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(-) Description

Title :  THIOPURINE S-METHYLTRANSFERASE
 
Authors :  Y. Peng, V. C. Yee
Date :  26 Nov 07  (Deposition) - 10 Jun 08  (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 :  Methyltransferase, Cytoplasm, S-Adenosyl-L-Methionine (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Peng, Q. Feng, D. Wilk, A. A. Adjei, O. E. Salavaggione, R. M. Weinshilboum, V. C. Yee
Structural Basis Of Substrate Recognition In Thiopurine S-Methyltransferase
Biochemistry V. 47 ( 6216 2008
PubMed-ID: 18484748  |  Reference-DOI: 10.1021/BI800102X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THIOPURINE S-METHYLTRANSFERASE
    ChainsA, B
    EC Number2.1.1.67
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-28A
    Expression System StrainBL21(DE3)
    Expression System Vector TypePLASMID
    GeneTPMT
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    SynonymTHIOPURINE METHYLTRANSFERASE

 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, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1PM64Ligand/Ion9H-PURINE-6-THIOL
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1PM62Ligand/Ion9H-PURINE-6-THIOL
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1PM62Ligand/Ion9H-PURINE-6-THIOL
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:21 , TRP A:24 , TRP A:28 , PHE A:35 , LEU A:64 , CYS A:65 , GLU A:85 , ILE A:86 , CYS A:128 , SER A:129 , ILE A:130 , ARG A:147 , GLY A:148 , HOH A:310 , HOH A:321 , HOH A:323 , HOH A:336BINDING SITE FOR RESIDUE SAH A 300
2AC2SOFTWARELEU B:21 , TRP B:24 , TRP B:28 , PHE B:35 , LEU B:64 , CYS B:65 , GLU B:85 , ILE B:86 , CYS B:128 , SER B:129 , ILE B:130 , ARG B:147 , GLY B:148 , HOH B:310 , HOH B:322 , HOH B:381 , HOH B:394BINDING SITE FOR RESIDUE SAH B 300
3AC3SOFTWAREPHE A:35 , ARG A:147 , GLY A:148 , ALA A:152 , PRO A:191BINDING SITE FOR RESIDUE PM6 A 301
4AC4SOFTWAREHIS A:47 , THR A:50 , PHE A:51 , GLN A:174 , LEU A:212 , LEU A:236BINDING SITE FOR RESIDUE PM6 A 302
5AC5SOFTWAREPHE B:35 , ARG B:147 , GLY B:148 , PRO B:191 , ARG B:221BINDING SITE FOR RESIDUE PM6 B 301
6AC6SOFTWAREHIS B:47 , THR B:50 , GLN B:174 , LEU B:212 , LEU B:236BINDING SITE FOR RESIDUE PM6 B 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:189 -Pro A:190
2Pro A:190 -Pro A:191
3Gly B:189 -Pro B:190
4Pro B:190 -Pro B:191

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_TPMT_MOUSE_001 *I69VTPMT_MOUSE  ---  ---A/BI69V
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_TPMT_MOUSE_001 *I69VTPMT_MOUSE  ---  ---AI69V
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_TPMT_MOUSE_001 *I69VTPMT_MOUSE  ---  ---BI69V
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_MT_TPMTPS51585 Thiopurine or thiol or thiocyanate S-methyltransferase (TPMT) family profile.TPMT_MOUSE21-235
 
  2A:21-235
B:21-235
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_MT_TPMTPS51585 Thiopurine or thiol or thiocyanate S-methyltransferase (TPMT) family profile.TPMT_MOUSE21-235
 
  1A:21-235
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_MT_TPMTPS51585 Thiopurine or thiol or thiocyanate S-methyltransferase (TPMT) family profile.TPMT_MOUSE21-235
 
  1-
B:21-235

(-) Exons   (0, 0)

(no "Exon" information available for 3BGD)

(-) 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:232
 aligned with TPMT_MOUSE | O55060 from UniProtKB/Swiss-Prot  Length:240

    Alignment length:232
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238  
           TPMT_MOUSE     9 PDAEVQKNQVLTLEDWKEKWVTRHISFHQEQGHQLLKKHLDTFLKGQSGLRVFFPLCGKAIEMKWFADRGHTVVGVEISEIGIREFFAEQNLSYTEEPLAEIAGAKVFKSSSGSISLYCCSIFDLPRANIGKFDRIWDRGALVAINPGDHDRYADIILSLLRKEFQYLVAVLSYDPTKHAGPPFYVPSAELKRLFGTKCSMQCLEEVDALEERHKAWGLDYLFEKLYLLTEK 240
               SCOP domains d3bgda_ A: Thiopurine S-methyltransferase                                                                                                                                                                                                SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh......hhhhhhhhhhhh.........hhhhhhhhhhhhh.....eeee......hhhhhhhh...eeeee..hhhhhhhhhhhh...eeeee.......eeeee....eeeee....hhhhhh...eeeeeee......hhhhhhhhhhhhhhheeeeeeeeeeeee.............hhhhhhhhhh...eeeeeeeee..hhhhhh......eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------V--------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------SAM_MT_TPMT  PDB: A:21-235 UniProt: 21-235                                                                                                                                                                             ----- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bgd A   9 PDAEVQKNQVLTLEDWKEKWVTRHISFHQEQGHQLLKKHLDTFLKGQSGLRVFFPLCGKAIEMKWFADRGHTVVGVEISEIGIREFFAEQNLSYTEEPLAEIAGAKVFKSSSGSISLYCCSIFDLPRANIGKFDRIWDRGALVAINPGDHDRYADIILSLLRKEFQYLVAVLSYDPTKHAGPPFYVPSAELKRLFGTKCSMQCLEEVDALEERHKAWGLDYLFEKLYLLTEK 240
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238  

Chain B from PDB  Type:PROTEIN  Length:232
 aligned with TPMT_MOUSE | O55060 from UniProtKB/Swiss-Prot  Length:240

    Alignment length:232
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238  
           TPMT_MOUSE     9 PDAEVQKNQVLTLEDWKEKWVTRHISFHQEQGHQLLKKHLDTFLKGQSGLRVFFPLCGKAIEMKWFADRGHTVVGVEISEIGIREFFAEQNLSYTEEPLAEIAGAKVFKSSSGSISLYCCSIFDLPRANIGKFDRIWDRGALVAINPGDHDRYADIILSLLRKEFQYLVAVLSYDPTKHAGPPFYVPSAELKRLFGTKCSMQCLEEVDALEERHKAWGLDYLFEKLYLLTEK 240
               SCOP domains d3bgdb_ B: Thiopurine S-methyltransferase                                                                                                                                                                                                SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh......hhhhhhhhhhh..........hhhhhhhhhhhh......eeee......hhhhhhhhh..eeeee..hhhhhhhhhhhhh..eeeee.......eeeee....eeeee....hhhhhh...eeeeee.......hhhhhhhhhhhhhhheeeeeeeeeeeee.hhhhh.......hhhhhhhhhh..eeeeeeeeee..hhhhhh......eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------V--------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------SAM_MT_TPMT  PDB: B:21-235 UniProt: 21-235                                                                                                                                                                             ----- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bgd B   9 PDAEVQKNQVLTLEDWKEKWVTRHISFHQEQGHQLLKKHLDTFLKGQSGLRVFFPLCGKAIEMKWFADRGHTVVGVEISEIGIREFFAEQNLSYTEEPLAEIAGAKVFKSSSGSISLYCCSIFDLPRANIGKFDRIWDRGALVAINPGDHDRYADIILSLLRKEFQYLVAVLSYDPTKHAGPPFYVPSAELKRLFGTKCSMQCLEEVDALEERHKAWGLDYLFEKLYLLTEK 240
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238  

   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  (0, 0)

(no "CATH Domain" information available for 3BGD)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (TPMT_MOUSE | O55060)
molecular function
    GO:0008757    S-adenosylmethionine-dependent methyltransferase activity    Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a substrate.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0008119    thiopurine S-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + a thiopurine = S-adenosyl-L-homocysteine + a thiopurine S-methylether.
    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:0006139    nucleobase-containing compound metabolic process    Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TPMT_MOUSE | O550602gb4 3bgi

(-) Related Entries Specified in the PDB File

3bgi 3bke 3bko