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(-) Description

Title :  T. THERMOPHILUS 16S RRNA G527 METHYLTRANSFERASE IN COMPLEX WITH ADOMET IN SPACE GROUP I222
 
Authors :  H. Demirci, S. T. Gregory, R. Belardinelli, C. Gualerzi, A. E. Dahlberg, G. Jogl
Date :  11 Feb 09  (Deposition) - 30 Jun 09  (Release) - 08 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Methyltransferase, 16S Rrna Methyltransferase, Translation, Cytoplasm, Rrna Processing, S-Adenosyl-L-Methionine, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. T. Gregory, H. Demirci, R. Belardinelli, T. Monshupanee, C. Gualerzi, A. E. Dahlberg, G. Jogl
Structural And Functional Studies Of The Thermus Thermophilus 16S Rrna Methyltransferase Rsmg
Rna V. 15 1693 2009
PubMed-ID: 19622680  |  Reference-DOI: 10.1261/RNA.1652709
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBOSOMAL RNA SMALL SUBUNIT METHYLTRANSFERASE G
    Chains: A, B
    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: GIDB, RSMG, TTHA1971
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8
    Synonym: 16S RRNA 7-METHYLGUANOSINE METHYLTRANSFERASE, 16S RRNA M7G METHYLTRANSFERASE, GLUCOSE-INHIBITED DIVISION PROTEIN B

 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  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1SAM2Ligand/IonS-ADENOSYLMETHIONINE
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1SAM1Ligand/IonS-ADENOSYLMETHIONINE
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SAM1Ligand/IonS-ADENOSYLMETHIONINE
2SO4-1Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:88 , THR A:89 , GLY A:90 , PHE A:93 , ASP A:111 , ALA A:112 , THR A:113 , LYS A:116 , GLY A:137 , ARG A:138 , ALA A:139 , GLU A:140 , ARG A:158 , ALA A:159 , HOH A:256 , HOH A:287 , HOH A:393 , HOH A:416 , HOH A:452 , ASN B:51BINDING SITE FOR RESIDUE SAM A 303
2AC2SOFTWARESER A:47 , HOH A:334 , HOH A:395BINDING SITE FOR RESIDUE SO4 A 250
3AC3SOFTWAREHOH A:415 , GLY B:88 , THR B:89 , PHE B:93 , ASP B:111 , ALA B:112 , THR B:113 , LYS B:116 , GLY B:137 , ARG B:138 , ALA B:139 , GLU B:140 , ARG B:158 , ALA B:159 , HOH B:252 , HOH B:253 , HOH B:281BINDING SITE FOR RESIDUE SAM B 303

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:164 -A:249
2B:164 -B:249

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Phe A:93 -Pro A:94
2Tyr A:236 -Pro A:237
3Phe B:93 -Pro B:94
4Tyr B:236 -Pro B:237

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3G8B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3G8B)

(-) Exons   (0, 0)

(no "Exon" information available for 3G8B)

(-) 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:241
 aligned with RSMG_THET8 | Q9LCY2 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:241
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248 
           RSMG_THET8     9 GLSERGRALLLEGGKALGLDLKPHLEAFSRLYALLQEASGKVNLTALRGEEEVVVKHFLDSLTLLRLPLWQGPLRVLDLGTGAGFPGLPLKIVRPELELVLVDATRKKVAFVERAIEVLGLKGARALWGRAEVLAREAGHREAYARAVARAVAPLCVLSELLLPFLEVGGAAVAMKGPRVEEELAPLPPALERLGGRLGEVLALQLPLSGEARHLVVLEKTAPTPPAYPRRPGVPERHPLC 249
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3g8bA00 A:9-249 Vaccinia Virus protein VP39                                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh.......eeeee......hhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh...eeeee.hhhhhh........eeeeeee...hhhhhhhhhh..eeeeeeeeeee...hhhhhhhhhhhhhhh.eeeeeeeeee......eeeeeeeee............hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g8b A   9 GLSERGRALLLEGGKALGLDLKPHLEAFSRLYALLQEASGKVNLTALRGEEEVVVKHFLDSLTLLRLPLWQGPLRVLDLGTGAGFPGLPLKIVRPELELVLVDATRKKVAFVERAIEVLGLKGARALWGRAEVLAREAGHREAYARAVARAVAPLCVLSELLLPFLEVGGAAVAMKGPRVEEELAPLPPALERLGGRLGEVLALQLPLSGEARHLVVLEKTAPTPPAYPRRPGVPERHPLC 249
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248 


Chain B from PDB  Type:PROTEIN  Length:242
 aligned with RSMG_THET8 | Q9LCY2 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:242
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247  
           RSMG_THET8     8 GGLSERGRALLLEGGKALGLDLKPHLEAFSRLYALLQEASGKVNLTALRGEEEVVVKHFLDSLTLLRLPLWQGPLRVLDLGTGAGFPGLPLKIVRPELELVLVDATRKKVAFVERAIEVLGLKGARALWGRAEVLAREAGHREAYARAVARAVAPLCVLSELLLPFLEVGGAAVAMKGPRVEEELAPLPPALERLGGRLGEVLALQLPLSGEARHLVVLEKTAPTPPAYPRRPGVPERHPLC 249
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3g8bB00 B:8-249 Vaccinia Virus protein VP39                                                                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.......eeeee......hhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh....eeeee.hhhhhh........eeeeeee...hhhhhhhhhh..eeeeeeeeeee...hhhhhhhhhhhhhhh.eeeeeeeeee......eeeeeeeee............hhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g8b B   8 GGLSERGRALLLEGGKALGLDLKPHLEAFSRLYALLQEASGKVNLTALRGEEEVVVKHFLDSLTLLRLPLWQGPLRVLDLGTGAGFPGLPLKIVRPELELVLVDATRKKVAFVERAIEVLGLKGARALWGRAEVLAREAGHREAYARAVARAVAPLCVLSELLLPFLEVGGAAVAMKGPRVEEELAPLPPALERLGGRLGEVLALQLPLSGEARHLVVLEKTAPTPPAYPRRPGVPERHPLC 249
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247
   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  (0, 0)

(no "SCOP Domain" information available for 3G8B)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3G8B)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RSMG_THET8 | Q9LCY2)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0070043    rRNA (guanine-N7-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N7-methylguanine.
    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:0070476    rRNA (guanine-N7)-methylation    The addition of a methyl group to the N7 atom in the base portion of a guanine nucleotide residue in an rRNA molecule.
    GO:0031167    rRNA methylation    The posttranscriptional addition of methyl groups to specific residues in an rRNA molecule.
    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

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        RSMG_THET8 | Q9LCY2: 3g88 3g89 3g8a

(-) Related Entries Specified in the PDB File

3g88 3g89 3g8a