DB code: T00407

RLCP classification	6.30.97700.5320 : Double-bonded atom exchange
	8.1121121.660330.5528 : Isomerization
	5.524.3198500.5541 : Elimination
	6.40.521000.5530 : Double-bonded atom exchange
CATH domain	2.10.25.30 : Laminin	Catalytic domain
	3.40.640.10 : Aspartate Aminotransferase; domain 2	Catalytic domain
	3.90.1150.10 : Aspartate Aminotransferase, domain 1
E.C.	4.4.1.4
CSA
M-CSA
MACiE

CATH domain	Related DB codes (homologues)

Uniprot Enzyme Name
UniprotKB	Protein name	Synonyms	Pfam
Q01594	Alliin lyase 1	Alliinase-1 EC 4.4.1.4 Cysteine sulphoxide lyase 1	PF04864 (Alliinase_C) PF04863 (EGF_alliinase) [Graphical View]

KEGG enzyme name
Alliin 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

UniprotKB: Accession Number	Entry name	Activity	Subunit	Subcellular location	Cofactor
Q01594	ALLN1_ALLSA	An S-alkyl-L-cysteine S-oxide = an alkyl sulfenate + 2-aminoacrylate.	Homodimer.	Vacuole.	Pyridoxal phosphate.

KEGG Pathways
Map code	Pathways	E.C.

Compound table
	Cofactors		Substrates	Products		Intermediates
KEGG-id	C00018	C00698	C03726	C02245	C02218	I00185	I00071	I00184	I00171
E.C.
Compound	Pyridoxal phosphate	Cl-	S-alkyl-L-cysteine S-oxide	alkyl sulfenate	2-aminoacrylate	Geminal-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)
Type	aromatic ring (with nitrogen atoms),phosphate group/phosphate ion	halide	amino acids,sulfoxide group	sulfenic acid	amino acids
ChEBI	18405 18405	17996 17996			17123 76565 17123 76565
PubChem	1051 1051	312 312			123991 72551549 123991 72551549

1lk9A01	Unbound	Bound:_CL	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
1lk9B01	Unbound	Bound:_CL	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
2horA01	Unbound	Bound:_CL	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
2hoxA01	Unbound	Bound:_CL	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
2hoxB01	Unbound	Bound:_CL	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
2hoxC01	Unbound	Bound:_CL	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
2hoxD01	Unbound	Bound:_CL	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
1lk9A02	Bound:PLP	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
1lk9B02	Bound:PLP	Unbound	Unbound	Unbound	Unbound	Transition-state-analogue:PLP-DHA-LYS_251	Unbound	Unbound	Unbound
2horA02	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
2hoxA02	Analogue:P1T	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Intermediate-bound:P1T
2hoxB02	Analogue:P1T	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Intermediate-bound:P1T
2hoxC02	Analogue:P1T	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Intermediate-bound:P1T
2hoxD02	Analogue:P1T	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Intermediate-bound:P1T
1lk9A03	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
1lk9B03	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
2horA03	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
2hoxA03	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
2hoxB03	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
2hoxC03	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
2hoxD03	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound

Reference for Active-site residues
resource	references	E.C.
Literature [3], [4]

Active-site residues
PDB	Catalytic residues	Cofactor-binding residues	Modified residues	Main-chain involved in catalysis	Comment

1lk9A01	SER 63;TYR 92	PHE 94;SER 98;PHE 100 (Chloride binding)		GLY 64
1lk9B01	SER 63;TYR 92	PHE 94;SER 98;PHE 100 (Chloride binding)		GLY 64
2horA01	SER 63;TYR 92	PHE 94;SER 98;PHE 100 (Chloride binding)		GLY 64
2hoxA01	SER 63;TYR 92	PHE 94;SER 98;PHE 100 (Chloride binding)		GLY 64
2hoxB01	SER 63;TYR 92	PHE 94;SER 98;PHE 100 (Chloride binding)		GLY 64
2hoxC01	SER 63;TYR 92	PHE 94;SER 98;PHE 100 (Chloride binding)		GLY 64
2hoxD01	SER 63;TYR 92	PHE 94;SER 98;PHE 100 (Chloride binding)		GLY 64
1lk9A02	TYR 165;ASP 225;TYR 228;LYS 251	LYS 251 (PLP binding)
1lk9B02	TYR 165;ASP 225;TYR 228;LYS 251	LYS 251 (PLP binding)
2horA02	TYR 165;ASP 225;TYR 228;LYS 251	LYS 251 (PLP binding)
2hoxA02	TYR 165;ASP 225;TYR 228;LYS 251	LYS 251 (PLP binding)
2hoxB02	TYR 165;ASP 225;TYR 228;LYS 251	LYS 251 (PLP binding)
2hoxC02	TYR 165;ASP 225;TYR 228;LYS 251	LYS 251 (PLP binding)
2hoxD02	TYR 165;ASP 225;TYR 228;LYS 251	LYS 251 (PLP binding)
1lk9A03
1lk9B03
2horA03
2hoxA03
2hoxB03
2hoxC03
2hoxD03

References for Catalytic Mechanism
References	Sections	No. of steps in catalysis
[1]	Scheme 1
[4]	Scheme 1

References
[1]
Resource
Comments
Medline ID
PubMed ID	9799098
Journal	Eur J Biochem
Year	1998
Volume	257
Pages	21-30
Authors	Manabe T, Hasumi A, Sugiyama M, Yamazaki M, Saito K
Title	Alliinase [S-alk(en)yl-L-cysteine sulfoxide lyase] from Allium tuberosum (Chinese chive)--purification, localization, cDNA cloning and heterologous functional expression.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID	9914259
Journal	Curr Opin Struct Biol
Year	1998
Volume	8
Pages	759-69
Authors	Jansonius JN
Title	Structure, evolution and action of vitamin B6-dependent enzymes.
Related PDB
Related UniProtKB
[3]
Resource
Comments	X-RAY CRYSTALLOGRAPHY (1.53 ANGSTROMS) OF 39-465, SUBUNIT.
Medline ID
PubMed ID	12235163
Journal	J Biol Chem
Year	2002
Volume	277
Pages	46402-7
Authors	Kuettner EB, Hilgenfeld R, Weiss MS
Title	The active principle of garlic at atomic resolution.
Related PDB	1lk9
Related UniProtKB	Q01594
[4]
Resource
Comments	X-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS) OF 39-465, SUBUNIT.
Medline ID
PubMed ID	17174334
Journal	J Mol Biol
Year	2007
Volume	366
Pages	611-25
Authors	Shimon LJ, Rabinkov A, Shin I, Miron T, Mirelman D, Wilchek M, Frolow F
Title	Two structures of alliinase from Alliium sativum L.: apo form and ternary complex with aminoacrylate reaction intermediate covalently bound to the PLP cofactor.
Related PDB	2hor 2hox
Related UniProtKB	Q01594

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.

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.

Created	Updated
2010-08-05	2015-07-29