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Q945K2

- MDL2_PRUDU

UniProt

Q945K2 - MDL2_PRUDU

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
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    • History
      Entry version 61 (01 Oct 2014)
      Sequence version 1 (01 Dec 2001)
      Previous versions | rss
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    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

    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

    MEKSTMSAIL LVLYIFVLHL QYSEVHSLAT TSDHDFSYLS FAYDATDLEL    50
    EGSYDYVIVG GGTSGCPLAA TLSEKYKVLV LERGSLPTAY PNVLTADGFV 100
    YNLQQEDDGK TPVERFVSED GIDNVRGRVL GGTSIINAGV YARANTSIYS 150
    ASGVDWDMDL VNQTYEWVED TIVYKPNSQS WQSVTKTAFL EAGVHPNHGF 200
    SLDHEEGTRI TGSTFDNKGT RHAADELLNK GNSNNLRVGV HASVEKIIFS 250
    NAPGLTATGV IYRDSNGTPH QAFVRSKGEV IVSAGTIGTP QLLLLSGVGP 300
    ESYLSSLNIP VVLSHPYVGQ FLHDNPRNFI NILPPNPIEP TIVTVLGISN 350
    DFYQCSFSSL PFTTPPFGFF PSASYPLPNS TFAHFASKVA GPLSYGSLTL 400
    KSSSNVRVSP NVKFNYYSNL TDLSHCVSGM KKIGELLSTD ALKPYKVEDL 450
    PGVEGFNILG IPLPKDQTDD AAFETFCRES VASYWHYHGG CLVGKVLDGD 500
    FRVTGINALR VVDGSTFPYT PASHPQGFYL MLGRYVGIKI LQERSASDLK 550
    ILDSLKSAAS LVL 563
    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