EzCatDB: T00407
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DB codeT00407
RLCP classification6.30.97700.5320 : Double-bonded atom exchange
8.1121121.660330.5528 : Isomerization
5.524.3198500.5541 : Elimination
6.40.521000.5530 : Double-bonded atom exchange
CATH domainDomain 12.10.25.30 : LamininCatalytic domain
Domain 23.40.640.10 : Aspartate Aminotransferase; domain 2Catalytic domain
Domain 33.90.1150.10 : Aspartate Aminotransferase, domain 1
E.C.4.4.1.4


Enzyme Name
UniProtKBKEGG

Q01594
Protein nameAlliin lyase 1Alliin lyase
Alliinase
Cysteine sulfoxide lyase
Alkylcysteine sulfoxide lyase
S-alkylcysteine sulfoxide lyase
L-cysteine sulfoxide lyase
S-alkyl-L-cysteine sulfoxide lyase
Alliin alkyl-sulfenate-lyase
SynonymsAlliinase-1
EC 4.4.1.4
Cysteine sulphoxide lyase 1
PfamPF04864 (Alliinase_C)
PF04863 (EGF_alliinase)
[Graphical view]


UniProtKB:Accession NumberQ01594
Entry nameALLN1_ALLSA
ActivityAn S-alkyl-L-cysteine S-oxide = an alkyl sulfenate + 2-aminoacrylate.
SubunitHomodimer.
Subcellular locationVacuole.
CofactorPyridoxal phosphate.

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProductsintermediates
KEGG-idC00018C00698C03726C02245C02218I00185I00071I00184I00171
CompoundPyridoxal phosphateCl-S-alkyl-L-cysteine S-oxidealkyl sulfenate2-aminoacrylateGeminal-diamine transition-state (active-site Lys-PLP-S-alkyl-L-cysteine S-oxide)External aldimine intermediate (PLP-S-alkyl-L-cysteine S-oxide)Quinonoid intermediate (PLP-S-alkyl-cysteine S-oxide)Aminoacrylate intermediate (PLP-dehydroAla)
Typearomatic ring (with nitrogen atoms),phosphate group/phosphate ionhalideamino acids,sulfoxide groupsulfenic acidamino acids



ChEBI18405
17996


17123
76565




PubChem1051
312


72551549
123991




                 
1lk9A01UnboundBound:_CLUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1lk9B01UnboundBound:_CLUnboundUnboundUnboundUnboundUnboundUnboundUnbound
2horA01UnboundBound:_CLUnboundUnboundUnboundUnboundUnboundUnboundUnbound
2hoxA01UnboundBound:_CLUnboundUnboundUnboundUnboundUnboundUnboundUnbound
2hoxB01UnboundBound:_CLUnboundUnboundUnboundUnboundUnboundUnboundUnbound
2hoxC01UnboundBound:_CLUnboundUnboundUnboundUnboundUnboundUnboundUnbound
2hoxD01UnboundBound:_CLUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1lk9A02Bound:PLPUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1lk9B02Bound:PLPUnboundUnboundUnboundUnboundTransition-state-analogue:PLP-DHA-LYS 251UnboundUnboundUnbound
2horA02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
2hoxA02Analogue:P1TUnboundUnboundUnboundUnboundUnboundUnboundUnboundIntermediate-bound:P1T
2hoxB02Analogue:P1TUnboundUnboundUnboundUnboundUnboundUnboundUnboundIntermediate-bound:P1T
2hoxC02Analogue:P1TUnboundUnboundUnboundUnboundUnboundUnboundUnboundIntermediate-bound:P1T
2hoxD02Analogue:P1TUnboundUnboundUnboundUnboundUnboundUnboundUnboundIntermediate-bound:P1T
1lk9A03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1lk9B03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
2horA03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
2hoxA03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
2hoxB03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
2hoxC03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
2hoxD03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
Literature [3], [4]
pdbCatalytic residuesCofactor-binding residuesMain-chain involved in catalysis
           
1lk9A01SER 63;TYR 92
PHE 94;SER 98;PHE 100 (Chloride binding)
GLY 64
1lk9B01SER 63;TYR 92
PHE 94;SER 98;PHE 100 (Chloride binding)
GLY 64
2horA01SER 63;TYR 92
PHE 94;SER 98;PHE 100 (Chloride binding)
GLY 64
2hoxA01SER 63;TYR 92
PHE 94;SER 98;PHE 100 (Chloride binding)
GLY 64
2hoxB01SER 63;TYR 92
PHE 94;SER 98;PHE 100 (Chloride binding)
GLY 64
2hoxC01SER 63;TYR 92
PHE 94;SER 98;PHE 100 (Chloride binding)
GLY 64
2hoxD01SER 63;TYR 92
PHE 94;SER 98;PHE 100 (Chloride binding)
GLY 64
1lk9A02TYR 165;ASP 225;TYR 228;LYS 251
LYS 251 (PLP binding)
 
1lk9B02TYR 165;ASP 225;TYR 228;LYS 251
LYS 251 (PLP binding)
 
2horA02TYR 165;ASP 225;TYR 228;LYS 251
LYS 251 (PLP binding)
 
2hoxA02TYR 165;ASP 225;TYR 228;LYS 251
LYS 251 (PLP binding)
 
2hoxB02TYR 165;ASP 225;TYR 228;LYS 251
LYS 251 (PLP binding)
 
2hoxC02TYR 165;ASP 225;TYR 228;LYS 251
LYS 251 (PLP binding)
 
2hoxD02TYR 165;ASP 225;TYR 228;LYS 251
LYS 251 (PLP binding)
 
1lk9A03               
 
 
1lk9B03               
 
 
2horA03               
 
 
2hoxA03               
 
 
2hoxB03               
 
 
2hoxC03               
 
 
2hoxD03               
 
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]Scheme 1
[4]Scheme 1

references
[1]
PubMed ID9799098
JournalEur J Biochem
Year1998
Volume257
Pages21-30
AuthorsManabe T, Hasumi A, Sugiyama M, Yamazaki M, Saito K
TitleAlliinase [S-alk(en)yl-L-cysteine sulfoxide lyase] from Allium tuberosum (Chinese chive)--purification, localization, cDNA cloning and heterologous functional expression.
[2]
PubMed ID9914259
JournalCurr Opin Struct Biol
Year1998
Volume8
Pages759-69
AuthorsJansonius JN
TitleStructure, evolution and action of vitamin B6-dependent enzymes.
[3]
CommentsX-RAY CRYSTALLOGRAPHY (1.53 ANGSTROMS) OF 39-465, SUBUNIT.
PubMed ID12235163
JournalJ Biol Chem
Year2002
Volume277
Pages46402-7
AuthorsKuettner EB, Hilgenfeld R, Weiss MS
TitleThe active principle of garlic at atomic resolution.
Related PDB1lk9
Related UniProtKBQ01594
[4]
CommentsX-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS) OF 39-465, SUBUNIT.
PubMed ID17174334
JournalJ Mol Biol
Year2007
Volume366
Pages611-25
AuthorsShimon LJ, Rabinkov A, Shin I, Miron T, Mirelman D, Wilchek M, Frolow F
TitleTwo structures of alliinase from Alliium sativum L.: apo form and ternary complex with aminoacrylate reaction intermediate covalently bound to the PLP cofactor.
Related PDB2hor,2hox
Related UniProtKBQ01594

comments
This enzyme belongs to the class-I of PLP-dependent enzymes superfamily (see [3]).
This enzyme cleaves the beta-carbon-gamma-sulfur bond of sulfoxide derivatives of cysteine to produce allicin, with its C-S lyase activity (see [3], [4]).
This enzyme catalyzes the following reactions (see [2], [3], [4]):
(A) Formation of external aldimine (with amine group of S-alkyl-L-cysteine sulfoxide); Exchange of double-bonded atoms (or transaldimination)
(B) Isomerization (shift of double-bond position) forming a quinonoid intermediate (I00184)
(C) Eliminative double-bond formation (C-S lysis from the intermediate) leading to formation of an aminoacrylate-PLP intermediate (I00171) and a product, alkyl sulfenate
(D) Formation of internal aldimine of PLP with active-site Lys, releasing another product, 2-aminoacrylate; Exchange of double-bonded atoms (or transaldimination)
These reactions proceed in the following way (see [3], [4], and D00101, D00085):
(A) Formation of external aldimine (with amine group of S-alkyl-L-cysteine sulfoxide); Exchange of double-bonded atoms (or transaldimination)
(A1) Tyr228 interacts with O3' atom of PLP, modulating and keeping the O3' of PLP negatively charged. The negatively charged O3 atom of PLP modulates the pKa of the amine group of substrate, S-alkyl-L-cysteine sulfoxie, and also the pKa of the internal aldimine with Lys251. The difference in the pKa values facilitates the proton transfer from the amine group of the substrate to the epsilon-nitrogen of Lys251.
(A2) The amine group of the substrate makes a nucleophilic attak on the C4' of the internal aldimine, and Lys251 is released from the Schiff-base (or the internal aldimine), forming a geminal-diamine transition-state (I00185).
(A3) Proton transfer from the substrate-derived amine group to epsilon-nitrogen atom of Lys251 must occur.
(A4) The lone pair of the amine group of the substrate makes a nucleophilic attack on the C4' atom to form a double-bond, releasing the amine of Lys251, leading to the formation of the external aldimine (I00071).
(B) Isomerization (shift of double-bond position) forming a quinonoid intermediate (I00184)
(B0) Asp225 interacts with the N1 atom of PLP, modulating and enhancing the activity of the PLP cofactor as an electron sink, which facilitates the abstraction of alpha-proton from the substrate covalently bound to the PLP (I00071). At the same time, Tyr228 also interacts with the O3' atom of the PLP, modulating the activity of the PLP, whereas Tyr165 stabilizes the PLP through ring stacking interactions.
(B1) The protonated sidechain of Lys251 must be activated. Either Tyr228 or Tyr92' from adjacent subunit may activate Lys251.
(B2) The activated Lys251 acts as a general base to deprotonate alpha-carbon of the external aldimine intermediate (I00071), forming a quinonoid intermediate (I00184).
(C) Eliminative double-bond formation (C-S lysis from the intermediate) leading to formation of an aminoacrylate-PLP intermediate (I00171) and a product, alkyl sulfenate
(C0) Asp225 interacts with the N1 atom of PLP, modulating and enhancing the activity of the PLP cofactor, which facilitates the following elimination reaction. At the same time, Tyr228 also interacts with the O3' atom of the PLP, modulating the activity of the PLP, whereas Tyr165 stabilizes the PLP through ring stacking interactions. Meanwhile, sidechain of Ser63 and mainchain amide of Gly64 may stabilize the eliminated sulfoxide group.
(C1) The protonated Lys251 may act as a general acid to protonate the eliminated sulfoxide group, releasing alkyl sulfenate and leading to the elimination and formation of an aminoacrylate-PLP intermediate (I00171).
(D) Formation of internal aldimine of PLP with active-site Lys, releasing another product, 2-aminoacrylate; Exchange of double-bonded atoms (or transaldimination)
## This reaction is the reverse reaction of reaction (A).
(D1) Tyr228 interacts with O3' atom of PLP, modulating and keeping the O3' of PLP negatively charged.
(D2) The amine group of the Lys251 makes a nucleophilic attak on the C4' of the external aldimine, and the aminoacrylate is released from the Schiff-base (or the external aldimine), forming a geminal-diamine transition-state.
(D3) Proton transfer from the epsilon-nitrogen atom of Lys251 to the amine group of the leaving group must occur.
(D4) The lone pair of the amine group of Lys251 makes a nucleophilic attack on the C4' atom to form a double-bond, releasing the amine group of aminoacrylate, leading to the formation of the internal aldimine.

createdupdated
2010-08-052015-07-29


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