Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  APO-FORM OF T. THERMOPHILUS 16S RRNA A1518 AND A1519 METHYLTRANSFERASE (KSGA) IN SPACE GROUP P43212
 
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 :  1.95
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (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, C
    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

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A  
Biological Unit 2 (1x) B 
Biological Unit 3 (1x)  C

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3FUV)

(-) Sites  (0, 0)

(no "Site" information available for 3FUV)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1Arg A:44 -Pro A:45
2Phe A:185 -Pro A:186
3Ala A:270 -Val A:271
4Arg B:44 -Pro B:45
5Phe B:185 -Pro B:186
6Arg C:44 -Pro C:45
7Phe C:185 -Pro C:186

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 6)

Asymmetric Unit (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_RNA_A_N6_MTPS51689 rRNA adenine N(6)-methyltransferase family profile.RSMA_THET821-271
 
 
  3A:26-271
B:27-268
C:28-268
2RRNA_A_DIMETHPS01131 Ribosomal RNA adenine dimethylases signature.RSMA_THET850-77
 
 
  3A:50-77
B:50-77
C: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:26-271
-
-
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:27-268
-
2RRNA_A_DIMETHPS01131 Ribosomal RNA adenine dimethylases signature.RSMA_THET850-77
 
 
  1-
B:50-77
-
Biological Unit 3 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_RNA_A_N6_MTPS51689 rRNA adenine N(6)-methyltransferase family profile.RSMA_THET821-271
 
 
  1-
-
C:28-268
2RRNA_A_DIMETHPS01131 Ribosomal RNA adenine dimethylases signature.RSMA_THET850-77
 
 
  1-
-
C:50-77

(-) Exons   (0, 0)

(no "Exon" information available for 3FUV)

(-) 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:260
 aligned with RSMA_THET8 | Q5SM60 from UniProtKB/Swiss-Prot  Length:271

    Alignment length:266
                                    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 SPQSVRALLERHGLFADKRFGQNFLVSEAHLRRIVEAARPFTGPVFEVGPGLGALTRALLEAGAEVTAIEKDLRLRPVLEETLSGLPVRLVFQDALLYPWEEVPQGSLLVANLPYHIATPLVTRLLKTGRFARLVFLVQKEVAERMTARPKTPAYGVLTLRVAHHAVAERLFDLPPGAFFPPPKVWSSLVRLTPTGALDDPGLFRLVEAAFGKRRKTLLNALAAAGYPKARVEEALRALGLPPRVRAEELDLEAFRRLREGLEGAV 271
               SCOP domains d3fuva_ A: aut      omated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains 3fuvA01 A:6-20      3 Vaccinia Virus protein VP39                                                                                                                                                     -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.------...ee.hhhhhhhhhhhhh.....eeee....hhhhhhhhhh...eeeee.hhhhhhhhhhhh.....eeee......hhhhh...eeeeee.hhhhhhhhhhhhhhhh.eeeeeeeeehhhhhhhh........hhhhhhhhhheeeeeeeeehhh.ee......eeeeeeee.....hhhhhhhhhhhh.....hhhhhhhh...hhhhhhhhhhhh......hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------SAM_RNA_A_N6_MT  PDB: A:26-271 UniProt: 21-271                                                                                                                                                                                                              PROSITE (1)
                PROSITE (2) --------------------------------------------RRNA_A_DIMETH  PDB: A:50-77 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fuv A   6 SPQSVRALLERHGL------GQNFLVSEAHLRRIVEAARPFTGPVFEVGPGLGALTRALLEAGAEVTAIEKDLRLRPVLEETLSGLPVRLVFQDALLYPWEEVPQGSLLVANLPYHIATPLVTRLLKTGRFARLVFLVQKEVAERMTARPKTPAYGVLTLRVAHHAVAERLFDLPPGAFFPPPKVWSSLVRLTPTGALDDPGLFRLVEAAFGKRRKTLLNALAAAGYPKARVEEALRALGLPPRVRAEELDLEAFRRLREGLEGAV 271
                                    15   |     -|       35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265      
                                        19     26                                                                                                                                                                                                                                                     

Chain B from PDB  Type:PROTEIN  Length:256
 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 d3fuvb_ B: aut       omated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains 3fuvB01 B:6-20       3 Vaccinia Virus protein VP39                                                                                                                                                    ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh..-------..ee.hhhhhhhhhhhhh.....eeee....hhhhhhhhhh...eeee..hhhhhhhhhhhh.....eee.......hhhhh...eeeeee.hhhhhhhhhhhhhhhh.eeeeeeeeehhhhhhhh........hhhhhhhhhheeeeeeeeehhh.ee......eeeeeeee.....hhhhhhhhhhhh.....hhhhhhhh.....hhhhhhhhhh......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------SAM_RNA_A_N6_MT  PDB: B:27-268 UniProt: 21-271                                                                                                                                                                                                           PROSITE (1)
                PROSITE (2) --------------------------------------------RRNA_A_DIMETH  PDB: B:50-77 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fuv B   6 SPQSVRALLERHGL-------QNFLVSEAHLRRIVEAARPFTGPVFEVGPGLGALTRALLEAGAEVTAIEKDLRLRPVLEETLSGLPVRLVFQDALLYPWEEVPQGSLLVANLPYHIATPLVTRLLKTGRFARLVFLVQKEVAERMTARPKTPAYGVLTLRVAHHAVAERLFDLPPGAFFPPPKVWSSLVRLTPTGALDDPGLFRLVEAAFGKRRKTLLNALAAAGYPKARVEEALRALGLPPRVRAEELDLEAFRRLREGLE 268
                                    15   |     - |      35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265   
                                        19      27                                                                                                                                                                                                                                                 

Chain C from PDB  Type:PROTEIN  Length:252
 aligned with RSMA_THET8 | Q5SM60 from UniProtKB/Swiss-Prot  Length:271

    Alignment length:261
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267 
           RSMA_THET8     8 QSVRALLERHGLFADKRFGQNFLVSEAHLRRIVEAARPFTGPVFEVGPGLGALTRALLEAGAEVTAIEKDLRLRPVLEETLSGLPVRLVFQDALLYPWEEVPQGSLLVANLPYHIATPLVTRLLKTGRFARLVFLVQKEVAERMTARPKTPAYGVLTLRVAHHAVAERLFDLPPGAFFPPPKVWSSLVRLTPTGALDDPGLFRLVEAAFGKRRKTLLNALAAAGYPKARVEEALRALGLPPRVRAEELDLEAFRRLREGLE 268
               SCOP domains d3fuvc_ C:          automated matches                                                                                                                                                                                                                                 SCOP domains
               CATH domains 3fuvC01 C:8         -203 Vaccinia Virus protein VP39                                                                                                                                                ----------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh---------.ee.hhhhhhhhhhhhh.....eeee....hhhhhhhhhh...eeee....hhhhhhhhhh.....eee.......hhhhh...eeeeee.....hhhhhhhhhhhh.eeeeeeeeehhhhhhhhh.......hhhhhhhhhheeeeeeeeehhh.ee......eeeeeeee.....hhhhhhhhhhhh.....hhhhhhhh...hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------SAM_RNA_A_N6_MT  PDB: C:28-268 UniProt: 21-271                                                                                                                                                                                                           PROSITE (1)
                PROSITE (2) ------------------------------------------RRNA_A_DIMETH  PDB: C:50-77 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fuv C   8 QSVRALLERHG---------NFLVSEAHLRRIVEAARPFTGPVFEVGPGLGALTRALLEAGAEVTAIEKDLRLRPVLEETLSGLPVRLVFQDALLYPWEEVPQGSLLVANLPYHIATPLVTRLLKTGRFARLVFLVQKEVAERMTARPKTPAYGVLTLRVAHHAVAERLFDLPPGAFFPPPKVWSSLVRLTPTGALDDPGLFRLVEAAFGKRRKTLLNALAAAGYPKARVEEALRALGLPPRVRAEELDLEAFRRLREGLE 268
                                    17|        -|       37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267 
                                     18        28                                                                                                                                                                                                                                                

   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, 3)

Asymmetric Unit

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3fuv)
 
  Sites
(no "Sites" information available for 3fuv)
 
  Cis Peptide Bonds
    Ala A:270 - Val A:271   [ RasMol ]  
    Arg A:44 - Pro A:45   [ RasMol ]  
    Arg B:44 - Pro B:45   [ RasMol ]  
    Arg C:44 - Pro C:45   [ RasMol ]  
    Phe A:185 - Pro A:186   [ RasMol ]  
    Phe B:185 - Pro B:186   [ RasMol ]  
    Phe C:185 - Pro C:186   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3fuv
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  RSMA_THET8 | Q5SM60
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.1.1.-
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  RSMA_THET8 | Q5SM60
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        RSMA_THET8 | Q5SM603fut 3fuu 3fuw 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
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