2BZG - JenaLib

Title :   CRYSTAL STRUCTURE OF THIOPURINE S-METHYLTRANSFERASE.

Authors :   K. P. Battaile, H. Wu, H. Zeng, P. Loppnau, A. Dong, J. Weigelt, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, A. N. Plotnikov, Structural Genomics Consortium (Sgc)

Date :   17 Aug 05 (Deposition) - 25 Aug 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.58

Chains :   Asym./Biol. Unit : A

Keywords :   Methyltransferase, Polymorphism, Transferase, Psi, Protein Structure Initiative, Structural Genomics Consortium (Sgc) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Wu, J. R. Horton, K. P. Battaile, A. Allali-Hassani, F. Martin, H. Zeng, P. Loppnau, M. Vedadi, A. Bochkarev, A. N. Plotnikov, X. Cheng
Structural Basis Of Allele Variation Of Human Thiopurine-S-Methyltransferase.
Proteins V. 67 198 2007
PubMed-ID: 17243178 | Reference-DOI: 10.1002/PROT.21272

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (8, 8)

Asymmetric/Biological Unit (8, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_005636	L	49	S	TPMT_HUMAN	Polymorphism	72552740	A	L	49	S
2	UniProt	VAR_005637	A	80	P	TPMT_HUMAN	Polymorphism	1800462	A	A	80	P
3	UniProt	VAR_005638	A	154	T	TPMT_HUMAN	Polymorphism	1800460	A	A	154	T
4	UniProt	VAR_052368	Q	179	H	TPMT_HUMAN	Polymorphism	6921269	A	Q	179	H
5	UniProt	VAR_005639	Y	180	F	TPMT_HUMAN	Polymorphism	75543815	A	Y	180	F
6	UniProt	VAR_008715	R	215	H	TPMT_HUMAN	Polymorphism	56161402	A	R	215	H
7	UniProt	VAR_005640	H	227	Q	TPMT_HUMAN	Polymorphism	72552736	A	H	227	Q
8	UniProt	VAR_005641	Y	240	C	TPMT_HUMAN	Polymorphism	1142345	A	Y	240	C

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

PROSITE Motifs (1, 1)

Exons (8, 8)

Asymmetric/Biological Unit (8, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000309983	1	ENSE00001478514	chr6:18155305-18155264	42	TPMT_HUMAN	-	0	0	-	-
1.2	ENST00000309983	2	ENSE00000928742	chr6:18149402-18149219	184	TPMT_HUMAN	1-47	47	1	A:17-47	31
1.3	ENST00000309983	3	ENSE00000928741	chr6:18148146-18148054	93	TPMT_HUMAN	47-78	32	1	A:47-78	32
1.4	ENST00000309983	4	ENSE00000928740	chr6:18143959-18143827	133	TPMT_HUMAN	78-122	45	1	A:78-122	45
1.5	ENST00000309983	5	ENSE00000928739	chr6:18139948-18139896	53	TPMT_HUMAN	123-140	18	1	A:123-140	18
1.6	ENST00000309983	6	ENSE00000928738	chr6:18139268-18139194	75	TPMT_HUMAN	140-165	26	1	A:140-165	26
1.7	ENST00000309983	7	ENSE00000928737	chr6:18134120-18134035	86	TPMT_HUMAN	165-194	30	1	A:165-194	30
1.8	ENST00000309983	8	ENSE00000928736	chr6:18132408-18132364	45	TPMT_HUMAN	194-209	16	1	A:194-209	16
1.9	ENST00000309983	9	ENSE00001209706	chr6:18131011-18128542	2470	TPMT_HUMAN	209-245	37	1	A:209-245	37

Sequences/Alignments

Asymmetric/Biological 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:229
 aligned with TPMT_HUMAN | P51580 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:229
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236         
           TPMT_HUMAN    17 EVQKNQVLTLEEWQDKWVNGKTAFHQEQGHQLLKKHLDTFLKGKSGLRVFFPLCGKAVEMKWFADRGHSVVGVEISELGIQEFFTEQNLSYSEEPITEIPGTKVFKSSSGNISLYCCSIFDLPRTNIGKFDMIWDRGALVAINPGDRKCYADTMFSLLGKKFQYLLCVLSYDPTKHPGPPFYVPHAEIERLFGKICNIRCLEKVDAFEERHKSWGIDCLFEKLYLLTEK 245
               SCOP domains d2bzga1 A:17-245 Thiopurine S-methyltransferase                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhh.........hhhhhhhhhhhhh.....eeee......hhhhhhhhh..eeeee..hhhhhhhhhhhh..eeeeee.....eeeeeee....eeeee.hhhhhhhh.....eeeee.hhhhhh...hhhhhhhhhhhh...eeeeeeeeee.............hhhhhhhhhh...eeeeeeeee..hhhhhhhh.eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------S------------------------------P-------------------------------------------------------------------------T------------------------HF----------------------------------H-----------Q------------C----- SAPs(SNPs)
                    PROSITE ---------SAM_MT_TPMT  PDB: A:26-240 UniProt: 26-240                                                                                                                                                                             ----- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:17-47         ------------------------------Exon 1.4  PDB: A:78-122 UniProt: 78-122      Exon 1.5          ------------------------Exon 1.7  PDB: A:165-194      --------------Exon 1.9  PDB: A:209-245              Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.3  PDB: A:47-78          -------------------------------------------------------------Exon 1.6  PDB: A:140-165  ----------------------------Exon 1.8        ------------------------------------ Transcript 1 (2)
                 2bzg A  17 EVQKNQVLTLEEWQDKWVNGKTAFHQEQGHQLLKKHLDTFLKGKSGLRVFFPLCGKAVEmKWFADRGHSVVGVEISELGIQEFFTEQNLSYSEEPITEIPGTKVFKSSSGNISLYCCSIFDLPRTNIGKFDmIWDRGALVAINPGDRKCYADTmFSLLGKKFQYLLCVLSYDPTKHPGPPFYVPHAEIERLFGKICNIRCLEKVDAFEERHKSWGIDCLFEKLYLLTEK 245
                                    26        36        46        56        66        76        86        96       106       116       126       136       146 |     156       166   |   176       186       196       206       216       226       236         
                                                                                      76-MSE                                                                 148-MSE               170-MSE

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, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TPMT_HUMAN | P51580)

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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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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	2bzg
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