DB code: S00358

RLCP classification 5.191.546000.23 : Elimination
CATH domain 3.40.50.1820 : Rossmann fold Catalytic domain
E.C. 4.1.2.47
CSA 1qj4 1dwo
M-CSA 1qj4 1dwo
MACiE

CATH domain Related DB codes (homologues)
3.40.50.1820 : Rossmann fold S00544 S00344 S00517 S00525 S00526 S00720 S00723 S00724 S00725 S00919 S00057 S00374 S00345 S00347 S00348 S00346 S00350 S00352 S00353 S00355 S00356 D00189 D00210 D00539 T00253

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam
P52704 Hydroxynitrilase
EC 4.1.2.37
EC 4.1.2.37) ((S)-acetone-cyanohydrin lyase
S)-acetone-cyanohydrin lyase) ((S)-hydroxynitrile lyase
Oxynitrilase
[Graphical View]
P52705 Hydroxynitrilase
EC 4.1.2.37
EC 4.1.2.37) ((S)-acetone-cyanohydrin lyase
S)-acetone-cyanohydrin lyase) ((S)-hydroxynitrile lyase
Oxynitrilase
PF00561 (Abhydrolase_1)
[Graphical View]

KEGG enzyme name
(S)-hydroxynitrile lyase
(S)-cyanohydrin producing hydroxynitrile lyase
(S)-oxynitrilase
(S)-HbHNL
(S)-MeHNL
hydroxynitrile lyase
oxynitrilase
HbHNL
MeHNL
(S)-selective hydroxynitrile lyase
(S)-cyanohydrin carbonyl-lyase (cyanide forming)

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P52704 HNL_HEVBR An aliphatic (S)-hydroxynitrile = cyanide + an aliphatic aldehyde or ketone. An aromatic (S)-hydroxynitrile = cyanide + an aromatic aldehyde. Homodimer.
P52705 HNL_MANES An aliphatic (S)-hydroxynitrile = cyanide + an aliphatic aldehyde or ketone. An aromatic (S)-hydroxynitrile = cyanide + an aromatic aldehyde. Homotrimer.

KEGG Pathways
Map code Pathways E.C.
MAP00460 Cyanoamino acid metabolism

Compound table
Substrates Products Intermediates
KEGG-id C18797 C00177 C00071 C01450
E.C.
Compound (S)-Hydroxynitrile cyanide Aldehyde Ketone
Type carbohydrate organic ion carbohydrate carbohydrate
ChEBI 17514
PubChem 5975
1dwoA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:ACN
1dwoB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1dwpA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Analogue:ACT
1dwpB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Analogue:ACT
1dwqA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:ATO
1dwqB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1e89A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1e89B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1e8dA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:CNH Unbound Unbound Unbound
1e8dB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:CNH Unbound Unbound Unbound
1eb8A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1eb8B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1eb9A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:HBA Unbound
1eb9B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:HBA Unbound
1qj4A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1yasA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Analogue:HIS
2yasA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:SCN Unbound Unbound
3yasA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:ACN
4yasA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
5yasA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Analogue:FAC
6yasA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
7yasA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot;P52704, P52705 & literature [8], [11] & [12]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1dwoA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 11;SER 80;ASP 208;HIS 236
1dwoB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 11;SER 80;ASP 208;HIS 236
1dwpA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 11;SER 80;ASP 208;HIS 236
1dwpB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 11;SER 80;ASP 208;HIS 236
1dwqA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 11;SER 80;ASP 208;HIS 236 CSA 81(acetonylation)
1dwqB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 11;SER 80;ASP 208;HIS 236 CSA 81(acetonylation)
1e89A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 11; ;ASP 208;HIS 236 mutant S80A
1e89B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 11; ;ASP 208;HIS 236 mutant S80A
1e8dA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 11; ;ASP 208;HIS 236 mutant S80A
1e8dB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 11; ;ASP 208;HIS 236 mutant S80A
1eb8A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 11;SER 80;ASP 208;HIS 236
1eb8B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 11;SER 80;ASP 208;HIS 236
1eb9A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 11;SER 80;ASP 208;HIS 236
1eb9B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 11;SER 80;ASP 208;HIS 236
1qj4A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 11;SER 80;ASP 207;HIS 235;LYS 236
1yasA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 11;SER 80;ASP 207;HIS 235;LYS 236
2yasA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 11;SER 80;ASP 207;HIS 235;LYS 236
3yasA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 11;SER 80;ASP 207;HIS 235;LYS 236
4yasA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 11;SER 80;ASP 207;HIS 235;LYS 236
5yasA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 11;SER 80;ASP 207;HIS 235;LYS 236
6yasA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 11;SER 80;ASP 207;HIS 235;LYS 236
7yasA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 11;SER 80;ASP 207;HIS 235;LYS 236

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
Fig.2 3
[2]
Fig.8, p.813-819 3
[3]
Fig.4, p.25833 3
[5]
Fig. 6, p.447-448 3
[6]
Scheme 3, p.186, p.193 5
[7]
Fig.2, p.997-998 4
[8]
Fig.6, p.1997 2
[11]
Fig.5, p.199 3
[12]
Fig.2, p.1019-1020 3
[13]
Fig.5, p.295-298 1

References
[1]
Resource
Comments
Medline ID
PubMed ID 8958122
Journal Ann N Y Acad Sci
Year 1996
Volume 799
Pages 707-12
Authors Hasslacher M, Schall M, Hayn M, Griengl H, Kohlwein SD, Schwab H
Title (S)-hydroxynitrile lyase from Hevea brasiliensis.
Related PDB
Related UniProtKB
[2]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
Medline ID 96434327
PubMed ID 8805565
Journal Structure
Year 1996
Volume 4
Pages 811-22
Authors Wagner UG, Hasslacher M, Griengl H, Schwab H, Kratky C
Title Mechanism of cyanogenesis: the crystal structure of hydroxynitrile lyase from Hevea brasiliensis.
Related PDB 1yas
Related UniProtKB P52704
[3]
Resource
Comments
Medline ID
PubMed ID 8824213
Journal J Biol Chem
Year 1996
Volume 271
Pages 25830-4
Authors Wajant H, Pfizenmaier K
Title Identification of potential active-site residues in the hydroxynitrile lyase from Manihot esculenta by site-directed mutagenesis.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 9325140
Journal Protein Expr Purif
Year 1997
Volume 11
Pages 61-71
Authors Hasslacher M, Schall M, Hayn M, Bona R, Rumbold K, Luckl J, Griengl H, Kohlwein SD, Schwab H
Title High-level intracellular expression of hydroxynitrile lyase from the tropical rubber tree Hevea brasiliensis in microbial hosts.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 9094745
Journal Proteins
Year 1997
Volume 27
Pages 438-49
Authors Hasslacher M, Kratky C, Griengl H, Schwab H, Kohlwein SD
Title Hydroxynitrile lyase from Hevea brasiliensis: molecular characterization and mechanism of enzyme catalysis.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 10407140
Journal Biochim Biophys Acta
Year 1999
Volume 1432
Pages 185-93
Authors Hanefeld U, Straathof AJ, Heijnen JJ
Title Study of the (S)-hydroxynitrile lyase from Hevea brasiliensis: mechanistic implications.
Related PDB
Related UniProtKB
[7]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.1 ANGSTROMS)
Medline ID 99423043
PubMed ID 10494852
Journal Biol Chem
Year 1999
Volume 380
Pages 993-1000
Authors Gruber K, Gugganig M, Wagner UG, Kratky C
Title Atomic resolution crystal structure of hydroxynitrile lyase from Hevea brasiliensis.
Related PDB 1qj4
Related UniProtKB P52704
[8]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.72 ANGSTROMS).
Medline ID 20014021
PubMed ID 10548044
Journal Protein Sci
Year 1999
Volume 8
Pages 1990-2000
Authors Zuegg J, Gruber K, Gugganig M, Wagner UG, Kratky C
Title Three-dimensional structures of enzyme-substrate complexes of the hydroxynitrile lyase from Hevea brasiliensis.
Related PDB 2yas 3yas 4yas 5yas 6yas 7yas
Related UniProtKB P52704
[9]
Resource
Comments
Medline ID
PubMed ID 11102786
Journal Curr Opin Biotechnol
Year 2000
Volume 11
Pages 532-9
Authors Effenberger F, Forster S, Wajant H
Title Hydroxynitrile lyases in stereoselective catalysis.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 10679367
Journal Curr Opin Chem Biol
Year 2000
Volume 4
Pages 103-9
Authors Johnson DV, Zabelinskaja-Mackova AA, Griengl H
Title Oxynitrilases for asymmetric C-C bond formation.
Related PDB
Related UniProtKB
[11]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 11173464
Journal Acta Crystallogr D Biol Crystallogr
Year 2001
Volume 57
Pages 194-200
Authors Lauble H, Forster S, Miehlich B, Wajant H, Effenberger F
Title Structure of hydroxynitrile lyase from Manihot esculenta in complex with substrates acetone and chloroacetone: implications for the mechanism of cyanogenesis.
Related PDB 1dwo 1dwp 1dwq
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 11316882
Journal Protein Sci
Year 2001
Volume 10
Pages 1015-22
Authors Lauble H, Miehlich B, Forster S, Wajant H, Effenberger F
Title Mechanistic aspects of cyanogenesis from active-site mutant Ser80Ala of hydroxynitrile lyase from Manihot esculenta in complex with acetone cyanohydrin.
Related PDB 1e89 1e8d
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 11790839
Journal Protein Sci
Year 2002
Volume 11
Pages 292-300
Authors Dreveny I, Kratky C, Gruber K
Title The active site of hydroxynitrile lyase from Prunus amygdalus: modeling studies provide new insights into the mechanism of cyanogenesis.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 11742123
Journal Protein Sci
Year 2002
Volume 11
Pages 65-71
Authors Lauble H, Miehlich B, Forster S, Kobler C, Wajant H, Effenberger F
Title Structure determinants of substrate specificity of hydroxynitrile lyase from Manihot esculenta.
Related PDB 1eb8 1eb9
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 12889812
Journal Biotechnol Lett
Year 2003
Volume 25
Pages 1041-7
Authors Yan G, Cheng S, Zhao G, Wu S, Liu Y, Sun W
Title A single residual replacement improves the folding and stability of recombinant cassava hydroxynitrile lyase in E. coil.
Related PDB
Related UniProtKB

Comments
This enzyme belongs to the alpha/beta hydrolase superfamily, which has a catalytic triad (Ser/Asp/His).
The earlier literature ([1], [2] & [5]) proposed a catalytic mechanism, in which Ser80 acts as a nucleophilic residue to form a tetrahedral intermediate with substrate, as that in serine proteases.
However, more recent papers ([3], [6], [7], [8], [11] & [12]) proposed an alternative mechanism, in which catalytic residues act as acid/base or stabilizers.
This enzyme catalyzes a reversible reaction. In the forward direction, cyanohydrin will be degradaded into acetone and cyanide, accompanied by elimination and double-bond formation, whilst cyanohydrin will be synthesized from acetone and cyanide, by addition to the double-bond, in the reverse direction.
The forward reaction (elimination and double-bond formation reaction) proceeds as follows (see ([3], [6], [7], [8], [11] & [12]):
(1) Ser80, modulated by His235, acts as a general base, to abstract a proton from cyanohydrin OH-group, leading to the elimination of the cyanide (or nitrile). During this reaction, Thr11 stabilizes the oxygen atom of the OH-group, whilst His235 and Lys236 (PDB; 1qj4; enzyme from Havea brasiliensis) stabilize the eliminated group, cyanide (or nitrile).
(2) His235 acts as a general acid, to donate a proton to the eliminated group, the cyanide ion.
In the enzyme from Manihot esculenta, however, the corresponding lysine residue, Lys237, does not seem to be involved in the stabilization, according to the literature [11] & [12].
The reverse reaction (addition to double-bond) adopts an analogous mechanism, using the same catalytic residues.

Created Updated
2004-04-04 2012-10-03