3KPV - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HPNMT IN COMPLEX ADOHCY AND ADENINE

Authors :   N. Drinkwater, J. L. Martin

Date :   17 Nov 09 (Deposition) - 29 Sep 10 (Release) - 29 Sep 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Methyltransferase, Fragment Screening, Catecholamine Biosynthesis, S- Adenosyl-L-Methionine, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Drinkwater, H. Vu, K. M. Lovell, K. R. Criscione, B. M. Collins, T. E. Prisinzano, S. A. Poulsen, M. J. Mcleish, G. L. Grunewald, J. L. Martin
Fragment-Based Screening By X-Ray Crystallography, Ms And Isothermal Titration Calorimetry To Identify Pnmt (Phenylethanolamine N-Methyltransferase) Inhibitors.
Biochem. J. V. 431 51 2010
PubMed-ID: 20642456 | Reference-DOI: 10.1042/BJ20100651

Molecule 1 - PHENYLETHANOLAMINE N-METHYLTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.1.1.28
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET17 PNMT-HIS
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PNMT, PENT
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PNMTASE, NORADRENALINE N-METHYLTRANSFERASE

		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	ADE	2	Ligand/Ion	ADENINE
2	SAH	2	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 , LEU A:103 , 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 2001
2	AC2	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 , ASP B:158 , VAL B:159 , HIS B:160 , ALA B:181 , PHE B:182 , CYS B:183 , VAL B:187 , HOH B:2015 , HOH B:2101 , HOH B:2197	BINDING SITE FOR RESIDUE SAH B 2002
3	AC3	SOFTWARE	TYR A:35 , ASN A:39 , TYR A:40 , ARG A:44 , PHE A:182 , GLU A:219 , TYR A:222 , ASP A:267 , HOH A:2232 , HOH A:2233 , HOH A:2235 , HOH A:2237	BINDING SITE FOR RESIDUE ADE A 290
4	AC4	SOFTWARE	TYR B:35 , ASN B:39 , TYR B:40 , ARG B:44 , PHE B:182 , GLU B:219 , TYR B:222 , ASP B:267 , HOH B:2101 , HOH B:2244 , HOH B:2245	BINDING SITE FOR RESIDUE ADE B 290

Asymmetric/Biological Unit

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

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, 3)

	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	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:24-68 B:14-68	45 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/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:257
 aligned with PNMT_HUMAN | P11086 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:257
                                    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    24 ASAYQRFEPRAYLRNNYAPPRGDLCNPNGVGPWKLRCLAQTFATGEVSGRTLIDIGSGPTVYQLLSACSHFEDITMTDFLEVNRQELGRWLQEEPGAFNWSMYSQHACLIEGKGECWQDKERQLRARVKRVLPIDVHQPQPLGAGSPAPLPADALVSAFCLEAVSPDLASFQRALDHITTLLRPGGHLLLIGALEESWYLAGEARLTVVPVSEEEVREALVRSGYKVRDLRTYIMPAHLQTGVDDVKGVFFAWAQKV 280
               SCOP domains d3kpva_ A: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.hhhhhhhhhhh..........hhhhhhhhhhhhhhhh......eeeee.....hhhhhhhhhhh.eeeee..hhhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhhhheeeee...................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: - UniProt: 23-282                                                                                                                                                                                                                     PROSITE (1)
                PROSITE (2) ---------------------------------------------------NNMT_PNMT_TEMT   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: A:24-68 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)
                 3kpv A  24 ASAYQRFEPRAYLRNNYAPPRGDLCNPNGVGPWKLRCLAQTFATGEVSGRTLIDIGSGPTVYQLLSACSHFEDITMTDFLEVNRQELGRWLQEEPGAFNWSMYSQHACLIEGKGECWQDKERQLRARVKRVLPIDVHQPQPLGAGSPAPLPADALVSAFCLEAVSPDLASFQRALDHITTLLRPGGHLLLIGALEESWYLAGEARLTVVPVSEEEVREALVRSGYKVRDLRTYIMPAHLQTGVDDVKGVFFAWAQKV 280
                                    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

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 d3kpvb_ B: automated matches                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) NNMT_PNMT_TEMT-3kpvB01 B:14-279                                                                                                                                                                                                                                           -- Pfam domains (1)
           Pfam domains (2) NNMT_PNMT_TEMT-3kpvB02 B:14-279                                                                                                                                                                                                                                           -- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhh..hhhhhhhhhhh..........hhhhhhhhhhhhhhhh......eeee......hhhhhhhhhhh.eeeee..hhhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhhhheeeee...................eeeeeee.hhhhhh.hhhhhhhhhhhhhh.eeeeeeeeeeeee...eeee..eeee....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: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)
                 3kpv 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)
		→ 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	d3kpva_	A:
1b	d3kpvb_	B:

(no "CATH Domain" information available for 3KPV)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: NNMT_PNMT_TEMT (24)

Homo sapiens (Human) (24)

1a	NNMT_PNMT_TEMT-3kpvB01	B:14-279
1b	NNMT_PNMT_TEMT-3kpvB02	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
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		ADE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SAH	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	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 ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3kpv
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	PNMT_HUMAN \| P11086
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	2.1.1.28
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	PNMT_HUMAN \| P11086
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (2, 2)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (8, 16)

PROSITE Motifs (2, 3)

Exons (3, 6)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (7, 7)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File