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(-) Description

Title :  CRYSTAL STRUCTURE OF A PREDICTED S-ADENOSYLMETHIONINE-DEPENDENT METHYLTRANSFERASE TT1512 FROM THERMUS THERMOPHILUS HB8.
 
Authors :  S. Kishishita, K. Murayama, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  27 May 04  (Deposition) - 27 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  S-Adenosyl-Methyltransferase, Mraw, Thermus Thermophilus, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Kishishita, K. Murayama, M. Shirouzu, S. Yokoyama
Crystal Structure Of A Predicted S-Adenosylmethionine-Dependent Methyltransferase Tt1512 From Thermus Thermophilus Hb8 At 2. 0 Ang. Resolution.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PREDICTED S-ADENOSYLMETHIONINE-DEPENDENT METHYLTRANSFERASE
    ChainsA, B
    EC Number2.1.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET11B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneTT1512
    Organism ScientificTHERMUS THERMOPHILUS
    Organism Taxid274

 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
1SAM2Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SAM1Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SAM1Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO B:8 , THR B:30 , LEU B:31 , GLY B:32 , GLY B:33 , ALA B:34 , GLY B:35 , HIS B:36 , ASP B:51 , GLN B:52 , GLY B:73 , ASN B:74 , PHE B:75 , ASP B:96 , GLY B:98 , SER B:100 , HIS B:103 , MET B:123 , HOH B:3158 , HOH B:3178 , HOH B:3192BINDING SITE FOR RESIDUE SAM B 3141
2AC2SOFTWAREPRO A:8 , THR A:30 , LEU A:31 , GLY A:32 , GLY A:33 , ALA A:34 , GLY A:35 , HIS A:36 , ASP A:51 , GLN A:52 , ASP A:53 , GLY A:73 , ASN A:74 , PHE A:75 , ASP A:96 , GLY A:98 , VAL A:99 , SER A:100 , HIS A:103 , MET A:123 , ARG A:271 , HOH A:3199 , HOH A:3235 , HOH A:3241 , HOH A:3242BINDING SITE FOR RESIDUE SAM A 3142

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WG8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WG8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WG8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1WG8)

(-) Exons   (0, 0)

(no "Exon" information available for 1WG8)

(-) 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:281
 aligned with RSMH_THET8 | Q5SJD8 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:281
                                    13        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       283 
           RSMH_THET8     4 MTHVPVLYQEALDLLAVRPGGVYVDATLGGAGHARGILERGGRVIGLDQDPEAVARAKGLHLPGLTVVQGNFRHLKRHLAALGVERVDGILADLGVSSFHLDDPSRGFSYQKEGPLDMRMGLEGPTAKEVVNRLPLEALARLLRELGEEPQAYRIARAIVAAREKAPIETTTQLAEIVRKAVGFRRAGHPARKTFQALRIYVNDELNALKEFLEQAAEVLAPGGRLVVIAFHSLEDRVVKRFLRESGLKVLTKKPLVPSEKEAAQNPRARSAKLRAAEKEA 284
               SCOP domains -d1wg8a2 A:5-108,A:207-284 TM0872, methyltransferase domain                                              d1wg8a1 A:109-206 Putative methyltransferase TM0872, insert domain                                d1wg8a2 A:5-108,A:207-284 TM0872, methyltransferase domain                     SCOP domains
               CATH domains 1wg8A01 A:4-106,A:208-284 Vaccinia Virus protein VP39                                                  1wg8A02 A:107-207  [code=1.10.150.170, no name defined]                                              1wg8A01 A:4-106,A:208-284 Vaccinia Virus protein VP39                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhh.....eeee.....hhhhhhhhhh..eeeeee.hhhhhhhhhhh....eeeee.hhhhhhhhhhhh....eeeeeee...hhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeeeeee.hhhhhhhhhhhhhhhh.ee........hhhhhhhhhhhhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wg8 A   4 MTHVPVLYQEALDLLAVRPGGVYVDATLGGAGHARGILERGGRVIGLDQDPEAVARAKGLHLPGLTVVQGNFRHLKRHLAALGVERVDGILADLGVSSFHLDDPSRGFSYQKEGPLDMRMGLEGPTAKEVVNRLPLEALARLLRELGEEPQAYRIARAIVAAREKAPIETTTQLAEIVRKAVGFRRAGHPARKTFQALRIYVNDELNALKEFLEQAAEVLAPGGRLVVIAFHSLEDRVVKRFLRESGLKVLTKKPLVPSEKEAAQNPRARSAKLRAAEKEA 284
                                    13        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       283 

Chain B from PDB  Type:PROTEIN  Length:280
 aligned with RSMH_THET8 | Q5SJD8 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:280
                                    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       274       284
           RSMH_THET8     5 THVPVLYQEALDLLAVRPGGVYVDATLGGAGHARGILERGGRVIGLDQDPEAVARAKGLHLPGLTVVQGNFRHLKRHLAALGVERVDGILADLGVSSFHLDDPSRGFSYQKEGPLDMRMGLEGPTAKEVVNRLPLEALARLLRELGEEPQAYRIARAIVAAREKAPIETTTQLAEIVRKAVGFRRAGHPARKTFQALRIYVNDELNALKEFLEQAAEVLAPGGRLVVIAFHSLEDRVVKRFLRESGLKVLTKKPLVPSEKEAAQNPRARSAKLRAAEKEA 284
               SCOP domains d1wg8b2 B:5-108,B:207-284 TM0872, methyltransferase domain                                              d1wg8b1 B:109-206 Putative methyltransferase TM0872, insert domain                                d1wg8b2 B:5-108,B:207-284 TM0872, methyltransferase domain                     SCOP domains
               CATH domains 1wg8B01 B:5-106,B:208-284 Vaccinia Virus protein VP39                                                 1wg8B02 B:107-207  [code=1.10.150.170, no name defined]                                              1wg8B01 B:5-106,B:208-284 Vaccinia Virus protein VP39                         CATH domains
           Pfam domains (1) Methyltransf_5-1wg8B01 B:5-283                                                                                                                                                                                                                                                         - Pfam domains (1)
           Pfam domains (2) Methyltransf_5-1wg8B02 B:5-283                                                                                                                                                                                                                                                         - Pfam domains (2)
         Sec.struct. author .....hhhhhhhhhh.....eeee.....hhhhhhhhhh..eeeeee.hhhhhhhhhhh....eeeee.hhhhhhhhhhhh....eeeeeee...hhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeeeeee.hhhhhhhhhhhhhh...ee........hhhhhhhh......eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wg8 B   5 THVPVLYQEALDLLAVRPGGVYVDATLGGAGHARGILERGGRVIGLDQDPEAVARAKGLHLPGLTVVQGNFRHLKRHLAALGVERVDGILADLGVSSFHLDDPSRGFSYQKEGPLDMRMGLEGPTAKEVVNRLPLEALARLLRELGEEPQAYRIARAIVAAREKAPIETTTQLAEIVRKAVGFRRAGHPARKTFQALRIYVNDELNALKEFLEQAAEVLAPGGRLVVIAFHSLEDRVVKRFLRESGLKVLTKKPLVPSEKEAAQNPRARSAKLRAAEKEA 284
                                    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       274       284

   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  (2, 4)

Asymmetric Unit

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RSMH_THET8 | Q5SJD8)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0071424    rRNA (cytosine-N4-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N4-methylcytosine.
    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:0070475    rRNA base methylation    The addition of a methyl group to an atom in the nucleoside base portion of a nucleotide residue 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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