2H11 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   AMINO-TERMINAL TRUNCATED THIOPURINE S-METHYLTRANSFERASE COMPLEXED WITH S-ADENOSYL-L-HOMOCYSTEINE

Authors :   J. R. Horton, X. Cheng

Date :   15 May 06 (Deposition) - 21 Nov 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.89

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

Keywords :   Binary Protein-Cofactor Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. R. Horton, X. Cheng
Amino-Terminal Truncated Thiopurine S-Methyltransferase Complexed With S-Adenosyl-L-Homocysteine
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 BL21(DE3)
	Expression System Plasmid	:	PGEX-4T-3
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	AMINO-TERMINAL TRUNCATED TPMT
	Gene	:	TPMT
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	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 (3, 9)

No.	Name	Count	Type	Full Name
1	B3P	3	Ligand/Ion	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2	SAH	2	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
3	SCN	4	Ligand/Ion	THIOCYANATE ION

Biological Unit 1 (3, 5)

No.	Name	Count	Type	Full Name
1	B3P	2	Ligand/Ion	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
3	SCN	2	Ligand/Ion	THIOCYANATE ION

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	B3P	1	Ligand/Ion	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
3	SCN	2	Ligand/Ion	THIOCYANATE ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:110 , PRO A:111 , HOH A:447 , ARG B:215	BINDING SITE FOR RESIDUE SCN A 4
2	AC2	SOFTWARE	ARG A:215 , GLU B:110 , PRO B:111 , HOH B:457	BINDING SITE FOR RESIDUE SCN B 5
3	AC3	SOFTWARE	ARG B:64 , LYS B:122 , SER B:129 , TYR B:131	BINDING SITE FOR RESIDUE SCN B 6
4	AC4	SOFTWARE	B3P A:1 , ARG A:64 , SER A:129 , TYR A:131 , HOH A:386	BINDING SITE FOR RESIDUE SCN A 7
5	AC5	SOFTWARE	LEU A:26 , TRP A:29 , TRP A:33 , PHE A:40 , LEU A:69 , CYS A:70 , GLU A:90 , ILE A:91 , CYS A:133 , SER A:134 , ILE A:135 , ARG A:152 , GLY A:153 , HOH A:309 , HOH A:315 , HOH A:319 , HOH A:379 , HOH A:385	BINDING SITE FOR RESIDUE SAH A 300
6	AC6	SOFTWARE	LEU B:26 , TRP B:29 , TRP B:33 , PHE B:40 , LEU B:69 , CYS B:70 , GLU B:90 , ILE B:91 , CYS B:133 , SER B:134 , ILE B:135 , ARG B:152 , GLY B:153 , HOH B:313 , HOH B:319 , HOH B:323 , HOH B:382 , HOH B:387	BINDING SITE FOR RESIDUE SAH B 301
7	AC7	SOFTWARE	SCN A:7 , ARG A:64 , PRO A:111 , ILE A:112 , THR A:113 , GLU A:114 , TYR A:131 , ASN A:142 , ILE A:143 , HOH A:350 , HOH A:397 , HOH A:402 , HOH A:403 , HOH A:439 , LYS B:228 , SER B:229	BINDING SITE FOR RESIDUE B3P A 1
8	AC8	SOFTWARE	LYS A:228 , SER A:229 , ARG B:64 , PRO B:111 , ILE B:112 , THR B:113 , GLU B:114 , LYS B:122 , TYR B:131 , THR B:141 , ASN B:142 , ILE B:143 , HOH B:354 , HOH B:396 , HOH B:400 , HOH B:401 , HOH B:437 , HOH B:438	BINDING SITE FOR RESIDUE B3P B 2
9	AC9	SOFTWARE	ILE A:115 , SER A:134 , ASP A:137 , HOH A:415 , HOH A:435 , ILE B:115 , ASP B:137	BINDING SITE FOR RESIDUE B3P A 3

(no "SS Bond" information available for 2H11)

Asymmetric Unit

No.	Residues
1	Gly A:194	-	Pro A:195
2	Pro A:195	-	Pro A:196
3	Gly B:194	-	Pro B:195
4	Pro B:195	-	Pro B:196

Asymmetric Unit (8, 16)

								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/B	L	49	S
2	UniProt	VAR_005637	A	80	P	TPMT_HUMAN	Polymorphism	1800462	A/B	A	80	P
3	UniProt	VAR_005638	A	154	T	TPMT_HUMAN	Polymorphism	1800460	A/B	A	154	T
4	UniProt	VAR_052368	Q	179	H	TPMT_HUMAN	Polymorphism	6921269	A/B	Q	179	H
5	UniProt	VAR_005639	Y	180	F	TPMT_HUMAN	Polymorphism	75543815	A/B	Y	180	F
6	UniProt	VAR_008715	R	215	H	TPMT_HUMAN	Polymorphism	56161402	A/B	R	215	H
7	UniProt	VAR_005640	H	227	Q	TPMT_HUMAN	Polymorphism	72552736	A/B	H	227	Q
8	UniProt	VAR_005641	Y	240	C	TPMT_HUMAN	Polymorphism	1142345	A/B	Y	240	C

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

Biological Unit 1 (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)

Biological Unit 2 (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	B	L	49	S
2	UniProt	VAR_005637	A	80	P	TPMT_HUMAN	Polymorphism	1800462	B	A	80	P
3	UniProt	VAR_005638	A	154	T	TPMT_HUMAN	Polymorphism	1800460	B	A	154	T
4	UniProt	VAR_052368	Q	179	H	TPMT_HUMAN	Polymorphism	6921269	B	Q	179	H
5	UniProt	VAR_005639	Y	180	F	TPMT_HUMAN	Polymorphism	75543815	B	Y	180	F
6	UniProt	VAR_008715	R	215	H	TPMT_HUMAN	Polymorphism	56161402	B	R	215	H
7	UniProt	VAR_005640	H	227	Q	TPMT_HUMAN	Polymorphism	72552736	B	H	227	Q
8	UniProt	VAR_005641	Y	240	C	TPMT_HUMAN	Polymorphism	1142345	B	Y	240	C

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_HUMAN	26-240	2	A:26-240 B:26-240

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_HUMAN	26-240	1	A:26-240 -

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_HUMAN	26-240	1	- B:26-240

Asymmetric Unit (8, 16)

	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	2	A:17-47 B:17-47	31 31
1.3	ENST00000309983	3	ENSE00000928741	chr6:18148146-18148054	93	TPMT_HUMAN	47-78	32	2	A:47-78 B:47-78	32 32
1.4	ENST00000309983	4	ENSE00000928740	chr6:18143959-18143827	133	TPMT_HUMAN	78-122	45	2	A:78-122 B:78-122	45 45
1.5	ENST00000309983	5	ENSE00000928739	chr6:18139948-18139896	53	TPMT_HUMAN	123-140	18	2	A:123-140 B:123-140	18 18
1.6	ENST00000309983	6	ENSE00000928738	chr6:18139268-18139194	75	TPMT_HUMAN	140-165	26	2	A:140-165 B:140-165	26 26
1.7	ENST00000309983	7	ENSE00000928737	chr6:18134120-18134035	86	TPMT_HUMAN	165-194	30	2	A:165-194 B:165-194	30 30
1.8	ENST00000309983	8	ENSE00000928736	chr6:18132408-18132364	45	TPMT_HUMAN	194-209	16	2	A:194-209 B:194-209	16 16
1.9	ENST00000309983	9	ENSE00001209706	chr6:18131011-18128542	2470	TPMT_HUMAN	209-245	37	2	A:209-245 B:209-245	37 37

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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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 d2h11a_ A: Thiopurine S-methyltransferase                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhh..........hhhhhhhhhhhh......eeee......hhhhhhhh...eeeee..hhhhhhhhhhhh...eeeee.......eeeee....eeeee.hhhhhhhh....eeeeee.......hhhhhhhhhhhhhh.eeeeeeeeeeeee.............hhhhhhhhhh..eeeeeeeeee..hhhhhhhh....eeeeeeeee. 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)
                 2h11 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

Chain B 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 d2h11b_ B: Thiopurine S-methyltransferase                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhh..........hhhhhhhhhhhh......eeeee.....hhhhhhhhh..eeeee..hhhhhhhhhhhh...eeeee.......eeeee....eeeee.hhhhhhhh....eeeeee.......hhhhhhhhhhhhhh.eeeeeeeeeeeee.............hhhhhhhhhh..eeeeeeeeee..hhhhhhhh....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------S------------------------------P-------------------------------------------------------------------------T------------------------HF----------------------------------H-----------Q------------C----- SAPs(SNPs)
                    PROSITE ---------SAM_MT_TPMT  PDB: B:26-240 UniProt: 26-240                                                                                                                                                                             ----- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: B:17-47         ------------------------------Exon 1.4  PDB: B:78-122 UniProt: 78-122      Exon 1.5          ------------------------Exon 1.7  PDB: B:165-194      --------------Exon 1.9  PDB: B:209-245              Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.3  PDB: B:47-78          -------------------------------------------------------------Exon 1.6  PDB: B:140-165  ----------------------------Exon 1.8        ------------------------------------ Transcript 1 (2)
                 2h11 B  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

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "CATH Domain" information available for 2H11)

(no "Pfam Domain" information available for 2H11)

Asymmetric Unit(hide GO term definitions)

Chain A,B (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.

Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:194 - Pro A:195	[ RasMol ]
		Gly B:194 - Pro B:195	[ RasMol ]
		Pro A:195 - Pro A:196	[ RasMol ]
		Pro B:195 - Pro B:196	[ RasMol ]

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Access by PDB/NDB ID
	2h11
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	TPMT_HUMAN \| P51580
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	2.1.1.67
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	TPMT_HUMAN \| P51580	:	2bzg

(no "Related Entries Specified in the PDB File" available for 2H11)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (8, 16)

PROSITE Motifs (1, 2)

Exons (8, 16)

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SCOP Domains (1, 2)

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