EzCatDB: S00214

DB codeS00214
RLCP classification1.60.55100.9000
CATH domainDomain 13.20.20.80Catalytic domain
E.C.3.2.1.147
CSA1myr

CATH domainRelated DB codes (homologues)
3.20.20.80S00202,S00210,S00748,S00906,S00907,S00911,S00912,S00915,M00134,M00160,D00479,S00204,S00205,S00206,S00207,S00203,S00208,S00209,S00211,S00213,M00113,T00307,D00165,D00166,D00169,D00176,D00501,D00502,D00503,D00844,D00861,D00864,M00026,M00112,M00193,M00346,T00057,T00062,T00063,T00066,T00067

Enzyme Name
Swiss-protKEGG

P29736
Protein nameMyrosinase MA1thioglucosidase
myrosinase
sinigrinase
sinigrase
SynonymsEC 3.2.1.147
Sinigrinase
Thioglucosidase

KEGG pathways
MAP codePathways
MAP00380Tryptophan metabolism

Swiss-prot:Accession NumberP29736
Entry nameMYRA_SINAL
ActivityA thioglucoside + H(2)O = a sugar + a thiol.
SubunitHomodimer.
Subcellular locationVacuole.
CofactorBinds 1 ascorbate molecule per subunit.


CofactorsSubstratesProductsintermediates
KEGG-idC00072C02085C00001C00145C11477


CompoundAscorbateThioglucosideH2OThiolSugarTransition-state in glycosylationIntermediateTransition-state in deglycosylation
Typecarbohydrate,aromatic ring (with hetero atoms other than nitrogen atoms)carbohydrate,sulfide groupH2Osulfhydryl groupcarbohydrate


1dwaMUnboundUnbound
UnboundAnalogue:GOL 24UnboundUnboundUnbound
1dwfMUnboundUnbound
UnboundAnalogue:GOL 24UnboundUnboundUnbound
1dwgMUnboundUnbound
UnboundAnalogue:GOL 24UnboundUnboundUnbound
1dwhMUnboundUnbound
UnboundAnalogue:GOL 24UnboundUnboundUnbound
1dwiMUnboundUnbound
UnboundAnalogue:GOL 24UnboundUnboundUnbound
1dwjMUnboundUnbound
UnboundAnalogue:GOL 24UnboundUnboundUnbound
1e4mMUnboundUnbound
UnboundAnalogue:GOL 1515UnboundUnboundUnbound
1e6qMUnboundUnbound
UnboundUnboundTransition-state-analogue:NTZUnboundUnbound
1e6sMUnboundUnbound
UnboundUnboundTransition-state-analogue:GOXUnboundUnbound
1e6xMUnboundUnbound
UnboundUnboundTransition-state-analogue:LGCUnboundUnbound
1e70MUnboundUnbound
UnboundUnboundUnboundUnboundTransition-state-analogue:G2F
1e71MBound:ASCUnbound
UnboundUnboundUnboundUnboundUnbound
1e72MBound:ASCUnbound
UnboundUnboundTransition-state-analogue:GOXUnboundUnbound
1e73MBound:ASCUnboundBound:HOH 998UnboundUnboundUnboundIntermediate-analogue:G2FUnbound
1myrAUnboundUnbound
UnboundAnalogue:GOL 22UnboundUnboundUnbound
2myrAUnboundUnbound
UnboundUnboundUnboundIntermediate-analogue:G2FUnbound

Active-site residues
resource
PDB;1e6q & literature [6], [9]
pdbCatalytic residuesCofactor-binding residues
1dwaMGLN 187;TYR 330;GLU 409
GLN 187;ARG 259(Ascorbate binding)
1dwfMGLN 187;TYR 330;GLU 409
GLN 187;ARG 259(Ascorbate binding)
1dwgMGLN 187;TYR 330;GLU 409
GLN 187;ARG 259(Ascorbate binding)
1dwhMGLN 187;TYR 330;GLU 409
GLN 187;ARG 259(Ascorbate binding)
1dwiMGLN 187;TYR 330;GLU 409
GLN 187;ARG 259(Ascorbate binding)
1dwjMGLN 187;TYR 330;GLU 409
GLN 187;ARG 259(Ascorbate binding)
1e4mMGLN 187;TYR 330;GLU 409
GLN 187;ARG 259(Ascorbate binding)
1e6qMGLN 187;TYR 330;GLU 409
GLN 187;ARG 259(Ascorbate binding)
1e6sMGLN 187;TYR 330;GLU 409
GLN 187;ARG 259(Ascorbate binding)
1e6xMGLN 187;TYR 330;GLU 409
GLN 187;ARG 259(Ascorbate binding)
1e70MGLN 187;TYR 330;GLU 409
GLN 187;ARG 259(Ascorbate binding)
1e71MGLN 187;TYR 330;GLU 409
GLN 187;ARG 259(Ascorbate binding)
1e72MGLN 187;TYR 330;GLU 409
GLN 187;ARG 259(Ascorbate binding)
1e73MGLN 187;TYR 330;GLU 409
GLN 187;ARG 259(Ascorbate binding)
1myrAGLN 187;TYR 330;GLU 409
GLN 187;ARG 259(Ascorbate binding)
2myrAGLN 187;TYR 330;GLU 409
GLN 187;ARG 259(Ascorbate binding)

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[3]Fig.3, p.15257
[4]Fig.4, p89
[6]Fig.1, p.671-673
[9]FIG.8, p39388-39393
[10]Fig.8, p.648

references
[1]
PubMed ID7759287
JournalHereditas
Year1995
Volume122
Pages95-8
AuthorsTaipalensuu J, Lundgren S, Rask L
TitleNo evidence for the ascorbic activation site of myrosinase being encoded by end of exon 9, beginning of exon 10.
[2]
PubMed ID7657629
JournalJ Biol Chem
Year1995
Volume270
Pages20530-5
AuthorsBotti MG, Taylor MG, Botting NP
TitleStudies on the mechanism of myrosinase. Investigation of the effect of glycosyl acceptors on enzyme activity.
[3]
PubMed ID8952475
JournalBiochemistry
Year1996
Volume35
Pages15256-9
AuthorsCottaz S, Henrissat B, Driguez H
TitleMechanism-based inhibition and stereochemistry of glucosinolate hydrolysis by myrosinase.
[4]
PubMed ID8641474
JournalFEBS Lett
Year1996
Volume385
Pages87-90
AuthorsIori R, Rollin P, Streicher H, Thiem J, Palmieri S
TitleThe myrosinase-glucosinolate interaction mechanism studied using some synthetic competitive inhibitors.
[5]
PubMed ID9354235
JournalBioorg Med Chem
Year1997
Volume5
Pages1799-806
AuthorsLeoni O, Iori R, Palmieri S, Esposito E, Menegatti E, Cortesi R, Nastruzzi C
TitleMyrosinase-generated isothiocyanate from glucosinolates: isolation, characterization and in vitro antiproliferative studies.
[6]
CommentsX-RAY CRYSTALLOGRAPHY (1.64 ANGSTROMS).
PubMed ID9195886
JournalStructure
Year1997
Volume5
Pages663-75
AuthorsBurmeister WP, Cottaz S, Driguez H, Iori R, Palmieri S, Henrissat B
TitleThe crystal structures of Sinapis alba myrosinase and a covalent glycosyl-enzyme intermediate provide insights into the substrate recognition and active-site machinery of an S-glycosidase.
Related PDB1myr,2myr
Related Swiss-protQ7SIB0
[7]
PubMed ID10417337
JournalBiochem J
Year1999
Volume341
Pages725-32
AuthorsShikita M, Fahey JW, Golden TR, Holtzclaw WD, Talalay P
TitleAn unusual case of 'uncompetitive activation' by ascorbic acid: purification and kinetic properties of a myrosinase from Raphanus sativus seedlings.
[8]
CommentsX-ray crystallography
PubMed ID10713520
JournalActa Crystallogr D Biol Crystallogr
Year2000
Volume56
Pages328-41
AuthorsBurmeister WP
TitleStructural changes in a cryo-cooled protein crystal owing to radiation damage.
Related PDB1dwa,1dwf,1dwg,1dwh,1dwi,1dwj
[9]
CommentsX-ray crystallography
PubMed ID10978344
JournalJ Biol Chem
Year2000
Volume275
Pages39385-93
AuthorsBurmeister WP, Cottaz S, Rollin P, Vasella A, Henrissat B
TitleHigh resolution X-ray crystallography shows that ascorbate is a cofactor for myrosinase and substitutes for the function of the catalytic base.
Related PDB1e4m,1e6q,1e6s,1e6x,1e70,1e71,1e72,1e73
[10]
PubMed ID11738173
JournalCurr Opin Chem Biol
Year2001
Volume5
Pages643-9
AuthorsZechel DL, Withers SG
TitleDissection of nucleophilic and acid-base catalysis in glycosidases.
[11]
PubMed ID11804799
JournalInsect Biochem Mol Biol
Year2002
Volume32
Pages275-84
AuthorsJones AM, Winge P, Bones AM, Cole R, Rossiter JT
TitleCharacterization and evolution of a myrosinase from the cabbage aphid Brevicoryne brassicae.
[12]
PubMed ID12696966
JournalJ Agric Food Chem
Year2003
Volume51
Pages2737-44
AuthorsBernardi R, Finiguerra MG, Rossi AA, Palmieri S
TitleIsolation and biochemical characterization of a basic myrosinase from ripe Crambe abyssinica seeds, highly specific for epi-progoitrin.

comments
This enzyme was transferred from E.C. 3.2.3.1 to E.C. 3.2.1.147.
This enzyme belongs to glycosidase family-1, a member family of 4/7 superfamily, which has got catalytic residues at the C-terminal ends of beta-4 and beta-7 on the (alpha/beta)8 barrel fold.
Moreover, comparing the structural data with that of the other family-1 enzyme, cellulase (E.C. 3.2.1.4) (S00203 in EzCatDB), Tyr330 might stabilize the leaving nucleophile, Glu409 in deglycosylation.
According to the literature [6] & [10], the S-glycoside is a good leaving group, so that a general acid is not required for the first step of Enzyme-substrate intermediate formation. On the other hand, at the second step of the hydrolysis, O3 atom of the ascorbate acts as a general base, which activates the water for the hydrolysis of the intermeidate (see [9] & [10]).
The catalytic reaction proceeds as follows (see [9] & [10]):
(1) Glu409 makes a nucleophilic attack on the C1 atom of the S-glycoside, releasing the thiolate, and forming a glycosyl-enzyme intermediate.
(2) An organic cofactor, Ascorbate, acts as a general base, to activate a water. Here, Gln187 seems to modulate the O3 oxygen of ascorbate by interacting with it.
(3) The activated water makes a nucleophilic attack on the C1 atom of the intermediate. Here, Tyr330 might stabilize the leaving Glu409.

createdupdated
2005-03-232009-02-26


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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