1N7I - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   THE STRUCTURE OF PHENYLETHANOLAMINE N-METHYLTRANSFERASE IN COMPLEX WITH S-ADENOSYLHOMOCYSTEINE AND THE INHIBITOR LY134046

Authors :   F. M. Mcmillan, J. Archbold, M. J. Mcleish, J. M. Caine, K. R. Criscione, G. L. Grunewald, J. L. Martin

Date :   15 Nov 02 (Deposition) - 23 Dec 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Methyltransferase, Catecholamine, Adrenaline, Epinephrine, S-Adenosylmethionine, S-Adenolsylhomocysteine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. M. Mcmillan, J. Archbold, M. J. Mcleish, J. M. Caine, K. R. Criscione, G. L. Grunewald, J. L. Martin
Molecular Recognition Of Sub-Micromolar Inhibitors By The Epinephrine-Synthesizing Enzyme Phenylethanolamine N-Methyltransferase.
J. Med. Chem. V. 47 37 2004
PubMed-ID: 14695818 | Reference-DOI: 10.1021/JM0205752
(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 BL21(DE3)
	Expression System Plasmid	:	PET17
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	PNMT OR PENT
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PNMTASE, NORADRENALINE N-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 (2, 4)

No.	Name	Count	Type	Full Name
1	LY1	2	Ligand/Ion	8,9-DICHLORO-2,3,4,5-TETRAHYDRO-1H-BENZO[C]AZEPINE
2	SAH	2	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	LY1	1	Ligand/Ion	8,9-DICHLORO-2,3,4,5-TETRAHYDRO-1H-BENZO[C]AZEPINE
2	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	LY1	1	Ligand/Ion	8,9-DICHLORO-2,3,4,5-TETRAHYDRO-1H-BENZO[C]AZEPINE
2	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:27 , 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 , ASN A:106 , ILE A:157 , ASP A:158 , VAL A:159 , HIS A:160 , ALA A:181 , PHE A:182 , CYS A:183 , VAL A:187	BINDING SITE FOR RESIDUE SAH A 2002
2	AC2	SOFTWARE	TYR B:527 , TYR B:535 , TYR B:540 , GLY B:579 , SER B:580 , GLY B:581 , THR B:583 , TYR B:585 , ASP B:601 , PHE B:602 , LEU B:603 , ASN B:606 , ILE B:657 , ASP B:658 , VAL B:659 , ALA B:681 , PHE B:682 , CYS B:683 , VAL B:687	BINDING SITE FOR RESIDUE SAH B 2003
3	AC3	SOFTWARE	TYR A:35 , ASN A:39 , TYR A:40 , ARG A:44 , VAL A:53 , LYS A:57 , PHE A:182 , MET A:258 , ASP A:267 , VAL A:269	BINDING SITE FOR RESIDUE LY1 A 3002
4	AC4	SOFTWARE	TYR B:535 , ASN B:539 , TYR B:540 , ARG B:544 , VAL B:553 , LYS B:557 , PHE B:682 , GLU B:719 , MET B:758 , ASP B:767 , VAL B:769	BINDING SITE FOR RESIDUE LY1 B 3003

(no "SS Bond" information available for 1N7I)

Asymmetric Unit

No.	Residues
1	Pro A:42	-	Pro A:43
2	Leu A:173	-	Pro A:174
3	Pro B:542	-	Pro B:543
4	Leu B:673	-	Pro B:674

Asymmetric 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	98 598	A
2	UniProt	VAR_036830	R	112	C	PNMT_HUMAN	Polymorphism	34530498	A B	R	112 612	C
3	UniProt	VAR_036831	A	175	T	PNMT_HUMAN	Polymorphism	34341496	A B	A	175 675	T
4	UniProt	VAR_037611	S	188	C	PNMT_HUMAN	Polymorphism	5639	A B	S	188 688	C
5	UniProt	VAR_037612	L	211	H	PNMT_HUMAN	Polymorphism	5640	A B	L	211 711	H
6	UniProt	VAR_037613	L	217	Q	PNMT_HUMAN	Polymorphism	5641	A B	L	217 717	Q
7	UniProt	VAR_037614	R	254	H	PNMT_HUMAN	Polymorphism	5642	A B	R	254 754	H
8	UniProt	VAR_024547	W	276	R	PNMT_HUMAN	Polymorphism	5643	A B	W	276 776	R

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_036829	T	98	A	PNMT_HUMAN	Polymorphism	36060376	A A	T	98 598	A
2	UniProt	VAR_036830	R	112	C	PNMT_HUMAN	Polymorphism	34530498	A A	R	112 612	C
3	UniProt	VAR_036831	A	175	T	PNMT_HUMAN	Polymorphism	34341496	A A	A	175 675	T
4	UniProt	VAR_037611	S	188	C	PNMT_HUMAN	Polymorphism	5639	A A	S	188 688	C
5	UniProt	VAR_037612	L	211	H	PNMT_HUMAN	Polymorphism	5640	A A	L	211 711	H
6	UniProt	VAR_037613	L	217	Q	PNMT_HUMAN	Polymorphism	5641	A A	L	217 717	Q
7	UniProt	VAR_037614	R	254	H	PNMT_HUMAN	Polymorphism	5642	A A	R	254 754	H
8	UniProt	VAR_024547	W	276	R	PNMT_HUMAN	Polymorphism	5643	A A	W	276 776	R

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_036829	T	98	A	PNMT_HUMAN	Polymorphism	36060376	A B	T	98 598	A
2	UniProt	VAR_036830	R	112	C	PNMT_HUMAN	Polymorphism	34530498	A B	R	112 612	C
3	UniProt	VAR_036831	A	175	T	PNMT_HUMAN	Polymorphism	34341496	A B	A	175 675	T
4	UniProt	VAR_037611	S	188	C	PNMT_HUMAN	Polymorphism	5639	A B	S	188 688	C
5	UniProt	VAR_037612	L	211	H	PNMT_HUMAN	Polymorphism	5640	A B	L	211 711	H
6	UniProt	VAR_037613	L	217	Q	PNMT_HUMAN	Polymorphism	5641	A B	L	217 717	Q
7	UniProt	VAR_037614	R	254	H	PNMT_HUMAN	Polymorphism	5642	A B	R	254 754	H
8	UniProt	VAR_024547	W	276	R	PNMT_HUMAN	Polymorphism	5643	A B	W	276 776	R

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

Asymmetric 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:23-282 B:523-780
2	NNMT_PNMT_TEMT	PS01100	NNMT/PNMT/TEMT family of methyltransferases signature.	PNMT_HUMAN	75-91	2	A:75-91 B:575-591

Biological Unit 1 (2, 2)

	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	1	A:23-282 -
2	NNMT_PNMT_TEMT	PS01100	NNMT/PNMT/TEMT family of methyltransferases signature.	PNMT_HUMAN	75-91	1	A:75-91 -

Biological Unit 2 (2, 2)

	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	1	- B:523-780
2	NNMT_PNMT_TEMT	PS01100	NNMT/PNMT/TEMT family of methyltransferases signature.	PNMT_HUMAN	75-91	1	- B:575-591

Asymmetric 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:22-68 B:514-568	47 55
1.3	ENST00000269582	3	ENSE00001682624	chr17:37825882-37826089	208	PNMT_HUMAN	68-137	70	2	A:68-137 B:568-637	70 70
1.4b	ENST00000269582	4b	ENSE00000950703	chr17:37826204-37826728	525	PNMT_HUMAN	137-282	146	2	A:137-282 B:637-780	146 144

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:261
 aligned with PNMT_HUMAN | P11086 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:261
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281 
           PNMT_HUMAN    22 AVASAYQRFEPRAYLRNNYAPPRGDLCNPNGVGPWKLRCLAQTFATGEVSGRTLIDIGSGPTVYQLLSACSHFEDITMTDFLEVNRQELGRWLQEEPGAFNWSMYSQHACLIEGKGECWQDKERQLRARVKRVLPIDVHQPQPLGAGSPAPLPADALVSAFCLEAVSPDLASFQRALDHITTLLRPGGHLLLIGALEESWYLAGEARLTVVPVSEEEVREALVRSGYKVRDLRTYIMPAHLQTGVDDVKGVFFAWAQKVGL 282
               SCOP domains d1n7ia_ A: Phenylethanolamine N-methyltransferase, PNMTase                                                                                                                                                                                                            SCOP domains
               CATH domains 1n7iA00 A:22-282 Vaccinia Virus protein VP39                                                                                                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..hhhhhhhhhh...........hhhhhhhhhhhhhhhh......eeeee..........hhhhhh.eeeeee.hhhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhhhheeeeee..................eeeeeee.hhhhhh.hhhhhhhhhhhhhh.eeeeeeeeeeeee...eeee..eeee.................eeeeeeeeee......................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -SAM_MT_NNMT_PNMT_TEMT  PDB: A:23-282 UniProt: 23-282                                                                                                                                                                                                                 PROSITE (1)
                PROSITE (2) -----------------------------------------------------NNMT_PNMT_TEMT   ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: A:22-68 UniProt: 1-68           --------------------------------------------------------------------Exon 1.4b  PDB: A:137-282 UniProt: 137-282                                                                                                         Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------Exon 1.3  PDB: A:68-137 UniProt: 68-137                               ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1n7i A  22 AVASAYQRFEPRAYLRNNYAPPRGDLCNPNGVGPWKLRCLAQTFATGEVSGRTLIDIGSGPTVYQLLSACSHFEDITMTDFLEVNRQELGRWLQEEPGAFNWSMYSQHACLIEGKGECWQDKERQLRARVKRVLPIDVHQPQPLGAGSPAPLPADALVSAFCLEAVSPDLASFQRALDHITTLLRPGGHLLLIGALEESWYLAGEARLTVVPVSEEEVREALVRSGYKVRDLRTYIMPAHLQTGVDDVKGVFFAWAQKVGL 282
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281

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 d1n7ib_ B: Phenylethanolamine N-methyltransferase, PNMTase                                                                                                                                                                                                                  SCOP domains
               CATH domains 1n7iB00 B:514-780 Vaccinia Virus protein VP39                                                                                                                                                                                                                               CATH domains
           Pfam domains (1) NNMT_PNMT_TEMT-1n7iB01 B:514-779                                                                                                                                                                                                                                          - Pfam domains (1)
           Pfam domains (2) NNMT_PNMT_TEMT-1n7iB02 B:514-779                                                                                                                                                                                                                                          - Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhh..hhhhhhhhhhh..........hhhhhhhhhhhhhhhh......eeee......hhhhh.......eeeeee.hhhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhhhheeeeee..................eeeeeee.hhhhhh.hhhhhhhhhhhhhh.eeeeeeeeeeeee...eee....eee....hhhhhhhhhhhhheeeeeeeeee.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:523-780 UniProt: 23-282                                                                                                                                                                                                              PROSITE (1)
                PROSITE (2) -------------------------------------------------------------NNMT_PNMT_TEMT   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: B:514-568 UniProt: 1-68 [INCOMPLETE]    --------------------------------------------------------------------Exon 1.4b  PDB: B:637-780 UniProt: 137-282 [INCOMPLETE]                                                                                          Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------Exon 1.3  PDB: B:568-637 UniProt: 68-137                              ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1n7i B 514 PDSAPGQAAVASAYQRFEPRAYLRNNYAPPRGDLCNPNGVGPWKLRCLAQTFATGEVSGRTLIDIGSGPTVYQLLSACSHFEDITMTDFLEVNRQELGRWLQEEPGAFNWSMYSQHACLIEGKGECWQDKERQLRARVKRVLPIDVHQPQPLGAGSPAPLPADALVSAFCLEAVSPDLASFQRALDHITTLLRPGGHLLLIGALEESWYLAGEARLTVVPVSEEEVREALVRSGYKVRDLRTYIMPAHLQTGVDDVKGVFFAWAQKV 780
                                   523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773

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 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	1n7iA00	A:22-282
1b	1n7iB00	B:514-780

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: NNMT_PNMT_TEMT (24)

Homo sapiens (Human) (24)

1a	NNMT_PNMT_TEMT-1n7iB01	B:514-779
1b	NNMT_PNMT_TEMT-1n7iB02	B:514-779

Asymmetric 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 Unit
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		Pro A:42 - Pro A:43	[ RasMol ]
		Pro B:542 - Pro B:543	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (2, 4)

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