3A7D - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURES OF RAT CATECHOL-O-METHYLTRANSFERASE COMPLEXED WITH NEW BI-SUBSTRATE TYPE INHIBITOR

Authors :   E. Tsuji

Date :   26 Sep 09 (Deposition) - 15 Sep 10 (Release) - 15 Sep 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym./Biol. Unit : A

Keywords :   Methyltransferase, Neurotransmitter Degradation, Alternative Initiation, Catecholamine Metabolism, S-Adenosyl-L-Methionine, Cell Membrane, Magnesium, Membrane, Metal-Binding, Phosphoprotein, Signal-Anchor, Transferase, Transmembrane (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Muranaka, M. Nakatsu, E. Tsuji, K. Okazaki
Hit To Lead: Comprehensive Strategy Of De Novo Scaffold Generation By Fbdd. Part 2: Ligand Fishing Using Mass Spectrometry By Detection Of Ligand-Protein Non-Covalent Complex After Matrix Click Chemistry
To Be Published
PubMed: search

Molecule 1 - CATECHOL O-METHYLTRANSFERASE
	Chains	:	A
	EC Number	:	2.1.1.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-2T
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	COMT
	Organism Common	:	RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 4)

No.	Name	Count	Type	Full Name
1	FBN	1	Ligand/Ion	5'-DEOXY-5'-[4-({[(2,3-DIHYDROXY-5-NITROPHENYL)CARBONYL]AMINO}METHYL)-1H-1,2,3-TRIAZOL-1-YL]ADENOSINE
2	MG	1	Ligand/Ion	MAGNESIUM ION
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:141 , ASP A:169 , ASN A:170 , FBN A:304 , HOH A:312	BINDING SITE FOR RESIDUE MG A 300
2	AC2	SOFTWARE	MET A:40 , ASN A:41 , VAL A:42 , ALA A:67 , TYR A:68 , TYR A:71 , SER A:72 , ASP A:141 , HOH A:311	BINDING SITE FOR RESIDUE SO4 A 303
3	AC3	SOFTWARE	GLY A:43 , ASP A:44 , ALA A:45 , GLU A:199 , TYR A:200 , HOH A:223 , HOH A:240	BINDING SITE FOR RESIDUE SO4 A 301
4	AC4	SOFTWARE	TRP A:38 , MET A:40 , TYR A:68 , MET A:89 , GLU A:90 , MET A:91 , ASN A:92 , TYR A:95 , ALA A:118 , SER A:119 , GLN A:120 , ASP A:141 , HIS A:142 , TRP A:143 , LYS A:144 , ASP A:169 , ASN A:170 , PRO A:174 , GLU A:199 , HOH A:224 , HOH A:229 , MG A:300 , HOH A:312	BINDING SITE FOR RESIDUE FBN A 304

(no "SS Bond" information available for 3A7D)

Asymmetric/Biological Unit

No.	Residues
1	Val A:173	-	Pro A:174

(no "SAP(SNP)/Variant" information available for 3A7D)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_OMT_I	PS51682	SAM-dependent O-methyltransferase class I-type profile.	COMT_RAT	45-256	1	A:2-213

Asymmetric/Biological Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSRNOT00000050269	1	ENSRNOE00000455167	chr11:84561591-84561757	167	COMT_RAT	-	0	0	-	-
1.2	ENSRNOT00000050269	2	ENSRNOE00000018229	chr11:84576767-84577034	268	COMT_RAT	1-90	90	1	A:2-47	46
1.3	ENSRNOT00000050269	3	ENSRNOE00000018230	chr11:84577399-84577592	194	COMT_RAT	90-154	65	1	A:47-111	65
1.4	ENSRNOT00000050269	4	ENSRNOE00000018231	chr11:84577902-84578033	132	COMT_RAT	155-198	44	1	A:112-155	44
1.5	ENSRNOT00000050269	5	ENSRNOE00000317236	chr11:84580831-84581705	875	COMT_RAT	199-264	66	1	A:156-215	60

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:214
 aligned with COMT_RAT | P22734 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:214
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254    
             COMT_RAT    45 GDTKEQRILRYVQQNAKPGDPQSVLEAIDTYCTQKEWAMNVGDAKGQIMDAVIREYSPSLVLELGAYCGYSAVRMARLLQPGARLLTMEMNPDYAAITQQMLNFAGLQDKVTILNGASQDLIPQLKKKYDVDTLDMVFLDHWKDRYLPDTLLLEKCGLLRKGTVLLADNVIVPGTPDFLAYVRGSSSFECTHYSSYLEYMKVVDGLEKAIYQGP 258
               SCOP domains d3a7da_ A: automated matches                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhh......eeeeee.hhhhhhhhhhhhhhhhhhh.eeeee.hhhhhh.hhhhhhh.....eeee..hhhhhhhhhhhhhhh.......eeee.......hhhhhhhhhhh..eeeeeeeee......eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE SAM_OMT_I  PDB: A:2-213 UniProt: 45-256                                                                                                                                                                             -- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:2-47 UniProt: 1-90           ----------------------------------------------------------------Exon 1.4  PDB: A:112-155 UniProt: 155-198   Exon 1.5  PDB: A:156-215 UniProt: 199-264 [INCOMPLETE]       Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------Exon 1.3  PDB: A:47-111 UniProt: 90-154                          -------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3a7d A   2 GDTKEQRILRYVQQNAKPGDPQSVLEAIDTYCTQKEWAMNVGDAKGQIMDAVIREYSPSLVLELGAYCGYSAVRMARLLQPGARLLTMEMNPDYAAITQQMLNFAGLQDKVTILNGASQDLIPQLKKKYDVDTLDMVFLDHWKDRYLPDTLLLEKCGLLRKGTVLLADNVIVPGTPDFLAYVRGSSSFECTHYSSYLEYMKVVDGLEKAIYQGP 215
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211

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(

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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: COMT-like (31)

Protein domain: automated matches (25)

Norway rat (Rattus norvegicus) [TaxId: 10116] (20)

d3a7da_

(no "CATH Domain" information available for 3A7D)

(no "Pfam Domain" information available for 3A7D)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (COMT_RAT | P22734)

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: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:0046498	S-adenosylhomocysteine metabolic process	The chemical reactions and pathways involving S-adenosylhomocysteine; the L-enantiomer is formed from S-adenosylmethionine and is a strong inhibitor of S-adenosylmethionine-mediated methylation reactions. It can be cleaved to form adenosine and homocysteine.
	GO:0046500	S-adenosylmethionine metabolic process	The chemical reactions and pathways involving S-adenosylmethionine, S-(5'-adenosyl)-L-methionine, an important intermediate in one-carbon metabolism.
	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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Val A:173 - Pro A:174	[ RasMol ]

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	3a7d
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	COMT_RAT \| P22734
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	2.1.1.6
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1jr4	RAT CATECHOL-O-METHYLTRANSFERASE COMPLEXED WITH BI- SUBSTRATE TYPE INHIBITOR
1vid	RAT CATECHOL-O-METHYLTRANSFERASE COMPLEXED WITH SAM AND 3, 5-DINITROCATECHOL
3a7e	HUMAN COMT CATECHOL-O-METHYLTRANSFERASE COMPLEXED WITH SAM AND 3,5-DINITROCATECHOL

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (4, 4)

Sequences/Alignments

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SCOP Domains (1, 1)

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Gene Ontology (42, 42)

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