MDL2_PRUDU
ID MDL2_PRUDU Reviewed; 563 AA.
AC Q945K2;
DT 28-NOV-2012, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 90.
DE RecName: Full=(R)-mandelonitrile lyase 2;
DE EC=4.1.2.10;
DE AltName: Full=Hydroxynitrile lyase 2;
DE Short=(R)-oxynitrilase 2;
DE Short=PaHNL1;
DE AltName: Full=R-oxynitrile lyase isoenzyme 2;
DE Flags: Precursor;
GN Name=MDL2; Synonyms=HNL1;
OS Prunus dulcis (Almond) (Amygdalus dulcis).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; fabids; Rosales; Rosaceae; Amygdaloideae; Amygdaleae; Prunus.
OX NCBI_TaxID=3755;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, X-RAY CRYSTALLOGRAPHY (1.47
RP ANGSTROMS) OF 28-563, GLYCOSYLATION AT ASN-145; ASN-162; ASN-379 AND
RP ASN-419, AND DISULFIDE BOND.
RC TISSUE=Seed;
RX PubMed=11566130; DOI=10.1016/s0969-2126(01)00639-6;
RA Dreveny I., Gruber K., Glieder A., Thompson A., Kratky C.;
RT "The hydroxynitrile lyase from almond: a lyase that looks like an
RT oxidoreductase.";
RL Structure 9:803-815(2001).
RN [2]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=6246955; DOI=10.1016/0005-2744(80)90206-5;
RA Jorns M.S.;
RT "Studies on the kinetics of cyanohydrin synthesis and cleavage by the the
RT flavoenzyme oxynitrilase.";
RL Biochim. Biophys. Acta 613:203-209(1980).
RN [3]
RP 3D-STRUCTURE MODELING.
RX PubMed=11790839; DOI=10.1110/ps.38102;
RA Dreveny I., Kratky C., Gruber K.;
RT "The active site of hydroxynitrile lyase from Prunus amygdalus: modeling
RT studies provide new insights into the mechanism of cyanogenesis.";
RL Protein Sci. 11:292-300(2002).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.57 ANGSTROMS) OF 28-548 IN COMPLEX WITH FAD AND
RP BENZALDEHYDE, SUBUNIT, CATALYTIC ACTIVITY, GLYCOSYLATION AT ASN-145;
RP ASN-162; ASN-379 AND ASN-419, DISULFIDE BOND, MUTAGENESIS OF HIS-486 AND
RP HIS-524, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=19256550; DOI=10.1021/bi802162s;
RA Dreveny I., Andryushkova A.S., Glieder A., Gruber K., Kratky C.;
RT "Substrate binding in the FAD-dependent hydroxynitrile lyase from almond
RT provides insight into the mechanism of cyanohydrin formation and explains
RT the absence of dehydrogenation activity.";
RL Biochemistry 48:3370-3377(2009).
CC -!- FUNCTION: Involved in cyanogenesis, the release of HCN from injured
CC tissues. Catalyzes the stereospecific addition of HCN to a variety of
CC aldehydes in vitro. Has no oxidase activity. The redox properties of
CC the FAD cofactor appear to be unimportant for catalysis.
CC {ECO:0000269|PubMed:11566130, ECO:0000269|PubMed:6246955}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(R)-mandelonitrile = benzaldehyde + hydrogen cyanide;
CC Xref=Rhea:RHEA:18313, ChEBI:CHEBI:17169, ChEBI:CHEBI:18407,
CC ChEBI:CHEBI:18450; EC=4.1.2.10;
CC Evidence={ECO:0000269|PubMed:19256550, ECO:0000269|PubMed:6246955};
CC -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692;
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 5.5. {ECO:0000269|PubMed:19256550};
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:19256550}.
CC -!- PTM: Glycosylated. Deglycosylation does not affect the enzymatic
CC activity. {ECO:0000269|PubMed:11566130, ECO:0000269|PubMed:19256550}.
CC -!- SIMILARITY: Belongs to the GMC oxidoreductase family. {ECO:0000305}.
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DR EMBL; AF412329; AAL11514.1; -; Genomic_DNA.
DR PDB; 1JU2; X-ray; 1.47 A; A/B=28-563.
DR PDB; 3GDN; X-ray; 1.67 A; A/B=28-548.
DR PDB; 3GDP; X-ray; 1.57 A; A/B=28-548.
DR PDBsum; 1JU2; -.
DR PDBsum; 3GDN; -.
DR PDBsum; 3GDP; -.
DR AlphaFoldDB; Q945K2; -.
DR SMR; Q945K2; -.
DR Allergome; 12337; Pru du 10.
DR iPTMnet; Q945K2; -.
DR EvolutionaryTrace; Q945K2; -.
DR GO; GO:0050660; F:flavin adenine dinucleotide binding; IDA:UniProtKB.
DR GO; GO:0046593; F:mandelonitrile lyase activity; TAS:UniProtKB.
DR GO; GO:0016614; F:oxidoreductase activity, acting on CH-OH group of donors; IEA:InterPro.
DR GO; GO:0050898; P:nitrile metabolic process; TAS:UniProtKB.
DR Gene3D; 3.50.50.60; -; 1.
DR InterPro; IPR036188; FAD/NAD-bd_sf.
DR InterPro; IPR012132; GMC_OxRdtase.
DR InterPro; IPR000172; GMC_OxRdtase_N.
DR InterPro; IPR007867; GMC_OxRtase_C.
DR Pfam; PF05199; GMC_oxred_C; 1.
DR Pfam; PF00732; GMC_oxred_N; 1.
DR PIRSF; PIRSF000137; Alcohol_oxidase; 1.
DR SUPFAM; SSF51905; SSF51905; 1.
DR PROSITE; PS00623; GMC_OXRED_1; 1.
DR PROSITE; PS00624; GMC_OXRED_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Disulfide bond; FAD; Flavoprotein; Glycoprotein; Lyase;
KW Signal.
FT SIGNAL 1..27
FT /evidence="ECO:0000255"
FT CHAIN 28..563
FT /note="(R)-mandelonitrile lyase 2"
FT /evidence="ECO:0000255"
FT /id="PRO_5000061321"
FT ACT_SITE 486
FT /note="Proton donor"
FT ACT_SITE 524
FT /note="Proton acceptor"
FT BINDING 63..64
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:19256550"
FT BINDING 82..83
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:19256550"
FT BINDING 129
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:19256550"
FT BINDING 133
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:19256550"
FT BINDING 137..140
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:19256550"
FT BINDING 244
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:19256550"
FT BINDING 355
FT /ligand="substrate"
FT BINDING 484
FT /ligand="substrate"
FT BINDING 485..486
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:19256550"
FT BINDING 514
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:19256550"
FT BINDING 525..526
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:19256550"
FT CARBOHYD 145
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000269|PubMed:11566130,
FT ECO:0000269|PubMed:19256550"
FT CARBOHYD 162
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000269|PubMed:11566130,
FT ECO:0000269|PubMed:19256550"
FT CARBOHYD 379
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000269|PubMed:11566130,
FT ECO:0000269|PubMed:19256550"
FT CARBOHYD 419
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000269|PubMed:11566130,
FT ECO:0000269|PubMed:19256550"
FT DISULFID 426..477
FT /evidence="ECO:0000269|PubMed:11566130,
FT ECO:0000269|PubMed:19256550"
FT MUTAGEN 486
FT /note="H->N: Loss of 95% of the catalytic activity."
FT /evidence="ECO:0000269|PubMed:19256550"
FT MUTAGEN 524
FT /note="H->N: Loss of 95% of the catalytic activity."
FT /evidence="ECO:0000269|PubMed:19256550"
FT CONFLICT 373
FT /note="A -> S (in Ref. 4; No nucleotide entry)"
FT /evidence="ECO:0000305"
FT HELIX 37..41
FT /evidence="ECO:0007829|PDB:1JU2"
FT STRAND 42..44
FT /evidence="ECO:0007829|PDB:1JU2"
FT HELIX 45..47
FT /evidence="ECO:0007829|PDB:1JU2"
FT STRAND 50..59
FT /evidence="ECO:0007829|PDB:1JU2"
FT HELIX 65..72
FT /evidence="ECO:0007829|PDB:1JU2"
FT TURN 73..75
FT /evidence="ECO:0007829|PDB:1JU2"
FT STRAND 78..81
FT /evidence="ECO:0007829|PDB:1JU2"
FT STRAND 83..85
FT /evidence="ECO:0007829|PDB:1JU2"
FT HELIX 87..89
FT /evidence="ECO:0007829|PDB:1JU2"
FT HELIX 91..94
FT /evidence="ECO:0007829|PDB:1JU2"
FT HELIX 96..98
FT /evidence="ECO:0007829|PDB:1JU2"
FT HELIX 99..104
FT /evidence="ECO:0007829|PDB:1JU2"
FT STRAND 109..117
FT /evidence="ECO:0007829|PDB:1JU2"
FT STRAND 123..127
FT /evidence="ECO:0007829|PDB:1JU2"
FT HELIX 132..135
FT /evidence="ECO:0007829|PDB:1JU2"
FT STRAND 152..154
FT /evidence="ECO:0007829|PDB:1JU2"
FT HELIX 158..172
FT /evidence="ECO:0007829|PDB:1JU2"
FT HELIX 180..191
FT /evidence="ECO:0007829|PDB:1JU2"
FT STRAND 197..200
FT /evidence="ECO:0007829|PDB:1JU2"
FT STRAND 206..210
FT /evidence="ECO:0007829|PDB:1JU2"
FT STRAND 212..215
FT /evidence="ECO:0007829|PDB:1JU2"
FT STRAND 219..221
FT /evidence="ECO:0007829|PDB:1JU2"
FT HELIX 224..230
FT /evidence="ECO:0007829|PDB:1JU2"
FT TURN 233..235
FT /evidence="ECO:0007829|PDB:1JU2"
FT STRAND 236..241
FT /evidence="ECO:0007829|PDB:1JU2"
FT STRAND 243..249
FT /evidence="ECO:0007829|PDB:1JU2"
FT STRAND 252..254
FT /evidence="ECO:0007829|PDB:1JU2"
FT STRAND 256..263
FT /evidence="ECO:0007829|PDB:1JU2"
FT STRAND 269..282
FT /evidence="ECO:0007829|PDB:1JU2"
FT HELIX 285..295
FT /evidence="ECO:0007829|PDB:1JU2"
FT HELIX 301..306
FT /evidence="ECO:0007829|PDB:1JU2"
FT STRAND 312..314
FT /evidence="ECO:0007829|PDB:1JU2"
FT TURN 316..319
FT /evidence="ECO:0007829|PDB:1JU2"
FT STRAND 320..323
FT /evidence="ECO:0007829|PDB:1JU2"
FT STRAND 326..332
FT /evidence="ECO:0007829|PDB:1JU2"
FT STRAND 345..348
FT /evidence="ECO:0007829|PDB:1JU2"
FT STRAND 350..359
FT /evidence="ECO:0007829|PDB:1JU2"
FT STRAND 370..373
FT /evidence="ECO:0007829|PDB:1JU2"
FT STRAND 382..391
FT /evidence="ECO:0007829|PDB:1JU2"
FT STRAND 396..399
FT /evidence="ECO:0007829|PDB:1JU2"
FT HELIX 420..437
FT /evidence="ECO:0007829|PDB:1JU2"
FT HELIX 440..445
FT /evidence="ECO:0007829|PDB:1JU2"
FT TURN 452..455
FT /evidence="ECO:0007829|PDB:3GDP"
FT STRAND 458..461
FT /evidence="ECO:0007829|PDB:1JU2"
FT HELIX 470..480
FT /evidence="ECO:0007829|PDB:1JU2"
FT STRAND 488..491
FT /evidence="ECO:0007829|PDB:1JU2"
FT TURN 494..496
FT /evidence="ECO:0007829|PDB:1JU2"
FT STRAND 501..503
FT /evidence="ECO:0007829|PDB:1JU2"
FT STRAND 509..511
FT /evidence="ECO:0007829|PDB:1JU2"
FT HELIX 514..516
FT /evidence="ECO:0007829|PDB:1JU2"
FT STRAND 521..524
FT /evidence="ECO:0007829|PDB:1JU2"
FT HELIX 526..547
FT /evidence="ECO:0007829|PDB:1JU2"
SQ SEQUENCE 563 AA; 61158 MW; E0F53C236F4B001C CRC64;
MEKSTMSAIL LVLYIFVLHL QYSEVHSLAT TSDHDFSYLS FAYDATDLEL EGSYDYVIVG
GGTSGCPLAA TLSEKYKVLV LERGSLPTAY PNVLTADGFV YNLQQEDDGK TPVERFVSED
GIDNVRGRVL GGTSIINAGV YARANTSIYS ASGVDWDMDL VNQTYEWVED TIVYKPNSQS
WQSVTKTAFL EAGVHPNHGF SLDHEEGTRI TGSTFDNKGT RHAADELLNK GNSNNLRVGV
HASVEKIIFS NAPGLTATGV IYRDSNGTPH QAFVRSKGEV IVSAGTIGTP QLLLLSGVGP
ESYLSSLNIP VVLSHPYVGQ FLHDNPRNFI NILPPNPIEP TIVTVLGISN DFYQCSFSSL
PFTTPPFGFF PSASYPLPNS TFAHFASKVA GPLSYGSLTL KSSSNVRVSP NVKFNYYSNL
TDLSHCVSGM KKIGELLSTD ALKPYKVEDL PGVEGFNILG IPLPKDQTDD AAFETFCRES
VASYWHYHGG CLVGKVLDGD FRVTGINALR VVDGSTFPYT PASHPQGFYL MLGRYVGIKI
LQERSASDLK ILDSLKSAAS LVL
