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(-) Description

Title :  APO-FORM OF T. THERMOPHILUS 16S RRNA A1518 AND A1519 METHYLTRANSFERASE (KSGA) IN SPACE GROUP P21212
 
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 :  1.52
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
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
    ChainsA, B
    EC Number2.1.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET26B
    Expression System StrainBL21 (DE3)STAR
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneKSGA, TTHA0083
    Organism ScientificTHERMUS THERMOPHILUS
    Organism Taxid300852
    StrainHB8
    SynonymS-ADENOSYLMETHIONINE-6-N', N'-ADENOSYL(RRNA) DIMETHYLTRANSFERASE, 16S RRNA DIMETHYLASE, HIGH LEVEL KASUGAMYCIN RESISTANCE PROTEIN KSGA, KASUGAMYCIN DIMETHYLTRANSFERASE

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1MSE1Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1MSE1Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3FUT)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Arg A:44 -Pro A:45
2Phe A:185 -Pro A:186
3Arg B:44 -Pro B:45
4Phe B:185 -Pro B:186

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_RNA_A_N6_MTPS51689 rRNA adenine N(6)-methyltransferase family profile.RSMA_THET821-271
 
  2A:21-268
B:25-268
2RRNA_A_DIMETHPS01131 Ribosomal RNA adenine dimethylases signature.RSMA_THET850-77
 
  2A:50-77
B:50-77
Biological Unit 1 (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
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_RNA_A_N6_MTPS51689 rRNA adenine N(6)-methyltransferase family profile.RSMA_THET821-271
 
  1-
B:25-268
2RRNA_A_DIMETHPS01131 Ribosomal RNA adenine dimethylases signature.RSMA_THET850-77
 
  1-
B:50-77

(-) Exons   (0, 0)

(no "Exon" information available for 3FUT)

(-) 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:264
 aligned with RSMA_THET8 | Q5SM60 from UniProtKB/Swiss-Prot  Length:271

    Alignment length:264
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264    
           RSMA_THET8     5 ASPQSVRALLERHGLFADKRFGQNFLVSEAHLRRIVEAARPFTGPVFEVGPGLGALTRALLEAGAEVTAIEKDLRLRPVLEETLSGLPVRLVFQDALLYPWEEVPQGSLLVANLPYHIATPLVTRLLKTGRFARLVFLVQKEVAERMTARPKTPAYGVLTLRVAHHAVAERLFDLPPGAFFPPPKVWSSLVRLTPTGALDDPGLFRLVEAAFGKRRKTLLNALAAAGYPKARVEEALRALGLPPRVRAEELDLEAFRRLREGLE 268
               SCOP domains d3futa_ A: automated matches                                                                                                                                                                                                                                             SCOP domains
               CATH domains 3futA01 A:5-203 Vaccinia Virus protein VP39                                                                                                                                                            ----------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhh...........ee.hhhhhhhhhhhhh.....eeee....hhhhhhhhhh...eeeee.hhhhhhhhhhhh.....eeee.hhhhhhhhhh...eeeeeee....hhhhhhhhhhhh.eeeeeeeeehhhhhhhh........hhhhhhhhhheeeeeeeeehhh.ee......eeeeeeee.....hhhhhhhhhhhh.....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
                 3fut A   5 ASPQSVRALLERHGLFADKRFGQNFLVSEAHLRRIVEAARPFTGPVFEVGPGLGALTRALLEAGAEVTAIEKDLRLRPVLEETLSGLPVRLVFQDALLYPWEEVPQGSLLVANLPYHIATPLVTRLLKTGRFARLVFLVQKEVAERmTARPKTPAYGVLTLRVAHHAVAERLFDLPPGAFFPPPKVWSSLVRLTPTGALDDPGLFRLVEAAFGKRRKTLLNALAAAGYPKARVEEALRALGLPPRVRAEELDLEAFRRLREGLE 268
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144      |154       164       174       184       194       204       214       224       234       244       254       264    
                                                                                                                                                                            151-MSE                                                                                                                 

Chain B from PDB  Type:PROTEIN  Length:260
 aligned with RSMA_THET8 | Q5SM60 from UniProtKB/Swiss-Prot  Length:271

    Alignment length:266
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262      
           RSMA_THET8     3 KLASPQSVRALLERHGLFADKRFGQNFLVSEAHLRRIVEAARPFTGPVFEVGPGLGALTRALLEAGAEVTAIEKDLRLRPVLEETLSGLPVRLVFQDALLYPWEEVPQGSLLVANLPYHIATPLVTRLLKTGRFARLVFLVQKEVAERMTARPKTPAYGVLTLRVAHHAVAERLFDLPPGAFFPPPKVWSSLVRLTPTGALDDPGLFRLVEAAFGKRRKTLLNALAAAGYPKARVEEALRALGLPPRVRAEELDLEAFRRLREGLE 268
               SCOP domains d3futb_ B: automat    ed matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains 3futB01 B:3-203 Va    ccinia Virus protein VP39                                                                                                                                                          ----------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh...----....ee.hhhhhhhhhhhhh.....eeee....hhhhhhhhhh...eeeee.hhhhhhhhhhhh....eeeee.hhhhhhhhhh...eeeeeee.--hhhhhhhhhhhhh.eeeeeeeeehhhhhhhh........hhhhhhhhhheeeeeeeeehhh.ee......eeeeeeee.....hhhhhhhhhhhhh....hhhhhhhh...hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------SAM_RNA_A_N6_MT  PDB: B:25-268 UniProt: 21-271                                                                                                                                                                                                           PROSITE (1)
                PROSITE (2) -----------------------------------------------RRNA_A_DIMETH  PDB: B:50-77 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fut B   3 KLASPQSVRALLERHGLF----FGQNFLVSEAHLRRIVEAARPFTGPVFEVGPGLGALTRALLEAGAEVTAIEKDLRLRPVLEETLSGLPVRLVFQDALLYPWEEVPQGSLLVANLP--IATPLVTRLLKTGRFARLVFLVQKEVAERmTARPKTPAYGVLTLRVAHHAVAERLFDLPPGAFFPPPKVWSSLVRLTPTGALDDPGLFRLVEAAFGKRRKTLLNALAAAGYPKARVEEALRALGLPPRVRAEELDLEAFRRLREGLE 268
                                    12       | -  |     32        42        52        62        72        82        92       102       112      |122       132       142       152       162       172       182       192       202       212       222       232       242       252       262      
                                            20   25                                                                                           119  |                          151-MSE                                                                                                                 
                                                                                                                                                 122                                                                                                                                                  

   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  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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 | Q5SM603fuu 3fuv 3fuw 3fux

(-) Related Entries Specified in the PDB File

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
3fuw T. THERMOPHILUS 16S RRNA A1518 AND A1519 METHYLTRANSFERASE (KSGA) IN COMPLEX WITH 5'-METHYLTHIOADENOSINE IN SPACE GROUP P212121
3fux T. THERMOPHILUS 16S RRNA A1518 AND A1519 METHYLTRANSFERASE (KSGA) IN COMPLEX WITH 5'-METHYLTHIOADENOSINE IN SPACE GROUP P212121