAVAERLFDLPPGAFFPPPKVWSSLVRLTPTGALDDPGLFRLVEAAFGKRRKTLLNALAAAGYPKARVEEALRALGLPPRVRAEELDLEAFRRLREGLE 268
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265
   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 3FUW)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RSMA_THET8 | Q5SM60)
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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 Related Entries

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

UniProtKB/Swiss-Prot
        RSMA_THET8 | Q5SM60: 3fut 3fuu 3fuv 3fux

(-) Related Entries Specified in the PDB File

3fut APO-FORM OF T. THERMOPHILUS 16S RRNA A1518 AND A1519 METHYLTRANSFERASE (KSGA) IN SPACE GROUP P21212
3fuu T. THERMOPHILUS 16S RRNA A1518 AND A1519 METHYLTRANSFERASE (KSGA) IN COMPLEX WITH ADENOSINE IN SPACE GROUP P212121
3fuv APO-FORM OF T. THERMOPHILUS 16S RRNA A1518 AND A1519 METHYLTRANSFERASE (KSGA) IN SPACE GROUP P43212
3fux T. THERMOPHILUS 16S RRNA A1518 AND A1519 METHYLTRANSFERASE (KSGA) IN COMPLEX WITH 5'-METHYLTHIOADENOSINE IN SPACE GROUP P212121