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Protein

(R)-mandelonitrile lyase 3

Gene

MDL3

Organism
Prunus serotina (Black cherry)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript 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 sitei356SubstrateBy similarity1
Binding sitei485SubstrateBy similarity1
Active sitei487Proton donorBy similarity1
Binding sitei515FAD; via amide nitrogenBy similarity1
Active sitei525Proton acceptorBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi63 – 64FADBy similarity2
Nucleotide bindingi82 – 83FADBy similarity2
Nucleotide bindingi137 – 140FADBy similarity4
Nucleotide bindingi486 – 487FADBy similarity2
Nucleotide bindingi526 – 527FADBy similarity2

GO - Molecular functioni

Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Ligandi

FAD, Flavoprotein

Names & Taxonomyi

Protein namesi
Recommended name:
(R)-mandelonitrile lyase 3 (EC:4.1.2.10)
Alternative name(s):
Hydroxynitrile lyase 3
Short name:
(R)-oxynitrilase 3
Gene namesi
Name:MDL3
OrganismiPrunus serotina (Black cherry)
Taxonomic identifieri23207 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsfabidsRosalesRosaceaeMaloideaeAmygdaleaePrunus

Subcellular locationi

  • Vacuolealeurone grain By similarity

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

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Vacuole

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 27Sequence analysisAdd BLAST27
ChainiPRO_000001234228 – 573(R)-mandelonitrile lyase 3Add BLAST546

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi30N-linked (GlcNAc...)Sequence analysis1
Glycosylationi75N-linked (GlcNAc...)Sequence analysis1
Glycosylationi145N-linked (GlcNAc...)Sequence analysis1
Glycosylationi150N-linked (GlcNAc...)Sequence analysis1
Glycosylationi162N-linked (GlcNAc...)Sequence analysis1
Glycosylationi218N-linked (GlcNAc...)Sequence analysis1
Glycosylationi252N-linked (GlcNAc...)Sequence analysis1
Glycosylationi267N-linked (GlcNAc...)Sequence analysis1
Glycosylationi309N-linked (GlcNAc...)Sequence analysis1
Glycosylationi380N-linked (GlcNAc...)Sequence analysis1
Glycosylationi402N-linked (GlcNAc...)Sequence analysis1
Glycosylationi420N-linked (GlcNAc...)Sequence analysis1
Disulfide bondi427 ↔ 478By similarity
Glycosylationi467N-linked (GlcNAc...)Sequence analysis1

Keywords - PTMi

Disulfide bond, Glycoprotein

Interactioni

Subunit structurei

Monomer.

Structurei

3D structure databases

ProteinModelPortaliP52707.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi293 – 296Poly-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.

P52707-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVKSTMSAVL LVLHIFVLHL QYSEVQSLAN TSSHDFSYLS FVYDATDPEL
60 70 80 90 100
EGSYDYIIVG GGTAGCPLAA TLSANYSVLV LERGSLPTEY PNLLISDGFV
110 120 130 140 150
YNLQQEDDGK TPVERFVSED GIDNVRGRVL GGTSMINAGV YVRANTSFFN
160 170 180 190 200
QTGIEWDMDL VNQTYEWVED TIVFEPDSQT WQTVIGTAYL EAGILPNNGF
210 220 230 240 250
SVDHLAGTRL TGSTFDNNGT RHASDELLNK GDPNNLRVAV QAAVEKIIFS
260 270 280 290 300
SNTSGVTAIG VIYTDSNGTT HQAFVRGEGE VILSAGPIGS PQLLLLSGVG
310 320 330 340 350
PESYLTSLNI SVVASHPYVG QYIYDNPRNF INILPPNPIE ASTVTVLGIT
360 370 380 390 400
SDFYQCSISS LPFDTPPFSF FPTTSYPLPN QTFAHIVNKV PGPLSHGTVT
410 420 430 440 450
LNSSSDVRVG PNVKFNYYSN LTDLSHCVSG MKKLGEVLST DALEPYKVED
460 470 480 490 500
LPGIDGFNIL GIPLPENQTD DAAFETFCRE SVASYWHYHG GCLVGKVLDD
510 520 530 540 550
GFRVTGINAL RVVDGSTFPS TPASHPQGFY LMLGRYMGIQ ILQERSASED
560 570
AIRNLGFQEN ILDSPKSTSS FAF
Length:573
Mass (Da):62,180
Last modified:October 1, 1996 - v1
Checksum:iDB181C68FED3F800
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U51562 Genomic DNA. Translation: AAA96782.1.
AF013161 mRNA. Translation: AAB67714.1.
PIRiT07948.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U51562 Genomic DNA. Translation: AAA96782.1.
AF013161 mRNA. Translation: AAB67714.1.
PIRiT07948.

3D structure databases

ProteinModelPortaliP52707.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

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 nameiMDL3_PRUSE
AccessioniPrimary (citable) accession number: P52707
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: October 5, 2016
This is version 87 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

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.