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Q945K2

- MDL2_PRUDU

UniProt

Q945K2 - MDL2_PRUDU

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Protein

(R)-mandelonitrile lyase 2

Gene

MDL2

Organism
Prunus dulcis (Almond) (Amygdalus dulcis)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Involved in cyanogenesis, the release of HCN from injured tissues. Catalyzes the stereospecific addition of HCN to a variety of aldehydes in vitro. Has no oxidase activity. The redox properties of the FAD cofactor appear to be unimportant for catalysis.2 Publications

Catalytic activityi

(R)-mandelonitrile = cyanide + benzaldehyde.2 Publications

Cofactori

FAD.

pH dependencei

Optimum pH is 5.5.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei129 – 1291FAD; via carbonyl oxygen1 Publication
Binding sitei133 – 1331FAD1 Publication
Binding sitei244 – 2441FAD; via amide nitrogen and carbonyl oxygen1 Publication
Binding sitei355 – 3551Substrate
Binding sitei484 – 4841Substrate
Active sitei486 – 4861Proton donor
Binding sitei514 – 5141FAD; via amide nitrogen1 Publication
Active sitei524 – 5241Proton acceptor

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi63 – 642FAD1 Publication
Nucleotide bindingi82 – 832FAD1 Publication
Nucleotide bindingi137 – 1404FAD1 Publication
Nucleotide bindingi485 – 4862FAD1 Publication
Nucleotide bindingi525 – 5262FAD1 Publication

GO - Molecular functioni

  1. choline dehydrogenase activity Source: InterPro
  2. flavin adenine dinucleotide binding Source: UniProtKB
  3. mandelonitrile lyase activity Source: UniProtKB

GO - Biological processi

  1. alcohol metabolic process Source: InterPro
  2. nitrile metabolic process Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Ligandi

FAD, Flavoprotein

Enzyme and pathway databases

BRENDAi4.1.2.10. 1961.

Names & Taxonomyi

Protein namesi
Recommended name:
(R)-mandelonitrile lyase 2 (EC:4.1.2.10)
Alternative name(s):
Hydroxynitrile lyase 2
Short name:
(R)-oxynitrilase 2
Short name:
PaHNL1
R-oxynitrile lyase isoenzyme 2
Gene namesi
Name:MDL2
Synonyms:HNL1
OrganismiPrunus dulcis (Almond) (Amygdalus dulcis)
Taxonomic identifieri3755 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsfabidsRosalesRosaceaeMaloideaeAmygdaleaePrunus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi486 – 4861H → N: Loss of 95% of the catalytic activity. 1 Publication
Mutagenesisi524 – 5241H → N: Loss of 95% of the catalytic activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2727Sequence AnalysisAdd
BLAST
Chaini28 – 563536(R)-mandelonitrile lyase 2Sequence AnalysisPRO_5000061321Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi145 – 1451N-linked (GlcNAc...)2 Publications
Glycosylationi162 – 1621N-linked (GlcNAc...)2 Publications
Glycosylationi379 – 3791N-linked (GlcNAc...)2 Publications
Glycosylationi419 – 4191N-linked (GlcNAc...)2 Publications
Disulfide bondi426 ↔ 4772 Publications

Post-translational modificationi

Glycosylated. Deglycosylation does not affect the enzymatic activity.2 Publications

Keywords - PTMi

Disulfide bond, Glycoprotein

Interactioni

Subunit structurei

Monomer.1 Publication

Structurei

Secondary structure

1
563
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi37 – 415
Beta strandi42 – 443
Helixi45 – 473
Beta strandi50 – 5910
Helixi65 – 728
Turni73 – 753
Beta strandi78 – 814
Beta strandi83 – 853
Helixi87 – 893
Helixi91 – 944
Helixi96 – 983
Helixi99 – 1046
Beta strandi109 – 1179
Beta strandi123 – 1275
Helixi132 – 1354
Beta strandi152 – 1543
Helixi158 – 17215
Helixi180 – 19112
Beta strandi197 – 2004
Beta strandi206 – 2105
Beta strandi212 – 2154
Beta strandi219 – 2213
Helixi224 – 2307
Turni233 – 2353
Beta strandi236 – 2416
Beta strandi243 – 2497
Beta strandi252 – 2543
Beta strandi256 – 2638
Beta strandi269 – 28214
Helixi285 – 29511
Helixi301 – 3066
Beta strandi312 – 3143
Turni316 – 3194
Beta strandi320 – 3234
Beta strandi326 – 3327
Beta strandi345 – 3484
Beta strandi350 – 35910
Beta strandi370 – 3734
Beta strandi382 – 39110
Beta strandi396 – 3994
Helixi420 – 43718
Helixi440 – 4456
Turni452 – 4554
Beta strandi458 – 4614
Helixi470 – 48011
Beta strandi488 – 4914
Turni494 – 4963
Beta strandi501 – 5033
Beta strandi509 – 5113
Helixi514 – 5163
Beta strandi521 – 5244
Helixi526 – 54722

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1JU2X-ray1.47A/B28-563[»]
3GDNX-ray1.67A/B28-548[»]
3GDPX-ray1.57A/B28-548[»]
ProteinModelPortaliQ945K2.
SMRiQ945K2. Positions 28-548.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ945K2.

Family & Domainsi

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi292 – 2954Poly-Leu

Sequence similaritiesi

Belongs to the GMC oxidoreductase family.Curated

Keywords - Domaini

Signal

Family and domain databases

InterProiIPR012132. GMC_OxRdtase.
IPR000172. GMC_OxRdtase_N.
IPR007867. GMC_OxRtase_C.
[Graphical view]
PfamiPF05199. GMC_oxred_C. 1 hit.
PF00732. GMC_oxred_N. 1 hit.
[Graphical view]
PIRSFiPIRSF000137. Alcohol_oxidase. 1 hit.
PROSITEiPS00623. GMC_OXRED_1. 1 hit.
PS00624. GMC_OXRED_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q945K2-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MEKSTMSAIL LVLYIFVLHL QYSEVHSLAT TSDHDFSYLS FAYDATDLEL
60 70 80 90 100
EGSYDYVIVG GGTSGCPLAA TLSEKYKVLV LERGSLPTAY PNVLTADGFV
110 120 130 140 150
YNLQQEDDGK TPVERFVSED GIDNVRGRVL GGTSIINAGV YARANTSIYS
160 170 180 190 200
ASGVDWDMDL VNQTYEWVED TIVYKPNSQS WQSVTKTAFL EAGVHPNHGF
210 220 230 240 250
SLDHEEGTRI TGSTFDNKGT RHAADELLNK GNSNNLRVGV HASVEKIIFS
260 270 280 290 300
NAPGLTATGV IYRDSNGTPH QAFVRSKGEV IVSAGTIGTP QLLLLSGVGP
310 320 330 340 350
ESYLSSLNIP VVLSHPYVGQ FLHDNPRNFI NILPPNPIEP TIVTVLGISN
360 370 380 390 400
DFYQCSFSSL PFTTPPFGFF PSASYPLPNS TFAHFASKVA GPLSYGSLTL
410 420 430 440 450
KSSSNVRVSP NVKFNYYSNL TDLSHCVSGM KKIGELLSTD ALKPYKVEDL
460 470 480 490 500
PGVEGFNILG IPLPKDQTDD AAFETFCRES VASYWHYHGG CLVGKVLDGD
510 520 530 540 550
FRVTGINALR VVDGSTFPYT PASHPQGFYL MLGRYVGIKI LQERSASDLK
560
ILDSLKSAAS LVL
Length:563
Mass (Da):61,158
Last modified:December 1, 2001 - v1
Checksum:iE0F53C236F4B001C
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti373 – 3731A → S No nucleotide entry (PubMed:19256550)Curated

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AF412329 Genomic DNA. Translation: AAL11514.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AF412329 Genomic DNA. Translation: AAL11514.1 .

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1JU2 X-ray 1.47 A/B 28-563 [» ]
3GDN X-ray 1.67 A/B 28-548 [» ]
3GDP X-ray 1.57 A/B 28-548 [» ]
ProteinModelPortali Q945K2.
SMRi Q945K2. Positions 28-548.
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Enzyme and pathway databases

BRENDAi 4.1.2.10. 1961.

Miscellaneous databases

EvolutionaryTracei Q945K2.

Family and domain databases

InterProi IPR012132. GMC_OxRdtase.
IPR000172. GMC_OxRdtase_N.
IPR007867. GMC_OxRtase_C.
[Graphical view ]
Pfami PF05199. GMC_oxred_C. 1 hit.
PF00732. GMC_oxred_N. 1 hit.
[Graphical view ]
PIRSFi PIRSF000137. Alcohol_oxidase. 1 hit.
PROSITEi PS00623. GMC_OXRED_1. 1 hit.
PS00624. GMC_OXRED_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "The hydroxynitrile lyase from almond: a lyase that looks like an oxidoreductase."
    Dreveny I., Gruber K., Glieder A., Thompson A., Kratky C.
    Structure 9:803-815(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, X-RAY CRYSTALLOGRAPHY (1.47 ANGSTROMS) OF 28-563, GLYCOSYLATION AT ASN-145; ASN-162; ASN-379 AND ASN-419, DISULFIDE BOND.
    Tissue: Seed.
  2. "Studies on the kinetics of cyanohydrin synthesis and cleavage by the the flavoenzyme oxynitrilase."
    Jorns M.S.
    Biochim. Biophys. Acta 613:203-209(1980) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY.
  3. "The active site of hydroxynitrile lyase from Prunus amygdalus: modeling studies provide new insights into the mechanism of cyanogenesis."
    Dreveny I., Kratky C., Gruber K.
    Protein Sci. 11:292-300(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: 3D-STRUCTURE MODELING.
  4. "Substrate binding in the FAD-dependent hydroxynitrile lyase from almond provides insight into the mechanism of cyanohydrin formation and explains the absence of dehydrogenation activity."
    Dreveny I., Andryushkova A.S., Glieder A., Gruber K., Kratky C.
    Biochemistry 48:3370-3377(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.57 ANGSTROMS) OF 28-548 IN COMPLEX WITH FAD AND BENZALDEHYDE, SUBUNIT, CATALYTIC ACTIVITY, GLYCOSYLATION AT ASN-145; ASN-162; ASN-379 AND ASN-419, DISULFIDE BOND, MUTAGENESIS OF HIS-486 AND HIS-524, BIOPHYSICOCHEMICAL PROPERTIES.

Entry informationi

Entry nameiMDL2_PRUDU
AccessioniPrimary (citable) accession number: Q945K2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 28, 2012
Last sequence update: December 1, 2001
Last modified: October 1, 2014
This is version 61 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3