EzCatDB: S00291

DB codeS00291
RLCP classification3.707.90500.391
CATH domainDomain 13.40.50.150Catalytic domain
E.C.2.1.1.6
CSA1vid

CATH domainRelated DB codes (homologues)
3.40.50.150S00637,S00639,S00262,S00261,S00412,D00075,D00076,D00079,D00080,D00082,D00083,D00823

Enzyme Name
Swiss-protKEGG

P22734P21964
Protein nameCatechol O-methyltransferaseCatechol O-methyltransferasecatechol O-methyltransferase
COMT I
COMT II
S-COMT (soluble form of catechol-O-methyltransferase)
MB-COMT (membrane-bound form of catechol-O-methyltransferase)
catechol methyltransferase
catecholamine O-methyltransferase
SynonymsEC 2.1.1.6
EC 2.1.1.6

KEGG pathways
MAP codePathways
MAP00350Tyrosine metabolism

Swiss-prot:Accession NumberP22734P21964
Entry nameCOMT_RATCOMT_HUMAN
ActivityS-adenosyl-L-methionine + a catechol = S-adenosyl-L-homocysteine + a guaiacol.S-adenosyl-L-methionine + a catechol = S-adenosyl-L-homocysteine + a guaiacol.
Subunit

Subcellular locationIsoform 2: Cytoplasm.,Isoform 1: Cell membrane, Single-pass type II membrane protein, Extracellular side.Isoform Soluble: Cytoplasm.,Isoform Membrane-bound: Cell membrane, Single-pass type II membrane protein, Extracellular side.
CofactorBinds 1 magnesium ion per subunit.Binds 1 magnesium ion per subunit.


CofactorsSubstratesProducts
KEGG-idC00305C00019C00090C02012C00788C00547C00021C01502
CompoundMagnesiumS-Adenosyl-L-methionineCatecholCatecholamine(R)-(-)-AdrenalineNoradrenalineS-Adenosyl-L-homocysteineGuaiacol
Typedivalent metal (Ca2+, Mg2+)amino acids,amine group,nucleoside,sulfonium ionaromatic ring (only carbon atom)amine group,aromatic ring (only carbon atom)amine group,aromatic ring (only carbon atom),carbohydrateamine group,aromatic ring (only carbon atom),carbohydrateamino acids,amine group,nucleoside,sulfide grouparomatic ring (only carbon atom),carbohydrate
1vidABound:_MGBound:SAMAnalogue:DNCUnboundUnboundUnboundUnboundUnbound
1h1dABound:_MGBound:SAMUnboundAnalogue:BIAUnboundUnboundUnboundUnbound
1jr4ABound:_MGAnalogue:CL4Analogue:CL4UnboundUnboundUnboundUnboundUnbound
2cl5ABound:_MGBound:SAMAnalogue:BIEUnboundUnboundUnboundUnboundUnbound
2cl5BBound:_MGBound:SAMAnalogue:BIEUnboundUnboundUnboundUnboundUnbound
2zlbAUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
2zthABound:_MGBound:SAMUnboundUnboundUnboundUnboundUnboundUnbound
2zvjABound:_MGBound:SAMAnalogue:KOMUnboundUnboundUnboundUnboundUnbound
3a7dABound:_MGAnalogue:FBNAnalogue:FBNUnboundUnboundUnboundUnboundUnbound
3hvhABound:_MGAnalogue:542Analogue:542UnboundUnboundUnboundUnboundUnbound
3hviABound:_MGAnalogue:619Analogue:619UnboundUnboundUnboundUnboundUnbound
3hvjABound:_MGAnalogue:705Analogue:705UnboundUnboundUnboundUnboundUnbound
3hvjBBound:_MGAnalogue:705Analogue:705UnboundUnboundUnboundUnboundUnbound
3hvkABound:_MGAnalogue:719Analogue:719UnboundUnboundUnboundUnboundUnbound
3a7eABound:_MGBound:SAMAnalogue:DNCUnboundUnboundUnboundUnboundUnbound
3bwmABound:_MGBound:SAMAnalogue:DNCUnboundUnboundUnboundUnboundUnbound
3bwyABound:_MGBound:SAMAnalogue:DNCUnboundUnboundUnboundUnboundUnbound

Active-site residues
pdbCatalytic residuesCofactor-binding residuescomment
1vidALYS 144;GLU 199
ASP 141;ASP 169;ASN 170(Magnesium binding)

1h1dALYS 144;GLU 199
ASP 141;ASP 169;ASN 170(Magnesium binding)

1jr4ALYS 144;GLU 199
ASP 141;ASP 169;ASN 170(Magnesium binding)

2cl5ALYS 144;GLU 199
ASP 141;ASP 169;ASN 170(Magnesium binding)

2cl5BLYS 144;GLU 199
ASP 141;ASP 169;ASN 170(Magnesium binding)

2zlbALYS 144;GLU 199
ASP 141;ASP 169;ASN 170(Magnesium binding)

2zthALYS 144;GLU 199
ASP 141;ASP 169;ASN 170(Magnesium binding)

2zvjALYS 144;GLU 199
ASP 141;ASP 169;ASN 170(Magnesium binding)

3a7dALYS 144;GLU 199
ASP 141;ASP 169;ASN 170(Magnesium binding)

3hvhALYS 187;GLU 242
ASP 184;ASP 212;ASN 213(Magnesium binding)

3hviALYS 187;GLU 242
ASP 184;ASP 212;ASN 213(Magnesium binding)

3hvjALYS 187;GLU 242
ASP 184;ASP 212;ASN 213(Magnesium binding)

3hvjBLYS 187;GLU 242
ASP 184;ASP 212;ASN 213(Magnesium binding)

3hvkALYS 187;GLU 242
ASP 184;ASP 212;ASN 213(Magnesium binding)

3a7eALYS 144;GLU 199
ASP 141;ASP 169;ASN 170(Magnesium binding)

3bwmALYS 144;GLU 199
ASP 141;ASP 169;ASN 170(Magnesium binding)

3bwyALYS 144;GLU 199
ASP 141;ASP 169;ASN 170(Magnesium binding)
mutant V108M

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[2]p.356
[4]Fig.1
[5]p.276-277
[7]p.804
[10]p.496
[11]p.136-138

references
[1]
PubMed ID1749777
JournalProteins
Year1991
Volume11
Pages233-6
AuthorsVidgren J, Tilgmann C, Lundstrom K, Liljas A
TitleCrystallization and preliminary X-ray investigation of a recombinant form of rat catechol O-methyltransferase.
[2]
CommentsX-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF SOLUBLE FORM.; rat
PubMed ID8127373
JournalNature
Year1994
Volume368
Pages354-8
AuthorsVidgren J, Svensson LA, Liljas A
TitleCrystal structure of catechol O-methyltransferase.
Related PDB1vid
Related Swiss-protP22734
[3]
PubMed ID7703232
JournalBiochemistry
Year1995
Volume34
Pages4202-10
AuthorsLotta T, Vidgren J, Tilgmann C, Ulmanen I, Melen K, Julkunen I, Taskinen J
TitleKinetics of human soluble and membrane-bound catechol O-methyltransferase: a revised mechanism and description of the thermolabile variant of the enzyme.
[4]
PubMed ID10785817
JournalChemistry
Year2000
Volume6
Pages971-82
AuthorsMasjost B, Ballmer P, Borroni E, Zurcher G, Winkler FK, Jakob-Roetne R, Diederich F
TitleStructure-based design, synthesis, and in vitro evaluation of bisubstrate inhibitors for catechol O-methyltransferase (COMT).
[5]
CommentsX-RAY CRYSTALLOGRAPHY; very distant homologue (plant)
PubMed ID11224575
JournalNat Struct Biol
Year2001
Volume8
Pages271-9
AuthorsZubieta C, He XZ, Dixon RA, Noel JP
TitleStructures of two natural product methyltransferases reveal the basis for substrate specificity in plant O-methyltransferases.
Related PDB1fpq,1fp1,1fpx,1fp2
[6]
PubMed ID12404486
JournalAngew Chem Int Ed Engl
Year2001
Volume40
Pages4040-4042
AuthorsLerner C, Ruf A, Gramlich V, Masjost B, Zurcher G, Jakob-Roetne R, Borroni E, Diederich F
TitleX-ray Crystal Structure of a Bisubstrate Inhibitor Bound to the Enzyme Catechol-O-methyltransferase: A Dramatic Effect of Inhibitor Preorganization on Binding Affinity We thank F. Hoffmann-La Roche for generous support of this work. We are grateful to P. Malherbe for the cloning of COMT, P. Caspers for the expression of COMT, A. Cesura for enzyme purification, B. Wipf for fermentation, and H. W. Lahm for sequencing. .
Related PDB1jr4
[7]
PubMed ID12237326
JournalMol Pharmacol
Year2002
Volume62
Pages795-805
AuthorsBonifacio MJ, Archer M, Rodrigues ML, Matias PM, Learmonth DA, Carrondo MA, Soares-Da-Silva P
TitleKinetics and crystal structure of catechol-o-methyltransferase complex with co-substrate and a novel inhibitor with potential therapeutic application.
Related PDB1h1d
[8]
PubMed ID16618795
JournalMol Pharmacol
Year2006
Volume70
Pages143-53
AuthorsPalma PN, Rodrigues ML, Archer M, Bonifacio MJ, Loureiro AI, Learmonth DA, Carrondo MA, Soares-da-Silva P
TitleComparative study of ortho- and meta-nitrated inhibitors of catechol-O-methyltransferase: interactions with the active site and regioselectivity of O-methylation.
Related PDB2cl5
[9]
PubMed ID18486144
JournalJ Mol Biol
Year2008
Volume380
Pages120-30
AuthorsRutherford K, Le Trong I, Stenkamp RE, Parson WW
TitleCrystal structures of human 108V and 108M catechol O-methyltransferase.
Related PDB3bwm,3bwy
[10]
PubMed ID19056347
JournalBiochem Biophys Res Commun
Year2009
Volume378
Pages494-7
AuthorsTsuji E, Okazaki K, Takeda K
TitleCrystal structures of rat catechol-O-methyltransferase complexed with coumarine-based inhibitor.
Related PDB2zvj
[11]
PubMed ID19111934
JournalJ Struct Biol
Year2009
Volume165
Pages133-9
AuthorsTsuji E, Okazaki K, Isaji M, Takeda K
TitleCrystal structures of the apo and holo form of rat catechol-O-methyltransferase.
Related PDB2zlb,2zth
[12]
PubMed ID19882607
JournalAngew Chem Int Ed Engl
Year2009
Volume48
Pages9092-6
AuthorsEllermann M, Jakob-Roetne R, Lerner C, Borroni E, Schlatter D, Roth D, Ehler A, Rudolph MG, Diederich F
TitleMolecular recognition at the active site of catechol-o-methyltransferase: energetically favorable replacement of a water molecule imported by a bisubstrate inhibitor.
Related PDB3hvh,3hvi,3hvj,3hvk

comments
According to the literature [5], which describes the mechanisms of the homologues of this enzymes, O-methyltransferases, methylation most likely proceeds via base-assisted deprotonation of the hydroxyl group followed by a nucleophilic attack of the newly generated phenolate anion of the substrate on the ractive methyl group of SAM. Because the sulfur of SAM is positively charged, the transmethylation process is easily facilitated by the deprotonation step. In catechol O-methyltransferase, O-methylation reaction is facilitated by metal-mediated deprotonation.
The literature [2] suggests that the methyl transfer from SAM to the catechol substrate catalysed by this enzyme is a direct bimolecular transfer of the methyl group from the sulfur of SAM to the oxygen of the catchol hydroxyl in an SN2-like transition state. One of the hydroxyl group of the substrate is surrounded by three positively charged groups inducing it to release its proton to become a negatively charged phenolate ion. These moieties are the Mg2+, the methyl group of SAM, and Lys144. The Mg2+ ion in particular probably lowers the pKa of the hydroxyl group significantly. In contrast, the proton of the other hydroxyl group is stabilized by the negatively charged carboxyl group of Glu199. The ionized hydroxyl makes a direct nucleophilic attack on the electron-deficient methyl of SAM.

createdupdated
2002-05-012010-12-02


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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