2AN5 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF HUMAN PNMT COMPLEXED WITH S-ADENOSYL-HOMOCYSTEINE AND AN INHIBITOR, TRANS-(1S,2S)-2-AMINO-1-TETRALOL

Authors :   C. L. Gee, J. D. A. Tyndall, G. L. Grunewald, Q. Wu, M. J. Mcleish, J. L. Martin

Date :   11 Aug 05 (Deposition) - 14 Mar 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Methyltransferase, Inhibitor Structure, S-Adenosyl-L- Methionine, Adrenaline Synthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. L. Gee, J. D. A. Tyndall, G. L. Grunewald, Q. Wu, M. J. Mcleish, J. L. Martin
Mode Of Binding Of Methyl Acceptor Substrates To The Adrenaline-Synthesizing Enzyme Phenylethanolamine N-Methyltransferase: Implications For Catalysis
Biochemistry V. 44 16875 2005
PubMed-ID: 16363801 | Reference-DOI: 10.1021/BI051636B
(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 Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PNMT
	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 (3, 5)

No.	Name	Count	Type	Full Name
1	PO4	1	Ligand/Ion	PHOSPHATE ION
2	SAH	2	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
3	TTL	2	Ligand/Ion	TRANS-(1S,2S)-2-AMINO-1,2,3,4-TETRAHYDRONAPHTHALEN-1-OL

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	PO4	-1	Ligand/Ion	PHOSPHATE ION
2	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
3	TTL	1	Ligand/Ion	TRANS-(1S,2S)-2-AMINO-1,2,3,4-TETRAHYDRONAPHTHALEN-1-OL

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	PO4	1	Ligand/Ion	PHOSPHATE ION
2	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
3	TTL	1	Ligand/Ion	TRANS-(1S,2S)-2-AMINO-1,2,3,4-TETRAHYDRONAPHTHALEN-1-OL

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN B:122 , GLU B:144 , ARG B:148 , HOH B:1021	BINDING SITE FOR RESIDUE PO4 B 1501
2	AC2	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 , LEU A:103 , ASN A:106 , 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 1301
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 , HIS B:160 , ALA B:181 , PHE B:182 , CYS B:183 , VAL B:187 , HOH B:1018	BINDING SITE FOR RESIDUE SAH B 2301
4	AC4	SOFTWARE	TYR A:35 , ASN A:39 , TYR A:40 , ARG A:44 , LYS A:57 , PHE A:182 , GLU A:219 , MET A:258 , ASP A:267 , HOH A:1049	BINDING SITE FOR RESIDUE TTL A 1401
5	AC5	SOFTWARE	TYR B:35 , ASN B:39 , ARG B:44 , LYS B:57 , PHE B:182 , GLU B:219 , MET B:258 , ASP B:267 , HOH B:1018	BINDING SITE FOR RESIDUE TTL B 2401

Asymmetric Unit

No.	Residues
1	A:48	-	B:139
2	A:139	-	B:48

Asymmetric 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 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)

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	T	98	A
2	UniProt	VAR_036830	R	112	C	PNMT_HUMAN	Polymorphism	34530498	A	R	112	C
3	UniProt	VAR_036831	A	175	T	PNMT_HUMAN	Polymorphism	34341496	A	A	175	T
4	UniProt	VAR_037611	S	188	C	PNMT_HUMAN	Polymorphism	5639	A	S	188	C
5	UniProt	VAR_037612	L	211	H	PNMT_HUMAN	Polymorphism	5640	A	L	211	H
6	UniProt	VAR_037613	L	217	Q	PNMT_HUMAN	Polymorphism	5641	A	L	217	Q
7	UniProt	VAR_037614	R	254	H	PNMT_HUMAN	Polymorphism	5642	A	R	254	H
8	UniProt	VAR_024547	W	276	R	PNMT_HUMAN	Polymorphism	5643	A	W	276	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	B	T	98	A
2	UniProt	VAR_036830	R	112	C	PNMT_HUMAN	Polymorphism	34530498	B	R	112	C
3	UniProt	VAR_036831	A	175	T	PNMT_HUMAN	Polymorphism	34341496	B	A	175	T
4	UniProt	VAR_037611	S	188	C	PNMT_HUMAN	Polymorphism	5639	B	S	188	C
5	UniProt	VAR_037612	L	211	H	PNMT_HUMAN	Polymorphism	5640	B	L	211	H
6	UniProt	VAR_037613	L	217	Q	PNMT_HUMAN	Polymorphism	5641	B	L	217	Q
7	UniProt	VAR_037614	R	254	H	PNMT_HUMAN	Polymorphism	5642	B	R	254	H
8	UniProt	VAR_024547	W	276	R	PNMT_HUMAN	Polymorphism	5643	B	W	276	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:23-280 B:23-281
2	NNMT_PNMT_TEMT	PS01100	NNMT/PNMT/TEMT family of methyltransferases signature.	PNMT_HUMAN	75-91	2	A:75-91 B:75-91

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:23-280 -
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:23-281
2	NNMT_PNMT_TEMT	PS01100	NNMT/PNMT/TEMT family of methyltransferases signature.	PNMT_HUMAN	75-91	1	- B:75-91

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:23-68 B:14-68	46 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:137-281	144 145

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:258
 aligned with PNMT_HUMAN | P11086 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:258
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272        
           PNMT_HUMAN    23 VASAYQRFEPRAYLRNNYAPPRGDLCNPNGVGPWKLRCLAQTFATGEVSGRTLIDIGSGPTVYQLLSACSHFEDITMTDFLEVNRQELGRWLQEEPGAFNWSMYSQHACLIEGKGECWQDKERQLRARVKRVLPIDVHQPQPLGAGSPAPLPADALVSAFCLEAVSPDLASFQRALDHITTLLRPGGHLLLIGALEESWYLAGEARLTVVPVSEEEVREALVRSGYKVRDLRTYIMPAHLQTGVDDVKGVFFAWAQKV 280
               SCOP domains d2an5a_ A: Phenylethanolamine N-methyltransferase, PNMTase                                                                                                                                                                                                         SCOP domains
               CATH domains 2an5A00 A:23-280 Vaccinia Virus protein VP39                                                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhh.hhhhhhhhhh...........hhhhhhhhhhhhhhh.......eeee......hhhhhhhhhh..eeeee..hhhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhheeeee...................eeeeeee.hhhhh..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: A:23-280 UniProt: 23-282                                                                                                                                                                                                               PROSITE (1)
                PROSITE (2) ----------------------------------------------------NNMT_PNMT_TEMT   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: A:23-68 UniProt: 1-68          --------------------------------------------------------------------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)
                 2an5 A  23 VASAYQRFEPRAYLRNNYAPPRGDLCNPNGVGPWKLRCLAQTFATGEVSGRTLIDIGSGPTVYQLLSACSHFEDITMTDFLEVNRQELGRWLQEEPGAFNWSMYSQHACLIEGKGECWQDKERQLRARVKRVLPIDVHQPQPLGAGSPAPLPADALVSAFCLEAVSPDLASFQRALDHITTLLRPGGHLLLIGALEESWYLAGEARLTVVPVSEEEVREALVRSGYKVRDLRTYIMPAHLQTGVDDVKGVFFAWAQKV 280
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272

Chain B from PDB  Type:PROTEIN  Length:268
 aligned with PNMT_HUMAN | P11086 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:268
                                    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 PDSAPGQAAVASAYQRFEPRAYLRNNYAPPRGDLCNPNGVGPWKLRCLAQTFATGEVSGRTLIDIGSGPTVYQLLSACSHFEDITMTDFLEVNRQELGRWLQEEPGAFNWSMYSQHACLIEGKGECWQDKERQLRARVKRVLPIDVHQPQPLGAGSPAPLPADALVSAFCLEAVSPDLASFQRALDHITTLLRPGGHLLLIGALEESWYLAGEARLTVVPVSEEEVREALVRSGYKVRDLRTYIMPAHLQTGVDDVKGVFFAWAQKVG 281
               SCOP domains d2an5b_ B: Phenylethanolamine N-methyltransferase, PNMTase                                                                                                                                                                                                                   SCOP domains
               CATH domains 2an5B00 B:14-281 Vaccinia Virus protein VP39                                                                                                                                                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh.......eeeee.....hhhhh.hhhhh.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:23-281 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:137-281 UniProt: 137-282 [INCOMPLETE]                                                                                           Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------Exon 1.3  PDB: B:68-137 UniProt: 68-137                               ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 2an5 B  14 PDSAPGQAAVASAYQRFEPRAYLRNNYAPPRGDLCNPNGVGPWKLRCLAQTFATGEVSGRTLIDIGSGPTVYQLLSACSHFEDITMTDFLEVNRQELGRWLQEEPGAFNWSMYSQHACLIEGKGECWQDKERQLRARVKRVLPIDVHQPQPLGAGSPAPLPADALVSAFCLEAVSPDLASFQRALDHITTLLRPGGHLLLIGALEESWYLAGEARLTVVPVSEEEVREALVRSGYKVRDLRTYIMPAHLQTGVDDVKGVFFAWAQKVG 281
                                    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)
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	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	2an5A00	A:23-280
1b	2an5B00	B:14-281

(no "Pfam Domain" information available for 2AN5)

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.

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	2an5
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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 (3, 5)

Sites (5, 5)

SS Bonds (2, 2)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (8, 16)

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Exons (3, 6)

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