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Protein

(R)-mandelonitrile lyase 1

Gene

MDL1

Organism
Prunus dulcis (Almond) (Amygdalus dulcis)
Status
Reviewed-Annotation score: Annotation score: 3 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 (By similarity).By similarity

Catalytic activityi

(R)-mandelonitrile = cyanide + benzaldehyde.

Cofactori

FADBy similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei133FADBy similarity1
Binding sitei244FAD; via amide nitrogen and carbonyl oxygenBy similarity1
Binding sitei485SubstrateBy similarity1
Active sitei487Proton donorBy 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

Enzyme and pathway databases

BRENDAi4.1.2.10. 5059.

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 dulcis (Almond) (Amygdalus dulcis)
Taxonomic identifieri3755 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsfabidsRosalesRosaceaeMaloideaeAmygdaleaePrunus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 27By similarityAdd BLAST27
ChainiPRO_000001234428 – 559(R)-mandelonitrile lyase 1Add BLAST532

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi30N-linked (GlcNAc...)Sequence analysis1
Glycosylationi44N-linked (GlcNAc...)Sequence analysis1
Glycosylationi145N-linked (GlcNAc...)Sequence analysis1
Glycosylationi162N-linked (GlcNAc...)Sequence analysis1
Glycosylationi178N-linked (GlcNAc...)Sequence analysis1
Glycosylationi218N-linked (GlcNAc...)Sequence analysis1
Glycosylationi252N-linked (GlcNAc...)Sequence analysis1
Glycosylationi255N-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.By similarity

Structurei

Secondary structure

1559
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi37 – 41Combined sources5
Beta strandi42 – 44Combined sources3
Helixi45 – 47Combined sources3
Beta strandi50 – 59Combined sources10
Helixi65 – 72Combined sources8
Turni73 – 75Combined sources3
Beta strandi78 – 81Combined sources4
Beta strandi83 – 85Combined sources3
Helixi87 – 89Combined sources3
Helixi91 – 94Combined sources4
Helixi96 – 98Combined sources3
Helixi99 – 104Combined sources6
Beta strandi109 – 117Combined sources9
Beta strandi123 – 127Combined sources5
Helixi132 – 135Combined sources4
Helixi147 – 152Combined sources6
Helixi158 – 172Combined sources15
Helixi180 – 191Combined sources12
Beta strandi197 – 200Combined sources4
Beta strandi206 – 210Combined sources5
Beta strandi212 – 215Combined sources4
Beta strandi219 – 221Combined sources3
Helixi224 – 230Combined sources7
Turni233 – 235Combined sources3
Beta strandi236 – 241Combined sources6
Beta strandi243 – 249Combined sources7
Beta strandi257 – 264Combined sources8
Beta strandi270 – 283Combined sources14
Helixi286 – 296Combined sources11
Helixi302 – 307Combined sources6
Beta strandi313 – 315Combined sources3
Turni317 – 320Combined sources4
Beta strandi321 – 324Combined sources4
Beta strandi327 – 334Combined sources8
Beta strandi346 – 350Combined sources5
Beta strandi353 – 360Combined sources8
Beta strandi371 – 374Combined sources4
Beta strandi383 – 389Combined sources7
Beta strandi397 – 400Combined sources4
Beta strandi402 – 405Combined sources4
Beta strandi407 – 409Combined sources3
Beta strandi412 – 414Combined sources3
Helixi421 – 438Combined sources18
Turni441 – 443Combined sources3
Helixi444 – 446Combined sources3
Helixi454 – 456Combined sources3
Beta strandi457 – 461Combined sources5
Helixi471 – 481Combined sources11
Beta strandi489 – 492Combined sources4
Turni495 – 497Combined sources3
Beta strandi502 – 504Combined sources3
Beta strandi510 – 512Combined sources3
Helixi515 – 517Combined sources3
Beta strandi522 – 525Combined sources4
Helixi527 – 545Combined sources19

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5EB4X-ray2.30A/B28-559[»]
5EB5X-ray2.80A/B28-559[»]
ProteinModelPortaliO24243.
SMRiO24243.
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. 3 hits.
InterProiIPR023753. FAD/NAD-binding_dom.
IPR001613. Flavin_amine_oxidase.
IPR000172. GMC_OxRdtase_N.
IPR007867. GMC_OxRtase_C.
[Graphical view]
PfamiPF05199. GMC_oxred_C. 1 hit.
PF00732. GMC_oxred_N. 1 hit.
[Graphical view]
PRINTSiPR00757. AMINEOXDASEF.
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.

O24243-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEKSTMSVIL FVLHLLVLHL QYSEVHSLAN TSAHDFSYLK FVYNATDTSL
60 70 80 90 100
EGSYDYIVIG GGTSGCPLAA TLSEKYKVLL LERGTIATEY PNTLTADGFA
110 120 130 140 150
YNLQQQDDGK TPVERFVSED GIDNVRARIL GGTTIINAGV YARANISFYS
160 170 180 190 200
QTGIEWDLDL VNKTYEWVED AIVVKPNNQS WQSVIGEGFL EAGILPDNGF
210 220 230 240 250
SLDHEAGTRL TGSTFDNNGT RHAADELLNK GDPNNLLVAV QASVEKILFS
260 270 280 290 300
SNTSNLSAIG VIYTDSDGNS HQAFVRGNGE VIVSAGTIGT PQLLLLSGVG
310 320 330 340 350
PESYLSSLNI TVVQPNPYVG QFLYNNPRNF INNFPPNPIE ASVVTVLGIR
360 370 380 390 400
SDYYQVSLSS LPFSTPPFSL FPTTSYPLPN STFAHIVSQV PGPLSHGSVT
410 420 430 440 450
LNSSSDVRIA PNIKFNYYSN STDLANCVSG MKKLGDLLRT KALEPYKARD
460 470 480 490 500
VLGIDGFNYL GVPLPENQTD DASFETFCLD NVASYWHYHG GSLVGKVLDD
510 520 530 540 550
SFRVMGIKAL RVVDASTFPY EPNSHPQGFY LMLGRYVGLQ ILQERSIRLE

AIHNIQESM
Length:559
Mass (Da):61,100
Last modified:January 1, 1998 - v1
Checksum:i58C2999EBF2E8A54
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y08211 mRNA. Translation: CAA69388.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y08211 mRNA. Translation: CAA69388.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5EB4X-ray2.30A/B28-559[»]
5EB5X-ray2.80A/B28-559[»]
ProteinModelPortaliO24243.
SMRiO24243.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

BRENDAi4.1.2.10. 5059.

Family and domain databases

Gene3Di3.50.50.60. 3 hits.
InterProiIPR023753. FAD/NAD-binding_dom.
IPR001613. Flavin_amine_oxidase.
IPR000172. GMC_OxRdtase_N.
IPR007867. GMC_OxRtase_C.
[Graphical view]
PfamiPF05199. GMC_oxred_C. 1 hit.
PF00732. GMC_oxred_N. 1 hit.
[Graphical view]
PRINTSiPR00757. AMINEOXDASEF.
SUPFAMiSSF51905. SSF51905. 1 hit.
PROSITEiPS00623. GMC_OXRED_1. 1 hit.
PS00624. GMC_OXRED_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiMDL1_PRUDU
AccessioniPrimary (citable) accession number: O24243
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: January 1, 1998
Last modified: November 2, 2016
This is version 83 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

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.