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(-) Description

Title :  STRUCTURE OF PNMT WITH S-ADENOSYL-L-HOMOCYSTEINE AND THE SEMI-RIGID ANALOGUE ACCEPTOR SUBSTRATE CIS-(1R,2S)-2-AMINO-1-TETRALOL.
 
Authors :  C. L. Gee, J. D. A. Tyndall, G. L. Grunewald, Q. Wu, M. J. Mcleish, J. L. Mar
Date :  11 Aug 05  (Deposition) - 14 Mar 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Methyltransferase, Substrate Structure, S-Adenosyl-L-Methionine, Adrenaline Synthesis, Transferase (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

(-) Compounds

Molecule 1 - PHENYLETHANOLAMINE N-METHYLTRANSFERASE
    ChainsA, B
    EC Number2.1.1.28
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET17PNMT-HIS
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GenePNMT
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPNMTASE, NORADRENALINE N-METHYLTRANSFERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B
Biological Unit 3 (1x)AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1CTL2Ligand/IonCIS-(1R,2S)-2-AMINO-1,2,3,4-TETRAHYDRONAPHTHALEN-1-OL
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CTL1Ligand/IonCIS-(1R,2S)-2-AMINO-1,2,3,4-TETRAHYDRONAPHTHALEN-1-OL
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1CTL1Ligand/IonCIS-(1R,2S)-2-AMINO-1,2,3,4-TETRAHYDRONAPHTHALEN-1-OL
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 3 (2, 4)
No.NameCountTypeFull Name
1CTL2Ligand/IonCIS-(1R,2S)-2-AMINO-1,2,3,4-TETRAHYDRONAPHTHALEN-1-OL
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 , GLN A:86 , 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:187BINDING SITE FOR RESIDUE SAH A 2001
2AC2SOFTWARETYR 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 , HIS B:660 , ALA B:681 , PHE B:682 , CYS B:683 , VAL B:687 , HOH B:1053 , HOH B:1071BINDING SITE FOR RESIDUE SAH B 2002
3AC3SOFTWARETYR A:35 , ARG A:44 , PHE A:182 , GLU A:219 , TYR A:222 , MET A:258 , ASP A:267 , HOH A:1044 , HOH A:1061BINDING SITE FOR RESIDUE CTL A 3001
4AC4SOFTWARETYR B:535 , ASN B:539 , ARG B:544 , PHE B:682 , GLU B:719 , TYR B:722 , MET B:758 , ASP B:767 , HOH B:1014 , HOH B:1058 , HOH B:1071BINDING SITE FOR RESIDUE CTL B 3002

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:48 -B:639
2A:139 -B:548

(-) Cis Peptide Bonds  (4, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (8, 16)

Asymmetric Unit (8, 16)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_036829T98APNMT_HUMANPolymorphism36060376A
B
T98
598
A
2UniProtVAR_036830R112CPNMT_HUMANPolymorphism34530498A
B
R112
612
C
3UniProtVAR_036831A175TPNMT_HUMANPolymorphism34341496A
B
A175
675
T
4UniProtVAR_037611S188CPNMT_HUMANPolymorphism5639A
B
S188
688
C
5UniProtVAR_037612L211HPNMT_HUMANPolymorphism5640A
B
L211
711
H
6UniProtVAR_037613L217QPNMT_HUMANPolymorphism5641A
B
L217
717
Q
7UniProtVAR_037614R254HPNMT_HUMANPolymorphism5642A
B
R254
754
H
8UniProtVAR_024547W276RPNMT_HUMANPolymorphism5643A
B
W276
776
R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (8, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_036829T98APNMT_HUMANPolymorphism36060376A
A
T98
598
A
2UniProtVAR_036830R112CPNMT_HUMANPolymorphism34530498A
A
R112
612
C
3UniProtVAR_036831A175TPNMT_HUMANPolymorphism34341496A
A
A175
675
T
4UniProtVAR_037611S188CPNMT_HUMANPolymorphism5639A
A
S188
688
C
5UniProtVAR_037612L211HPNMT_HUMANPolymorphism5640A
A
L211
711
H
6UniProtVAR_037613L217QPNMT_HUMANPolymorphism5641A
A
L217
717
Q
7UniProtVAR_037614R254HPNMT_HUMANPolymorphism5642A
A
R254
754
H
8UniProtVAR_024547W276RPNMT_HUMANPolymorphism5643A
A
W276
776
R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (8, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_036829T98APNMT_HUMANPolymorphism36060376A
B
T98
598
A
2UniProtVAR_036830R112CPNMT_HUMANPolymorphism34530498A
B
R112
612
C
3UniProtVAR_036831A175TPNMT_HUMANPolymorphism34341496A
B
A175
675
T
4UniProtVAR_037611S188CPNMT_HUMANPolymorphism5639A
B
S188
688
C
5UniProtVAR_037612L211HPNMT_HUMANPolymorphism5640A
B
L211
711
H
6UniProtVAR_037613L217QPNMT_HUMANPolymorphism5641A
B
L217
717
Q
7UniProtVAR_037614R254HPNMT_HUMANPolymorphism5642A
B
R254
754
H
8UniProtVAR_024547W276RPNMT_HUMANPolymorphism5643A
B
W276
776
R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (8, 16)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_036829T98APNMT_HUMANPolymorphism36060376A
A/B
T98
598
A
2UniProtVAR_036830R112CPNMT_HUMANPolymorphism34530498A
A/B
R112
612
C
3UniProtVAR_036831A175TPNMT_HUMANPolymorphism34341496A
A/B
A175
675
T
4UniProtVAR_037611S188CPNMT_HUMANPolymorphism5639A
A/B
S188
688
C
5UniProtVAR_037612L211HPNMT_HUMANPolymorphism5640A
A/B
L211
711
H
6UniProtVAR_037613L217QPNMT_HUMANPolymorphism5641A
A/B
L217
717
Q
7UniProtVAR_037614R254HPNMT_HUMANPolymorphism5642A
A/B
R254
754
H
8UniProtVAR_024547W276RPNMT_HUMANPolymorphism5643A
A/B
W276
776
R

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

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_MT_NNMT_PNMT_TEMTPS51681 SAM-dependent methyltransferase NNMT/PNMT/TEMT-type profile.PNMT_HUMAN23-282
 
  2A:23-280
B:523-781
2NNMT_PNMT_TEMTPS01100 NNMT/PNMT/TEMT family of methyltransferases signature.PNMT_HUMAN75-91
 
  2A:75-91
B:575-591
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_MT_NNMT_PNMT_TEMTPS51681 SAM-dependent methyltransferase NNMT/PNMT/TEMT-type profile.PNMT_HUMAN23-282
 
  1A:23-280
-
2NNMT_PNMT_TEMTPS01100 NNMT/PNMT/TEMT family of methyltransferases signature.PNMT_HUMAN75-91
 
  1A:75-91
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_MT_NNMT_PNMT_TEMTPS51681 SAM-dependent methyltransferase NNMT/PNMT/TEMT-type profile.PNMT_HUMAN23-282
 
  1-
B:523-781
2NNMT_PNMT_TEMTPS01100 NNMT/PNMT/TEMT family of methyltransferases signature.PNMT_HUMAN75-91
 
  1-
B:575-591
Biological Unit 3 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_MT_NNMT_PNMT_TEMTPS51681 SAM-dependent methyltransferase NNMT/PNMT/TEMT-type profile.PNMT_HUMAN23-282
 
  2A:23-280
B:523-781
2NNMT_PNMT_TEMTPS01100 NNMT/PNMT/TEMT family of methyltransferases signature.PNMT_HUMAN75-91
 
  2A:75-91
B:575-591

(-) Exons   (3, 6)

Asymmetric Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2ENST000002695822ENSE00000950701chr17:37824507-37824930424PNMT_HUMAN1-68682A:23-68
B:513-568
46
56
1.3ENST000002695823ENSE00001682624chr17:37825882-37826089208PNMT_HUMAN68-137702A:68-137
B:568-637
70
70
1.4bENST000002695824bENSE00000950703chr17:37826204-37826728525PNMT_HUMAN137-2821462A:137-280
B:637-781
144
145

(-) Sequences/Alignments

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 d2an3a_ A: Phenylethanolamine N-methyltransferase, PNMTase                                                                                                                                                                                                         SCOP domains
               CATH domains 2an3A00 A:23-280 Vaccinia Virus protein VP39                                                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh......eeeee.....hhhhhhhhhhh.eeeeee.hhhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhhhheeeeee..................eeeeeee........hhhhhhhhhhhhhh.eeeeeeeeeeeee...eeee..eeee....hhhhhhhhhhhh.eeeeeeeeee.hhhhh.......eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ 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)
                 2an3 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:269
 aligned with PNMT_HUMAN | P11086 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:269
                                    22        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    13 APDSAPGQAAVASAYQRFEPRAYLRNNYAPPRGDLCNPNGVGPWKLRCLAQTFATGEVSGRTLIDIGSGPTVYQLLSACSHFEDITMTDFLEVNRQELGRWLQEEPGAFNWSMYSQHACLIEGKGECWQDKERQLRARVKRVLPIDVHQPQPLGAGSPAPLPADALVSAFCLEAVSPDLASFQRALDHITTLLRPGGHLLLIGALEESWYLAGEARLTVVPVSEEEVREALVRSGYKVRDLRTYIMPAHLQTGVDDVKGVFFAWAQKVG 281
               SCOP domains d2an3b_ B: Phenylethanolamine N-methyltransferase, PNMTase                                                                                                                                                                                                                    SCOP domains
               CATH domains 2an3B00 B:513-781 Vaccinia Virus protein VP39                                                                                                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh..hhhhhhhhhhh..........hhhhhhhhhhhhhhh.......eeeee.....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:523-781 UniProt: 23-282                                                                                                                                                                                                               PROSITE (1)
                PROSITE (2) --------------------------------------------------------------NNMT_PNMT_TEMT   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: B:513-568 UniProt: 1-68 [INCOMPLETE]     --------------------------------------------------------------------Exon 1.4b  PDB: B:637-781 UniProt: 137-282 [INCOMPLETE]                                                                                           Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------Exon 1.3  PDB: B:568-637 UniProt: 68-137                              ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 2an3 B 513 APDSAPGQAAVASAYQRFEPRAYLRNNYAPPRGDLCNPNGVGPWKLRCLAQTFATGEVSGRTLIDIGSGPTVYQLLSACSHFEDITMTDFLEVNRQELGRWLQEEPGAFNWSMYSQHACLIEGKGECWQDKERQLRARVKRVLPIDVHQPQPLGAGSPAPLPADALVSAFCLEAVSPDLASFQRALDHITTLLRPGGHLLLIGALEESWYLAGEARLTVVPVSEEEVREALVRSGYKVRDLRTYIMPAHLQTGVDDVKGVFFAWAQKVG 781
                                   522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772         

   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 Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2AN3)

(-) Gene Ontology  (7, 7)

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

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

(-) Related Entries Specified in the PDB File

1hnn 1n7i 1n7j 1yz3 2an4 2an5