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Protein

(R)-mandelonitrile lyase 1

Gene

MDL1

Organism
Prunus serotina (Black cherry)
Status
Reviewed-Annotation score: 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. It is a major seed constituent, and could have the additional role of a storage form for reduced nitrogen.

Catalytic activityi

(R)-mandelonitrile = cyanide + benzaldehyde.

Cofactori

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei129FAD; via carbonyl oxygenBy similarity1
Binding sitei133FADBy similarity1
Binding sitei244FAD; via amide nitrogen and carbonyl oxygenBy similarity1
Binding sitei355SubstrateBy similarity1
Binding sitei484SubstrateBy similarity1
Active sitei486Proton donorBy similarity1
Binding sitei514FAD; via amide nitrogenBy similarity1
Active sitei524Proton acceptorBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi63 – 64FADBy similarity2
Nucleotide bindingi82 – 83FADBy similarity2
Nucleotide bindingi137 – 140FADBy similarity4
Nucleotide bindingi485 – 486FADBy similarity2
Nucleotide bindingi525 – 526FADBy similarity2

GO - Molecular functioni

Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Ligandi

FAD, Flavoprotein

Enzyme and pathway databases

BRENDAi4.1.2.10. 5069.

Names & Taxonomyi

Protein namesi
Recommended name:
(R)-mandelonitrile lyase 1 (EC:4.1.2.10)
Alternative name(s):
Hydroxynitrile lyase 1
Short name:
(R)-oxynitrilase 1
Gene namesi
Name:MDL1
OrganismiPrunus serotina (Black cherry)
Taxonomic identifieri23207 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsfabidsRosalesRosaceaeMaloideaeAmygdaleaePrunus

Subcellular locationi

  • Vacuolealeurone grain

  • Note: Primarily found within protein bodies of the cotyledonary parenchyma cells, with lesser amounts within the procambium.

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Vacuole

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 271 PublicationAdd BLAST27
ChainiPRO_000001234028 – 563(R)-mandelonitrile lyase 1Add BLAST536

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi145N-linked (GlcNAc...)Sequence analysis1
Glycosylationi162N-linked (GlcNAc...)Sequence analysis1
Glycosylationi379N-linked (GlcNAc...)Sequence analysis1
Disulfide bondi426 ↔ 477By similarity

Post-translational modificationi

Glycosylated.

Keywords - PTMi

Disulfide bond, Glycoprotein

Expressioni

Tissue specificityi

Seeds. Localized within cotyledonary parenchyma cells.1 Publication

Developmental stagei

Absent from maturing black cherry fruits until 6 weeks after flowering. Then, concomitant with cotyledon development, the level of enzyme increases with specificity for embryonal tissues.2 Publications

Interactioni

Subunit structurei

Monomer.

Structurei

3D structure databases

ProteinModelPortaliP52706.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi292 – 295Poly-Leu4

Sequence similaritiesi

Belongs to the GMC oxidoreductase family.Curated

Keywords - Domaini

Signal

Family and domain databases

Gene3Di3.50.50.60. 4 hits.
InterProiIPR023753. FAD/NAD-binding_dom.
IPR000172. GMC_OxRdtase_N.
IPR007867. GMC_OxRtase_C.
[Graphical view]
PfamiPF05199. GMC_oxred_C. 1 hit.
PF00732. GMC_oxred_N. 1 hit.
[Graphical view]
SUPFAMiSSF51905. SSF51905. 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.

P52706-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEKSTMSAIL LVLHLFVLLL QYSEVHSLAT TSNHDFSYLR FAYDATDLEL
60 70 80 90 100
EGSYDYVIVG GGTSGCPLAA TLSEKYKVLV LERGSLPTAY PNVLTADGFV
110 120 130 140 150
YNLQQEDDGK TPVERFVSED GIDNVRGRVL GGTSMINAGV YARANTSIYS
160 170 180 190 200
ASGVDWDMDL VNKTYEWVED TIVFKPNYQP WQSVTGTAFL EAGVDPNHGF
210 220 230 240 250
SLDHEAGTRI TGSTFDNKGT RHAADELLNK GNSNNLRVGV HASVEKIIFS
260 270 280 290 300
NAPGLTATGV IYRDSNGTPH RAFVRSKGEV IVSAGTIGTP QLLLLSGVGP
310 320 330 340 350
ESYLSSLNIP VVLSHPYVGQ FLHDNPRNFI NILPPNPIEP TIVTVLGISN
360 370 380 390 400
DFYQCSFSSL PFTTPPFSFF PSTSYPLPNS TFAHFASKVA GPLSYGSLTL
410 420 430 440 450
KSSSNVRVSP NVKFNYYSNP TDLSHCVSGM KKIGELLSTD ALKPYKVEDL
460 470 480 490 500
PGIEGFNILG IPLPKDQTDD AAFETFCRES VASYWHYHGG CLVGKVLDGD
510 520 530 540 550
FRVTGIDALR VVDGSTFPYT PASHPQGFYL MLGRYVGIKI LQERSASDLK
560
ILDSLKSAAS LVL
Length:563
Mass (Da):61,200
Last modified:October 1, 1996 - v1
Checksum:i152367E736AF5FDD
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X72617 mRNA. Translation: CAA51194.1.
U78814 Genomic DNA. Translation: AAB38536.1.
PIRiS32156.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X72617 mRNA. Translation: CAA51194.1.
U78814 Genomic DNA. Translation: AAB38536.1.
PIRiS32156.

3D structure databases

ProteinModelPortaliP52706.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

BRENDAi4.1.2.10. 5069.

Family and domain databases

Gene3Di3.50.50.60. 4 hits.
InterProiIPR023753. FAD/NAD-binding_dom.
IPR000172. GMC_OxRdtase_N.
IPR007867. GMC_OxRtase_C.
[Graphical view]
PfamiPF05199. GMC_oxred_C. 1 hit.
PF00732. GMC_oxred_N. 1 hit.
[Graphical view]
SUPFAMiSSF51905. SSF51905. 1 hit.
PROSITEiPS00623. GMC_OXRED_1. 1 hit.
PS00624. GMC_OXRED_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiMDL1_PRUSE
AccessioniPrimary (citable) accession number: P52706
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: October 5, 2016
This is version 89 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

Direct protein sequencing

Documents

  1. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.