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(-) Description

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

(-) Compounds

Molecule 1 - PHENYLETHANOLAMINE N-METHYLTRANSFERASE
    ChainsA, B
    EC Number2.1.1.28
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET17 PNMT-HIS
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GenePNMT, PENT
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPNMTASE, NORADRENALINE N-METHYLTRANSFERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1ADE2Ligand/IonADENINE
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR 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:187BINDING SITE FOR RESIDUE SAH A 2001
2AC2SOFTWARETYR 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:2197BINDING SITE FOR RESIDUE SAH B 2002
3AC3SOFTWARETYR 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:2237BINDING SITE FOR RESIDUE ADE A 290
4AC4SOFTWARETYR 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:2245BINDING SITE FOR RESIDUE ADE B 290

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:48 -B:139
2A:139 -B:48

(-) Cis Peptide Bonds  (4, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (8, 16)

Asymmetric/Biological Unit (8, 16)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_036829T98APNMT_HUMANPolymorphism36060376A/BT98A
2UniProtVAR_036830R112CPNMT_HUMANPolymorphism34530498A/BR112C
3UniProtVAR_036831A175TPNMT_HUMANPolymorphism34341496A/BA175T
4UniProtVAR_037611S188CPNMT_HUMANPolymorphism5639A/BS188C
5UniProtVAR_037612L211HPNMT_HUMANPolymorphism5640A/BL211H
6UniProtVAR_037613L217QPNMT_HUMANPolymorphism5641A/BL217Q
7UniProtVAR_037614R254HPNMT_HUMANPolymorphism5642A/BR254H
8UniProtVAR_024547W276RPNMT_HUMANPolymorphism5643A/BW276R

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

(-) PROSITE Motifs  (2, 3)

Asymmetric/Biological Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_MT_NNMT_PNMT_TEMTPS51681 SAM-dependent methyltransferase NNMT/PNMT/TEMT-type profile.PNMT_HUMAN23-282  1B:23-281
2NNMT_PNMT_TEMTPS01100 NNMT/PNMT/TEMT family of methyltransferases signature.PNMT_HUMAN75-91
 
  2A:75-91
B:75-91

(-) Exons   (3, 6)

Asymmetric/Biological Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2ENST000002695822ENSE00000950701chr17:37824507-37824930424PNMT_HUMAN1-68682A:24-68
B:14-68
45
55
1.3ENST000002695823ENSE00001682624chr17:37825882-37826089208PNMT_HUMAN68-137702A:68-137
B:68-137
70
70
1.4bENST000002695824bENSE00000950703chr17:37826204-37826728525PNMT_HUMAN137-2821462A:137-280
B:137-281
144
145

(-) Sequences/Alignments

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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (7, 7)

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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PNMT_HUMAN | P110861hnn 1n7i 1n7j 1yz3 2an3 2an4 2an5 2g70 2g71 2g72 2g8n 2obf 2ony 2onz 2opb 3hca 3hcb 3hcc 3hcd 3hce 3hcf 3kpj 3kpu 3kpw 3kpy 3kqm 3kqo 3kqp 3kqq 3kqs 3kqt 3kqv 3kqw 3kqy 3kr0 3kr1 3kr2 4dm3 4mik 4mq4

(-) Related Entries Specified in the PDB File

3kpj 3kpu 3kpw 3kpy 3kqm 3kqo 3kqp 3kqq 3kqs 3kqt 3kqv 3kqw 3kqy 3kr0 3kr1 3kr2