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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF HUMAN HISTAMINE METHYLTRANSFERASE (ILE105 POLYMORPHIC VARIANT) COMPLEXED WITH ADOHCY AND ANTIMALARIAL DRUG QUINACRINE
 
Authors :  J. R. Horton, K. Sawada, M. Nishibori, X. Zhang, X. Cheng
Date :  06 Aug 01  (Deposition) - 06 Aug 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.91
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Classic Methyltransferase Fold, Protein-Substrate-Cofactor Complex, Polymorphic Variant (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. R. Horton, K. Sawada, M. Nishibori, X. Zhang, X. Cheng
Two Polymorphic Forms Of Human Histamine Methyltransferase: Structural, Thermal, And Kinetic Comparisons.
Structure V. 9 837 2001
PubMed-ID: 11566133  |  Reference-DOI: 10.1016/S0969-2126(01)00643-8
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HISTAMINE N-METHYLTRANSFERASE
    ChainsA, B
    EC Number2.1.1.8
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-4T-3
    Expression System StrainDH5A
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneHNMT
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHNMT, HMT

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1QUN1Ligand/IonQUINACRINE
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
3UNX7Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1QUN1Ligand/IonQUINACRINE
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
3UNX-1Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1QUN-1Ligand/IonQUINACRINE
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
3UNX7Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:19 , HIS A:29 , GLY A:60 , GLY A:62 , GLU A:89 , PRO A:90 , SER A:91 , GLN A:94 , THR A:119 , SER A:120 , ILE A:142 , GLN A:143 , MET A:144 , TYR A:147 , QUN A:500 , HOH A:533 , HOH A:719 , HOH A:720 , HOH A:721 , HOH A:722 , HOH A:723 , HOH A:724BINDING SITE FOR RESIDUE SAH A 400
02AC2SOFTWAREHIS B:29 , GLY B:60 , GLY B:62 , ILE B:66 , GLU B:89 , PRO B:90 , SER B:91 , GLN B:94 , THR B:119 , SER B:120 , ILE B:142 , GLN B:143 , MET B:144 , TYR B:147 , HOH B:556 , HOH B:557 , HOH B:558BINDING SITE FOR RESIDUE SAH B 401
03AC3SOFTWARETYR A:15 , VAL A:16 , TYR A:146 , TYR A:147 , TRP A:179 , TRP A:183 , ASP A:193 , LEU A:195 , CYS A:196 , PHE A:243 , GLU A:246 , SAH A:400 , HOH A:725 , HOH A:726BINDING SITE FOR RESIDUE QUN A 500
04AC4SOFTWAREUNX B:403BINDING SITE FOR RESIDUE UNX B 402
05AC5SOFTWAREUNX B:402BINDING SITE FOR RESIDUE UNX B 403
06AC6SOFTWAREUNX B:376 , UNX B:405BINDING SITE FOR RESIDUE UNX B 404
07AC7SOFTWAREUNX B:404 , UNX B:406BINDING SITE FOR RESIDUE UNX B 405
08AC8SOFTWAREUNX B:405 , UNX B:407BINDING SITE FOR RESIDUE UNX B 406
09AC9SOFTWAREUNX B:404BINDING SITE FOR RESIDUE UNX B 376
10BC1SOFTWAREUNX B:406BINDING SITE FOR RESIDUE UNX B 407

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1JQE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 6)

Asymmetric Unit (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_076312G60DHNMT_HUMANDisease (MRT51)758252808A/BG60D
2UniProtVAR_010252T105IHNMT_HUMANPolymorphism1801105A/BI105I
3UniProtVAR_076313L208PHNMT_HUMANDisease (MRT51)745756308A/BL208P

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_076312G60DHNMT_HUMANDisease (MRT51)758252808AG60D
2UniProtVAR_010252T105IHNMT_HUMANPolymorphism1801105AI105I
3UniProtVAR_076313L208PHNMT_HUMANDisease (MRT51)745756308AL208P

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_076312G60DHNMT_HUMANDisease (MRT51)758252808BG60D
2UniProtVAR_010252T105IHNMT_HUMANPolymorphism1801105BI105I
3UniProtVAR_076313L208PHNMT_HUMANDisease (MRT51)745756308BL208P

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1JQE)

(-) Exons   (6, 12)

Asymmetric Unit (6, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000002800972aENSE00001824410chr2:138721880-138722198319HNMT_HUMAN1-46462A:13-46
B:13-46
34
34
1.5ENST000002800975ENSE00000995392chr2:138727735-13872778753HNMT_HUMAN46-64192A:46-64
B:46-64
19
19
1.9ENST000002800979ENSE00000995399chr2:138758488-138758595108HNMT_HUMAN64-100372A:64-100
B:64-100
37
37
1.10ENST0000028009710ENSE00000995393chr2:138759634-138759764131HNMT_HUMAN100-143442A:100-143
B:100-143
44
44
1.12ENST0000028009712ENSE00000995397chr2:138762702-13876279594HNMT_HUMAN144-175322A:144-175
B:144-175
32
32
1.13cENST0000028009713cENSE00001071685chr2:138771345-1387739302586HNMT_HUMAN175-2921182A:175-292
B:175-292
118
118

(-) 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:280
 aligned with HNMT_HUMAN | P50135 from UniProtKB/Swiss-Prot  Length:292

    Alignment length:280
                                    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       282       292
           HNMT_HUMAN    13 GKYVESFRRFLNHSTEHQCMQEFMDKKLPGIIGRIGDTKSEIKILSIGGGAGEIDLQILSKVQAQYPGVCINNEVVEPSAEQIAKYKELVAKTSNLENVKFAWHKETSSEYQSRMLEKKELQKWDFIHMIQMLYYVKDIPATLKFFHSLLGTNAKMLIIVVSGSSGWDKLWKKYGSRFPQDDLCQYITSDDLTQMLDNLGLKYECYDLLSTMDISDCFIDGNENGDLLWDFLTETCNFNATAPPDLRAELGKDLQEPEFSAKKEGKVLFNNTLSFIVIEA 292
               SCOP domains d1jqea_ A: Histamine methyltransferase                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1jqeA00 A:13-292 Vaccinia Virus protein VP39                                                                                                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh........eeeeeee....hhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhh.......eeeeee..hhhhhhhhhh.......eeeeeee.hhhhh.hhhhhhhhhhhheeeeeeeeeeee...hhhhhhhhhhhhhh.........hhhhhhhhhhhhh..eeeeee..eee.hhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.....eeee..eeeee..eeeeeee. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------D--------------------------------------------I------------------------------------------------------------------------------------------------------P------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: A:13-46           -----------------------------------------------------Exon 1.10  PDB: A:100-143 UniProt: 100-143  Exon 1.12  PDB: A:144-175       --------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------Exon 1.5           --------------------------------------------------------------------------------------------------------------Exon 1.13c  PDB: A:175-292 UniProt: 175-292                                                                            Transcript 1 (2)
           Transcript 1 (3) ---------------------------------------------------Exon 1.9  PDB: A:64-100              ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (3)
                 1jqe A  13 GKYVESFRRFLNHSTEHQCMQEFMDKKLPGIIGRIGDTKSEIKILSIGGGAGEIDLQILSKVQAQYPGVCINNEVVEPSAEQIAKYKELVAKISNLENVKFAWHKETSSEYQSRMLEKKELQKWDFIHMIQMLYYVKDIPATLKFFHSLLGTNAKMLIIVVSGSSGWDKLWKKYGSRFPQDDLCQYITSDDLTQMLDNLGLKYECYDLLSTMDISDCFIDGNENGDLLWDFLTETCNFNATAPPDLRAELGKDLQEPEFSAKKEGKVLFNNTLSFIVIEA 292
                                    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       282       292

Chain B from PDB  Type:PROTEIN  Length:280
 aligned with HNMT_HUMAN | P50135 from UniProtKB/Swiss-Prot  Length:292

    Alignment length:280
                                    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       282       292
           HNMT_HUMAN    13 GKYVESFRRFLNHSTEHQCMQEFMDKKLPGIIGRIGDTKSEIKILSIGGGAGEIDLQILSKVQAQYPGVCINNEVVEPSAEQIAKYKELVAKTSNLENVKFAWHKETSSEYQSRMLEKKELQKWDFIHMIQMLYYVKDIPATLKFFHSLLGTNAKMLIIVVSGSSGWDKLWKKYGSRFPQDDLCQYITSDDLTQMLDNLGLKYECYDLLSTMDISDCFIDGNENGDLLWDFLTETCNFNATAPPDLRAELGKDLQEPEFSAKKEGKVLFNNTLSFIVIEA 292
               SCOP domains d1jqeb_ B: Histamine methyltransferase                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1jqeB00 B:13-292 Vaccinia Virus protein VP39                                                                                                                                                                                                                                             CATH domains
           Pfam domains (1) ----------------Methyltransf_23-1jqeB01 B:29-217                                                                                                                                                             --------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----------------Methyltransf_23-1jqeB02 B:29-217                                                                                                                                                             --------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.......eeeeeee....hhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhh......eeeeeee.hhhhh.hhhhhhhhhhhheeeeeeeeeeee...hhhhhhhhhhh............hhhhhhhhhhhhh..eeeeee..eee.hhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.....eeee..eeeee..eeeeeee. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------D--------------------------------------------I------------------------------------------------------------------------------------------------------P------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: B:13-46           -----------------------------------------------------Exon 1.10  PDB: B:100-143 UniProt: 100-143  Exon 1.12  PDB: B:144-175       --------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------Exon 1.5           --------------------------------------------------------------------------------------------------------------Exon 1.13c  PDB: B:175-292 UniProt: 175-292                                                                            Transcript 1 (2)
           Transcript 1 (3) ---------------------------------------------------Exon 1.9  PDB: B:64-100              ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (3)
                 1jqe B  13 GKYVESFRRFLNHSTEHQCMQEFMDKKLPGIIGRIGDTKSEIKILSIGGGAGEIDLQILSKVQAQYPGVCINNEVVEPSAEQIAKYKELVAKISNLENVKFAWHKETSSEYQSRMLEKKELQKWDFIHMIQMLYYVKDIPATLKFFHSLLGTNAKMLIIVVSGSSGWDKLWKKYGSRFPQDDLCQYITSDDLTQMLDNLGLKYECYDLLSTMDISDCFIDGNENGDLLWDFLTETCNFNATAPPDLRAELGKDLQEPEFSAKKEGKVLFNNTLSFIVIEA 292
                                    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       282       292

   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  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (HNMT_HUMAN | P50135)
molecular function
    GO:0008170    N-methyltransferase activity    Catalysis of the transfer of a methyl group to the nitrogen atom of an acceptor molecule.
    GO:0046539    histamine N-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine(1+) + histamine = N(tau)-methylhistamine + S-adenosyl-L-homocysteine + H(+).
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    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:0007420    brain development    The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
    GO:0006548    histidine catabolic process    The chemical reactions and pathways resulting in the breakdown of histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid.
    GO:0006972    hyperosmotic response    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of detection of, or exposure to, a hyperosmotic environment, i.e. an environment with a higher concentration of solutes than the organism or cell.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:1903955    positive regulation of protein targeting to mitochondrion    Any process that activates or increases the frequency, rate or extent of protein targeting to mitochondrion.
    GO:0007585    respiratory gaseous exchange    The process of gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms.
    GO:0014075    response to amine    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amine stimulus. An amine is a compound formally derived from ammonia by replacing one, two or three hydrogen atoms by hydrocarbyl groups.
    GO:0042220    response to cocaine    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cocaine stimulus. Cocaine is a crystalline alkaloid obtained from the leaves of the coca plant.
    GO:0051384    response to glucocorticoid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucocorticoid stimulus. Glucocorticoids are hormonal C21 corticosteroids synthesized from cholesterol with the ability to bind with the cortisol receptor and trigger similar effects. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects.
    GO:0035902    response to immobilization stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of being rendered immobile.
    GO:0070555    response to interleukin-1    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interleukin-1 stimulus.
    GO:0002347    response to tumor cell    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a tumor cell.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HNMT_HUMAN | P501351icz 1jqd 2aot 2aou 2aov 2aow 2aox

(-) Related Entries Specified in the PDB File

1jqd 1JQD CONTAINS THE THR105 POLYMORPHIC VARIANT COMPLEXED WITH HISTAMINE INSTEAD OF QUINACRINE