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Q945K2 (MDL2_PRUDU) Reviewed, UniProtKB/Swiss-Prot

Last modified April 3, 2013. Version 57. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended 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 names
Name:MDL2
Synonyms:HNL1
OrganismPrunus dulcis (Almond) (Prunus amygdalus)
Taxonomic identifier3755 [NCBI]
Taxonomic lineageEukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › fabids › Rosales › Rosaceae › Amygdaloideae › Amygdaleae › Prunus

Protein attributes

Sequence length563 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.1 Ref.2

Catalytic activity

(R)-mandelonitrile = cyanide + benzaldehyde. Ref.2 Ref.4

Cofactor

FAD.

Subunit structure

Monomer. Ref.4

Post-translational modification

Glycosylated. Deglycosylation does not affect the enzymatic activity. Ref.1 Ref.4

Sequence similarities

Belongs to the GMC oxidoreductase family.

Biophysicochemical properties

pH dependence:

Optimum pH is 5.5. Ref.4

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 2727 Potential
Chain28 – 563536(R)-mandelonitrile lyase 2 Potential
PRO_5000061321

Regions

Nucleotide binding63 – 642FAD
Nucleotide binding82 – 832FAD
Nucleotide binding137 – 1404FAD
Nucleotide binding485 – 4862FAD
Nucleotide binding525 – 5262FAD
Compositional bias292 – 2954Poly-Leu

Sites

Active site4861Proton donor
Active site5241Proton acceptor
Binding site1291FAD; via carbonyl oxygen
Binding site1331FAD
Binding site2441FAD; via amide nitrogen and carbonyl oxygen
Binding site3551Substrate
Binding site4841Substrate
Binding site5141FAD; via amide nitrogen

Amino acid modifications

Glycosylation1451N-linked (GlcNAc...) Ref.1 Ref.4
Glycosylation1621N-linked (GlcNAc...) Ref.1 Ref.4
Glycosylation3791N-linked (GlcNAc...) Ref.1 Ref.4
Glycosylation4191N-linked (GlcNAc...) Ref.1 Ref.4
Disulfide bond426 ↔ 477 Ref.1 Ref.4

Experimental info

Mutagenesis4861H → N: Loss of 95% of the catalytic activity. Ref.4
Mutagenesis5241H → N: Loss of 95% of the catalytic activity. Ref.4
Sequence conflict3731A → S No nucleotide entry Ref.4

Secondary structure

1 ................................................................................................... 563
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q945K2 [UniParc].

Last modified December 1, 2001. Version 1.
Checksum: E0F53C236F4B001C

FASTA56361,158
        10         20         30         40         50         60 
MEKSTMSAIL LVLYIFVLHL QYSEVHSLAT TSDHDFSYLS FAYDATDLEL EGSYDYVIVG 

        70         80         90        100        110        120 
GGTSGCPLAA TLSEKYKVLV LERGSLPTAY PNVLTADGFV YNLQQEDDGK TPVERFVSED 

       130        140        150        160        170        180 
GIDNVRGRVL GGTSIINAGV YARANTSIYS ASGVDWDMDL VNQTYEWVED TIVYKPNSQS 

       190        200        210        220        230        240 
WQSVTKTAFL EAGVHPNHGF SLDHEEGTRI TGSTFDNKGT RHAADELLNK GNSNNLRVGV 

       250        260        270        280        290        300 
HASVEKIIFS NAPGLTATGV IYRDSNGTPH QAFVRSKGEV IVSAGTIGTP QLLLLSGVGP 

       310        320        330        340        350        360 
ESYLSSLNIP VVLSHPYVGQ FLHDNPRNFI NILPPNPIEP TIVTVLGISN DFYQCSFSSL 

       370        380        390        400        410        420 
PFTTPPFGFF PSASYPLPNS TFAHFASKVA GPLSYGSLTL KSSSNVRVSP NVKFNYYSNL 

       430        440        450        460        470        480 
TDLSHCVSGM KKIGELLSTD ALKPYKVEDL PGVEGFNILG IPLPKDQTDD AAFETFCRES 

       490        500        510        520        530        540 
VASYWHYHGG CLVGKVLDGD FRVTGINALR VVDGSTFPYT PASHPQGFYL MLGRYVGIKI 

       550        560 
LQERSASDLK ILDSLKSAAS LVL

« Hide

References

[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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		AF412329 Genomic DNA. Translation: AAL11514.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1JU2X-ray1.47A/B28-563[»]
3GDNX-ray1.67A/B28-548[»]
3GDPX-ray1.57A/B28-548[»]
ProteinModelPortalQ945K2.
SMRQ945K2. Positions 28-548.
ModBaseSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Enzyme and pathway databases

BRENDA4.1.2.10. 1961.

Family and domain databases

InterProIPR012132. GMC_OxRdtase.
IPR000172. GMC_OxRdtase_N.
IPR007867. GMC_OxRtase_C.
[Graphical view]
PfamPF05199. GMC_oxred_C. 1 hit.
PF00732. GMC_oxred_N. 1 hit.
[Graphical view]
PIRSFPIRSF000137. Alcohol_oxidase. 1 hit.
PROSITEPS00623. GMC_OXRED_1. 1 hit.
PS00624. GMC_OXRED_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ945K2.

Entry information

Entry nameMDL2_PRUDU
AccessionPrimary (citable) accession number: Q945K2
Entry history
Integrated into UniProtKB/Swiss-Prot: November 28, 2012
Last sequence update: December 1, 2001
Last modified: April 3, 2013
This is version 57 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

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