1YZ3 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   STRUCTURE OF HUMAN PNMT COMPLEXED WITH COFACTOR PRODUCT ADOHCY AND INHIBITOR SK&F 64139

Authors :   Q. Wu, C. L. Gee, F. Lin, J. L. Martin, G. L. Grunewald, M. J. Mcleish

Date :   27 Feb 05 (Deposition) - 07 Feb 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym./Biol. Unit : A,B

Keywords :   Enzyme, Product, Inhibitor Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Q. Wu, C. L. Gee, F. Lin, J. D. Tyndall, J. L. Martin, G. L. Grunewald, M. J. Mcleish
Structural, Mutagenic, And Kinetic Analysis Of The Binding Of Substrates And Inhibitors Of Human Phenylethanolamine N-Methyltransferase
J. Med. Chem. V. 48 7243 2005
PubMed-ID: 16279783 | Reference-DOI: 10.1021/JM050568O
(for further references see the PDB file header)

Molecule 1 - PHENYLETHANOLAMINE N-METHYLTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.1.1.28
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET17PNMT-HIS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	SAH	2	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
2	SKA	2	Ligand/Ion	7,8-DICHLORO-1,2,3,4-TETRAHYDROISOQUINOLINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:35 , ASN A:39 , TYR A:40 , VAL A:53 , LYS A:57 , PHE A:182 , GLU A:219 , MET A:258 , ASP A:267 , HOH A:1040	BINDING SITE FOR RESIDUE SKA A 3001
2	AC2	SOFTWARE	TYR B:35 , ASN B:39 , TYR B:40 , VAL B:53 , LYS B:57 , PHE B:182 , GLU B:219 , MET B:258 , ASP B:267 , VAL B:269 , VAL B:272 , HOH B:1068	BINDING SITE FOR RESIDUE SKA B 3002
3	AC3	SOFTWARE	TYR B:27 , TYR B:35 , TYR B:40 , GLY B:79 , SER B:80 , GLY B:81 , THR B:83 , TYR B:85 , ASP B:101 , PHE B:102 , LEU B:103 , ASN B:106 , ILE B:157 , ASP B:158 , VAL B:159 , ALA B:181 , PHE B:182 , CYS B:183 , VAL B:187 , HOH B:1080	BINDING SITE FOR RESIDUE SAH B 2001
4	AC4	SOFTWARE	TYR A:35 , TYR A:40 , GLY A:79 , SER A:80 , GLY A:81 , THR A:83 , TYR A:85 , ASP A:101 , PHE A:102 , LEU A:103 , ASN A:106 , ASP A:158 , VAL A:159 , ALA A:181 , PHE A:182 , CYS A:183 , VAL A:187 , HOH A:1039 , HOH A:1182	BINDING SITE FOR RESIDUE SAH A 2002

(no "SS Bond" information available for 1YZ3)

Asymmetric/Biological Unit

No.	Residues
1	Pro A:42	-	Pro A:43
2	Leu A:173	-	Pro A:174
3	Pro B:42	-	Pro B:43
4	Leu B:173	-	Pro B:174

Asymmetric/Biological Unit (8, 16)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_036829	T	98	A	PNMT_HUMAN	Polymorphism	36060376	A/B	T	98	A
2	UniProt	VAR_036830	R	112	C	PNMT_HUMAN	Polymorphism	34530498	A/B	R	112	C
3	UniProt	VAR_036831	A	175	T	PNMT_HUMAN	Polymorphism	34341496	A/B	A	175	T
4	UniProt	VAR_037611	S	188	C	PNMT_HUMAN	Polymorphism	5639	A/B	S	188	C
5	UniProt	VAR_037612	L	211	H	PNMT_HUMAN	Polymorphism	5640	A/B	L	211	H
6	UniProt	VAR_037613	L	217	Q	PNMT_HUMAN	Polymorphism	5641	A/B	L	217	Q
7	UniProt	VAR_037614	R	254	H	PNMT_HUMAN	Polymorphism	5642	A/B	R	254	H
8	UniProt	VAR_024547	W	276	R	PNMT_HUMAN	Polymorphism	5643	A/B	W	276	R

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

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_MT_NNMT_PNMT_TEMT	PS51681	SAM-dependent methyltransferase NNMT/PNMT/TEMT-type profile.	PNMT_HUMAN	23-282	2	A:23-280 B:23-280
2	NNMT_PNMT_TEMT	PS01100	NNMT/PNMT/TEMT family of methyltransferases signature.	PNMT_HUMAN	75-91	2	A:75-91 B:75-91

Asymmetric/Biological Unit (3, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2	ENST00000269582	2	ENSE00000950701	chr17:37824507-37824930	424	PNMT_HUMAN	1-68	68	2	A:18-68 B:14-68	51 55
1.3	ENST00000269582	3	ENSE00001682624	chr17:37825882-37826089	208	PNMT_HUMAN	68-137	70	2	A:68-137 B:68-137	70 70
1.4b	ENST00000269582	4b	ENSE00000950703	chr17:37826204-37826728	525	PNMT_HUMAN	137-282	146	2	A:137-280 B:137-280	144 144

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:263
 aligned with PNMT_HUMAN | P11086 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:263
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277   
           PNMT_HUMAN    18 PGQAAVASAYQRFEPRAYLRNNYAPPRGDLCNPNGVGPWKLRCLAQTFATGEVSGRTLIDIGSGPTVYQLLSACSHFEDITMTDFLEVNRQELGRWLQEEPGAFNWSMYSQHACLIEGKGECWQDKERQLRARVKRVLPIDVHQPQPLGAGSPAPLPADALVSAFCLEAVSPDLASFQRALDHITTLLRPGGHLLLIGALEESWYLAGEARLTVVPVSEEEVREALVRSGYKVRDLRTYIMPAHLQTGVDDVKGVFFAWAQKV 280
               SCOP domains d1yz3a_ A: automated matches                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1yz3A00 A:18-280 Vaccinia Virus protein VP39                                                                                                                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhh...hhhhhhhhhh...........hhhhhhhhhhhhhhhh.......eeee.....hhhhhhhhhh...eeee..hhhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhhhheeeee...................eeeeeee.hhhhhh.hhhhhhhhhhhhhh.eeeeeeeeeeeee...eeee..eeee....hhhhhhhhhhh......eeeeee.hhhhh.......eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------A-------------C--------------------------------------------------------------T------------C----------------------H-----Q------------------------------------H---------------------R---- SAPs(SNPs)
                PROSITE (1) -----SAM_MT_NNMT_PNMT_TEMT  PDB: A:23-280 UniProt: 23-282                                                                                                                                                                                                               PROSITE (1)
                PROSITE (2) ---------------------------------------------------------NNMT_PNMT_TEMT   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: A:18-68 UniProt: 1-68 [INCOMPLETE]  --------------------------------------------------------------------Exon 1.4b  PDB: A:137-280 UniProt: 137-282 [INCOMPLETE]                                                                                          Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------Exon 1.3  PDB: A:68-137 UniProt: 68-137                               ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1yz3 A  18 PGQAAVASAYQRFEPRAYLRNNYAPPRGDLCNPNGVGPWKLRCLAQTFATGEVSGRTLIDIGSGPTVYQLLSACSHFEDITMTDFLEVNRQELGRWLQEEPGAFNWSMYSQHACLIEGKGECWQDKERQLRARVKRVLPIDVHQPQPLGAGSPAPLPADALVSAFCLEAVSPDLASFQRALDHITTLLRPGGHLLLIGALEESWYLAGEARLTVVPVSEEEVREALVRSGYKVRDLRTYIMPAHLQTGVDDVKGVFFAWAQKV 280
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277

Chain B from PDB  Type:PROTEIN  Length:267
 aligned with PNMT_HUMAN | P11086 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:267
                                    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       
           PNMT_HUMAN    14 PDSAPGQAAVASAYQRFEPRAYLRNNYAPPRGDLCNPNGVGPWKLRCLAQTFATGEVSGRTLIDIGSGPTVYQLLSACSHFEDITMTDFLEVNRQELGRWLQEEPGAFNWSMYSQHACLIEGKGECWQDKERQLRARVKRVLPIDVHQPQPLGAGSPAPLPADALVSAFCLEAVSPDLASFQRALDHITTLLRPGGHLLLIGALEESWYLAGEARLTVVPVSEEEVREALVRSGYKVRDLRTYIMPAHLQTGVDDVKGVFFAWAQKV 280
               SCOP domains d1yz3b_ B: automated matches                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1yz3B00 B:14-280 Vaccinia Virus protein VP39                                                                                                                                                                                                                                CATH domains
           Pfam domains (1) NNMT_PNMT_TEMT-1yz3B01 B:14-279                                                                                                                                                                                                                                           - Pfam domains (1)
           Pfam domains (2) NNMT_PNMT_TEMT-1yz3B02 B:14-279                                                                                                                                                                                                                                           - Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhh..hhhhhhhhhhh..........hhhhhhhhhhhhhhh.......eeeee.....hhhhhhhhhh..eeeeee.hhhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhhhheeeeee..................eeeeeee.hhhhhh.hhhhhhhhhhhhhh.eeeeeeeeeeeee...eeee..eeee....hhhhhhhhhhhh.eeeeeeeeee.hhhhh.......eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------A-------------C--------------------------------------------------------------T------------C----------------------H-----Q------------------------------------H---------------------R---- SAPs(SNPs)
                PROSITE (1) ---------SAM_MT_NNMT_PNMT_TEMT  PDB: B:23-280 UniProt: 23-282                                                                                                                                                                                                               PROSITE (1)
                PROSITE (2) -------------------------------------------------------------NNMT_PNMT_TEMT   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: B:14-68 UniProt: 1-68 [INCOMPLETE]      --------------------------------------------------------------------Exon 1.4b  PDB: B:137-280 UniProt: 137-282 [INCOMPLETE]                                                                                          Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------Exon 1.3  PDB: B:68-137 UniProt: 68-137                               ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1yz3 B  14 PDSAPGQAAVASAYQRFEPRAYLRNNYAPPRGDLCNPNGVGPWKLRCLAQTFATGEVSGRTLIDIGSGPTVYQLLSACSHFEDITMTDFLEVNRQELGRWLQEEPGAFNWSMYSQHACLIEGKGECWQDKERQLRARVKRVLPIDVHQPQPLGAGSPAPLPADALVSAFCLEAVSPDLASFQRALDHITTLLRPGGHLLLIGALEESWYLAGEARLTVVPVSEEEVREALVRSGYKVRDLRTYIMPAHLQTGVDDVKGVFFAWAQKV 280
                                    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

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: S-adenosyl-L-methionine-dependent methyltransferases (533)

Superfamily: S-adenosyl-L-methionine-dependent methyltransferases (533)

Family: Arylamine N-methyltransferase (40)

Protein domain: automated matches (31)

Human (Homo sapiens) [TaxId: 9606] (31)

1a	d1yz3a_	A:
1b	d1yz3b_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: Vaccinia Virus protein VP39 (378)

Human (Homo sapiens) (49)

1a	1yz3A00	A:18-280
1b	1yz3B00	B:14-280

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: NNMT_PNMT_TEMT (24)

Homo sapiens (Human) (24)

1a	NNMT_PNMT_TEMT-1yz3B01	B:14-279
1b	NNMT_PNMT_TEMT-1yz3B02	B:14-279

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PNMT_HUMAN | P11086)

molecular function
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:0004603	phenylethanolamine N-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + phenylethanolamine = S-adenosyl-L-homocysteine + N-methylphenylethanolamine.
	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:0042423	catecholamine biosynthetic process	The chemical reactions and pathways resulting in the formation of any of a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine.
	GO:0042418	epinephrine biosynthetic process	The chemical reactions and pathways resulting in the formation of epinephrine, a hormone produced by the medulla of the adrenal glands that increases heart activity, improves the power and prolongs the action of muscles, and increases the rate and depth of breathing. It is synthesized by the methylation of norepinephrine.
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Leu A:173 - Pro A:174	[ RasMol ]
		Leu B:173 - Pro B:174	[ RasMol ]
		Pro A:42 - Pro A:43	[ RasMol ]
		Pro B:42 - Pro B:43	[ RasMol ]

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	1yz3
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	PNMT_HUMAN \| P11086
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	2.1.1.28
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (8, 16)

PROSITE Motifs (2, 4)

Exons (3, 6)

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