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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN COMT COMPLEXED WITH SAM AND 3,5-DINITROCATECHOL
 
Authors :  E. Tsuji
Date :  26 Sep 09  (Deposition) - 15 Sep 10  (Release) - 15 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Comt, Alternative Initiation, Catecholamine Metabolism, Magnesium, Methyltransferase, Neurotransmitter Degradation, S-Adenosyl-L- Methionine, Transferase, Cell Membrane, Membrane, Metal-Binding, Phosphoprotein, Signal-Anchor, Transmembrane (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Nonaka, T. Momose, T. Ozawa, M. Ozawa, M. Nakatsu, E. Tsuji, K. Okazaki, Y. Takase, T. Kiyotani
Hit To Lead: Comprehensive Strategy Of De Novo Scaffold Generation By Fbdd. Part 1: In Silico Fragments Linking And Verification Of Spatial Proximity Using Inter Ligand Noe Approachs
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CATECHOL O-METHYLTRANSFERASE
    ChainsA
    EC Number2.1.1.6
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-2T
    Expression System StrainBL21 CODON PLUS (DE3) RP
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 51-264
    GeneCOMT
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1DNC1Ligand/Ion3,5-DINITROCATECHOL
2MG1Ligand/IonMAGNESIUM ION
3SAM1Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:141 , ASP A:169 , ASN A:170 , SAM A:216 , DNC A:217BINDING SITE FOR RESIDUE MG A 215
2AC2SOFTWAREMET A:40 , VAL A:42 , GLU A:64 , GLY A:66 , ALA A:67 , TYR A:68 , TYR A:71 , SER A:72 , ILE A:89 , GLU A:90 , ILE A:91 , GLY A:117 , SER A:119 , GLN A:120 , ASP A:141 , HIS A:142 , TRP A:143 , ARG A:146 , MG A:215 , DNC A:217 , HOH A:251BINDING SITE FOR RESIDUE SAM A 216
3AC3SOFTWARETRP A:38 , ASP A:141 , HIS A:142 , TRP A:143 , LYS A:144 , ASP A:169 , ASN A:170 , PRO A:174 , GLU A:199 , MG A:215 , SAM A:216BINDING SITE FOR RESIDUE DNC A 217

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3A7E)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Cys A:173 -Pro A:174

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

Asymmetric/Biological Unit (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_013926A72SCOMT_HUMANPolymorphism6267AA22S
2UniProtVAR_020274A102TCOMT_HUMANPolymorphism5031015AA52T
3UniProtVAR_020275A146VCOMT_HUMANPolymorphism4986871AA96V
4UniProtVAR_005139V158MCOMT_HUMANPolymorphism4680AV108M

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3A7E)

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003616821aENSE00001871649chr22:19929130-19929420291COMT_HUMAN-00--
1.5bENST000003616825bENSE00001056469chr22:19948722-1994881291COMT_HUMAN-00--
1.7bENST000003616827bENSE00001656924chr22:19950050-19950338289COMT_HUMAN1-97971A:3-4745
1.9aENST000003616829aENSE00001295143chr22:19951089-19951282194COMT_HUMAN97-161651A:47-11165
1.10bENST0000036168210bENSE00001316383chr22:19951691-19951822132COMT_HUMAN162-205441A:112-15544
1.12gENST0000036168212gENSE00001297813chr22:19956059-199574981440COMT_HUMAN206-271661A:156-21459

(-) 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:212
 aligned with COMT_HUMAN | P21964 from UniProtKB/Swiss-Prot  Length:271

    Alignment length:212
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262  
           COMT_HUMAN    53 DTKEQRILNHVLQHAEPGNAQSVLEAIDTYCEQKEWAMNVGDKKGKIVDAVIQEHQPSVLLELGAYCGYSAVRMARLLSPGARLITIEINPDCAAITQRMVDFAGVKDKVTLVVGASQDIIPQLKKKYDVDTLDMVFLDHWKDRYLPDTLLLEECGLLRKGTVLLADNVICPGAPDFLAHVRGSSCFECTHYQSFLEYREVVDGLEKAIYKG 264
               SCOP domains d3a7ea_ A: automated matches                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh..eeeee....hhhhhhhhh......eeeeee.hhhhhhhhhhhhhhhh....eeeee.hhhhhh.hhhhhh....eeeeee..hhhhhhhhhhhhhhh..eeeeeeeee.......hhhhhhhhhhh..eeeeeeeee......eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------S-----------------------------T-------------------------------------------V-----------M---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.7b  PDB: A:3-47 UniProt: 1-97         ----------------------------------------------------------------Exon 1.10b  PDB: A:112-155 UniProt: 162-205 Exon 1.12g  PDB: A:156-214 UniProt: 206-271 [INCOMPLETE]    Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------Exon 1.9a  PDB: A:47-111 UniProt: 97-161                         ------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3a7e A   3 DTKEQRILNHVLQHAEPGNAQSVLEAIDTYCEQKEWAMNVGDKKGKIVDAVIQEHQPSVLLELGAYCGYSAVRMARLLSPGARLITIEINPDCAAITQRMVDFAGVKDKVTLVVGASQDIIPQLKKKYDVDTLDMVFLDHWKDRYLPDTLLLEECGLLRKGTVLLADNVICPGAPDFLAHVRGSSCFECTHYQSFLEYREVVDGLEKAIYKG 214
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212  

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3A7E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3A7E)

(-) Gene Ontology  (41, 41)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (COMT_HUMAN | P21964)
molecular function
    GO:0008171    O-methyltransferase activity    Catalysis of the transfer of a methyl group to the oxygen atom of an acceptor molecule.
    GO:0016206    catechol O-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + a catechol = S-adenosyl-L-homocysteine + a guaiacol.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0009712    catechol-containing compound metabolic process    The chemical reactions and pathways involving a compound containing a pyrocatechol (1,2-benzenediol) nucleus or substituent.
    GO:0006584    catecholamine metabolic process    The chemical reactions and pathways involving 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:0016036    cellular response to phosphate starvation    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of phosphate.
    GO:0032502    developmental process    A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition.
    GO:0042420    dopamine catabolic process    The chemical reactions and pathways resulting in the breakdown of dopamine, a catecholamine neurotransmitter and a metabolic precursor of noradrenaline and adrenaline.
    GO:0042417    dopamine metabolic process    The chemical reactions and pathways involving dopamine, a catecholamine neurotransmitter and a metabolic precursor of noradrenaline and adrenaline.
    GO:0008210    estrogen metabolic process    The chemical reactions and pathways involving estrogens, C18 steroid hormones that can stimulate the development of female sexual characteristics. Also found in plants.
    GO:0007565    female pregnancy    The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth.
    GO:0007612    learning    Any process in an organism in which a relatively long-lasting adaptive behavioral change occurs as the result of experience.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0048609    multicellular organismal reproductive process    The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs.
    GO:0045963    negative regulation of dopamine metabolic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving dopamine.
    GO:0035814    negative regulation of renal sodium excretion    Any process that decreases the amount of sodium excreted in urine over a unit of time.
    GO:0048662    negative regulation of smooth muscle cell proliferation    Any process that stops, prevents or reduces the rate or extent of smooth muscle cell proliferation.
    GO:0042135    neurotransmitter catabolic process    The chemical reactions and pathways resulting in the breakdown of any of a group of substances that are released on excitation from the axon terminal of a presynaptic neuron of the central or peripheral nervous system and travel across the synaptic cleft to either excite or inhibit the target cell.
    GO:0050668    positive regulation of homocysteine metabolic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving homocysteine.
    GO:0051930    regulation of sensory perception of pain    Any process that modulates the frequency, rate or extent of the sensory perception of pain, the series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal.
    GO:0042493    response to drug    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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0014070    response to organic cyclic compound    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 organic cyclic compound stimulus.
    GO:0048265    response to pain    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 pain stimulus. Pain stimuli cause activation of nociceptors, peripheral receptors for pain, include receptors which are sensitive to painful mechanical stimuli, extreme heat or cold, and chemical stimuli.
    GO:0007614    short-term memory    The memory process that deals with the storage, retrieval and modification of information received a short time (up to about 30 minutes) ago. This type of memory is typically dependent on direct, transient effects of second messenger activation.
cellular component
    GO:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    GO:0044297    cell body    The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections.
    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:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    GO:0043197    dendritic spine    A small, membranous protrusion from a dendrite that forms a postsynaptic compartment - typically receiving input from a single presynapse. They function as partially isolated biochemical and an electrical compartments. Spine morphology is variable including "thin", "stubby", "mushroom", and "branched", with a continuum of intermediate morphologies. They typically terminate in a bulb shape, linked to the dendritic shaft by a restriction. Spine remodeling is though to be involved in synaptic plasticity.
    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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0045211    postsynaptic membrane    A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane.

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 Related Entries

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

UniProtKB/Swiss-Prot
        COMT_HUMAN | P219643bwm 3bwy 4pyi 4pyj 4pyk 4xuc 4xud 4xue 5lsa

(-) Related Entries Specified in the PDB File

1vid RAT CATECHOL-O-METHYLTRANSFERASE COMPLEXED WITH SAM AND 3, 5-DINITROCATECHOL
3a7d RAT CATECHOL-O-METHYLTRANSFERASE COMPLEXED WITH BI- SUBSTRATE TYPE INHIBITOR
3bwm HUMAN CATECHOL-O-METHYLTRANSFERASE COMPLEXED WITH SAM AND 3,5-DINITROCATECHOL
3bwy HUMAN CATECHOL-O-METHYLTRANSFERASE COMPLEXED WITH SAM AND 3,5-DINITROCATECHOL