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Title :   CRYSTAL STRUCTURE OF THIOPURINE METHYLTRANSFERASE (18204406) FROM MUS MUSCULUS AT 1.35 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   09 Mar 06 (Deposition) - 19 Sep 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.25

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   18204406, Thiopurine Methyltransferase, Structural Genomics, Psi, Protein Structure Initiative, Joint Center For Structural Genomics, Jcsg (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Thiopurine Methyltransferase (18204406) From Mus Musculus At 1. 35 A Resolution
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - THIOPURINE S-METHYLTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.1.1.67
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TPMT
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	THIOPURINE METHYLTRANSFERASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	SAH	2	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:21 , TRP A:24 , TRP A:28 , PHE A:35 , LEU A:64 , CYS A:65 , GLY A:66 , GLU A:85 , ILE A:86 , CYS A:128 , SER A:129 , ILE A:130 , ARG A:147 , GLY A:148 , HOH A:302 , HOH A:309 , HOH A:316 , HOH A:339	BINDING SITE FOR RESIDUE SAH A 300
2	AC2	SOFTWARE	LEU B:21 , TRP B:24 , TRP B:28 , PHE B:35 , LEU B:64 , CYS B:65 , GLY B:66 , GLU B:85 , ILE B:86 , CYS B:128 , SER B:129 , ILE B:130 , ARG B:147 , GLY B:148 , HOH B:301 , HOH B:318 , HOH B:322 , HOH B:342	BINDING SITE FOR RESIDUE SAH B 300

(no "SS Bond" information available for 2GB4)

Asymmetric Unit

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

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_TPMT_MOUSE_001 *	I	69	V	TPMT_MOUSE	---	---	A/B	I	69	V
	* ID not provided by source

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

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_TPMT_MOUSE_001 *	I	69	V	TPMT_MOUSE	---	---	A	I	69	V
	* ID not provided by source

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

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_TPMT_MOUSE_001 *	I	69	V	TPMT_MOUSE	---	---	B	I	69	V
	* ID not provided by source

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_MT_TPMT	PS51585	Thiopurine or thiol or thiocyanate S-methyltransferase (TPMT) family profile.	TPMT_MOUSE	21-235	2	A:21-235 B:21-235

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_MT_TPMT	PS51585	Thiopurine or thiol or thiocyanate S-methyltransferase (TPMT) family profile.	TPMT_MOUSE	21-235	1	A:21-235 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_MT_TPMT	PS51585	Thiopurine or thiol or thiocyanate S-methyltransferase (TPMT) family profile.	TPMT_MOUSE	21-235	1	- B:21-235

(no "Exon" information available for 2GB4)

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:231
 aligned with TPMT_MOUSE | O55060 from UniProtKB/Swiss-Prot  Length:240

    Alignment length:231
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239 
           TPMT_MOUSE    10 DAEVQKNQVLTLEDWKEKWVTRHISFHQEQGHQLLKKHLDTFLKGQSGLRVFFPLCGKAIEMKWFADRGHTVVGVEISEIGIREFFAEQNLSYTEEPLAEIAGAKVFKSSSGSISLYCCSIFDLPRANIGKFDRIWDRGALVAINPGDHDRYADIILSLLRKEFQYLVAVLSYDPTKHAGPPFYVPSAELKRLFGTKCSMQCLEEVDALEERHKAWGLDYLFEKLYLLTEK 240
               SCOP domains d2gb4a_ A: Thiopurine S-methyltransferase                                                                                                                                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhh.........hhhhhhhhhhhhh.....eeee......hhhhhhhhh..eeeee..hhhhhhhhhhhh...eeeee.......eeeee....eeeee....hhhhhh...eeeeee.......hhhhhhhhhhhhhhheeeeeeeeeeeee.............hhhhhhhhhh..eeeeeeeeee..hhhhh.......eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------V--------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------SAM_MT_TPMT  PDB: A:21-235 UniProt: 21-235                                                                                                                                                                             ----- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gb4 A  10 DAEVQKNQVLTLEDWKEKWVTRHISFHQEQGHQLLKKHLDTFLKGQSGLRVFFPLCGKAIEMKWFADRGHTVVGVEISEIGIREFFAEQNLSYTEEPLAEIAGAKVFKSSSGSISLYCCSIFDLPRANIGKFDRIWDRGALVAINPGDHDRYADIILSLLRKEFQYLVAVLSYDPTKHAGPPFYVPSAELKRLFGTKCSMQCLEEVDALEERHKAWGLDYLFEKLYLLTEK 240
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239

Chain B from PDB  Type:PROTEIN  Length:230
 aligned with TPMT_MOUSE | O55060 from UniProtKB/Swiss-Prot  Length:240

    Alignment length:230
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
           TPMT_MOUSE    11 AEVQKNQVLTLEDWKEKWVTRHISFHQEQGHQLLKKHLDTFLKGQSGLRVFFPLCGKAIEMKWFADRGHTVVGVEISEIGIREFFAEQNLSYTEEPLAEIAGAKVFKSSSGSISLYCCSIFDLPRANIGKFDRIWDRGALVAINPGDHDRYADIILSLLRKEFQYLVAVLSYDPTKHAGPPFYVPSAELKRLFGTKCSMQCLEEVDALEERHKAWGLDYLFEKLYLLTEK 240
               SCOP domains d2gb4b_ B: Thiopurine S-methyltransferase                                                                                                                                                                                              SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhh.........hhhhhhhhhhhh......eeee......hhhhhhhhh..eeeee..hhhhhhhhhhhhh..eeeee.......eeeee....eeeee....hhhhhh...eeeeee.......hhhhhhhhhhhhhhheeeeeeeeeeeee.............hhhhhhhhhh..eeeeeeeeee..hhhhhhh.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------V--------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------SAM_MT_TPMT  PDB: B:21-235 UniProt: 21-235                                                                                                                                                                             ----- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gb4 B  11 AEVQKNQVLTLEDWKEKWVTRHISFHQEQGHQLLKKHLDTFLKGQSGLRVFFPLCGKAIEMKWFADRGHTVVGVEISEIGIREFFAEQNLSYTEEPLAEIAGAKVFKSSSGSISLYCCSIFDLPRANIGKFDRIWDRGALVAINPGDHDRYADIILSLLRKEFQYLVAVLSYDPTKHAGPPFYVPSAELKRLFGTKCSMQCLEEVDALEERHKAWGLDYLFEKLYLLTEK 240
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240

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 '\|'

(no "CATH Domain" information available for 2GB4)

(no "Pfam Domain" information available for 2GB4)

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.

Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:189 - Pro A:190	[ RasMol ]
		Gly B:189 - Pro B:190	[ RasMol ]
		Pro A:190 - Pro A:191	[ RasMol ]
		Pro B:190 - Pro B:191	[ RasMol ]

Biological Units
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(no "Related Entries Specified in the PDB File" available for 2GB4)

Description

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Ligands, Modified Residues, Ions (1, 2)

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SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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Exons (0, 0)

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