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Protein

(R)-mandelonitrile lyase 2

Gene

MDL2

Organism
Prunus dulcis (Almond) (Amygdalus dulcis)
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. 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

pH dependencei

Optimum pH is 5.5.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei129FAD; via carbonyl oxygen1 Publication1
Binding sitei133FAD1 Publication1
Binding sitei244FAD; via amide nitrogen and carbonyl oxygen1 Publication1
Binding sitei355Substrate1
Binding sitei484Substrate1
Active sitei486Proton donor1
Binding sitei514FAD; via amide nitrogen1 Publication1
Active sitei524Proton acceptor1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi63 – 64FAD1 Publication2
Nucleotide bindingi82 – 83FAD1 Publication2
Nucleotide bindingi137 – 140FAD1 Publication4
Nucleotide bindingi485 – 486FAD1 Publication2
Nucleotide bindingi525 – 526FAD1 Publication2

GO - Molecular functioni

  • flavin adenine dinucleotide binding Source: UniProtKB
  • mandelonitrile lyase activity Source: UniProtKB
  • oxidoreductase activity, acting on CH-OH group of donors Source: InterPro

GO - Biological processi

  • nitrile metabolic process Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Ligandi

FAD, Flavoprotein

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)DescriptionActionsGraphical viewLength
Mutagenesisi486H → N: Loss of 95% of the catalytic activity. 1 Publication1
Mutagenesisi524H → N: Loss of 95% of the catalytic activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 27Sequence analysisAdd BLAST27
ChainiPRO_500006132128 – 563(R)-mandelonitrile lyase 2Sequence analysisAdd BLAST536

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi145N-linked (GlcNAc...)2 Publications1
Glycosylationi162N-linked (GlcNAc...)2 Publications1
Glycosylationi379N-linked (GlcNAc...)2 Publications1
Glycosylationi419N-linked (GlcNAc...)2 Publications1
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

1563
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
Beta strandi152 – 154Combined sources3
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 strandi252 – 254Combined sources3
Beta strandi256 – 263Combined sources8
Beta strandi269 – 282Combined sources14
Helixi285 – 295Combined sources11
Helixi301 – 306Combined sources6
Beta strandi312 – 314Combined sources3
Turni316 – 319Combined sources4
Beta strandi320 – 323Combined sources4
Beta strandi326 – 332Combined sources7
Beta strandi345 – 348Combined sources4
Beta strandi350 – 359Combined sources10
Beta strandi370 – 373Combined sources4
Beta strandi382 – 391Combined sources10
Beta strandi396 – 399Combined sources4
Helixi420 – 437Combined sources18
Helixi440 – 445Combined sources6
Turni452 – 455Combined sources4
Beta strandi458 – 461Combined sources4
Helixi470 – 480Combined sources11
Beta strandi488 – 491Combined sources4
Turni494 – 496Combined sources3
Beta strandi501 – 503Combined sources3
Beta strandi509 – 511Combined sources3
Helixi514 – 516Combined sources3
Beta strandi521 – 524Combined sources4
Helixi526 – 547Combined sources22

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1JU2X-ray1.47A/B28-563[»]
3GDNX-ray1.67A/B28-548[»]
3GDPX-ray1.57A/B28-548[»]
ProteinModelPortaliQ945K2.
SMRiQ945K2.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ945K2.

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.

Q945K2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEKSTMSAIL LVLYIFVLHL QYSEVHSLAT TSDHDFSYLS FAYDATDLEL
60 70 80 90 100
EGSYDYVIVG GGTSGCPLAA TLSEKYKVLV LERGSLPTAY PNVLTADGFV
110 120 130 140 150
YNLQQEDDGK TPVERFVSED GIDNVRGRVL GGTSIINAGV YARANTSIYS
160 170 180 190 200
ASGVDWDMDL VNQTYEWVED TIVYKPNSQS WQSVTKTAFL EAGVHPNHGF
210 220 230 240 250
SLDHEEGTRI TGSTFDNKGT RHAADELLNK GNSNNLRVGV HASVEKIIFS
260 270 280 290 300
NAPGLTATGV IYRDSNGTPH QAFVRSKGEV IVSAGTIGTP QLLLLSGVGP
310 320 330 340 350
ESYLSSLNIP VVLSHPYVGQ FLHDNPRNFI NILPPNPIEP TIVTVLGISN
360 370 380 390 400
DFYQCSFSSL PFTTPPFGFF PSASYPLPNS TFAHFASKVA GPLSYGSLTL
410 420 430 440 450
KSSSNVRVSP NVKFNYYSNL TDLSHCVSGM KKIGELLSTD ALKPYKVEDL
460 470 480 490 500
PGVEGFNILG IPLPKDQTDD AAFETFCRES VASYWHYHGG CLVGKVLDGD
510 520 530 540 550
FRVTGINALR VVDGSTFPYT PASHPQGFYL MLGRYVGIKI LQERSASDLK
560
ILDSLKSAAS LVL
Length:563
Mass (Da):61,158
Last modified:December 1, 2001 - v1
Checksum:iE0F53C236F4B001C
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti373A → S No nucleotide entry (PubMed:19256550).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF412329 Genomic DNA. Translation: AAL11514.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF412329 Genomic DNA. Translation: AAL11514.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1JU2X-ray1.47A/B28-563[»]
3GDNX-ray1.67A/B28-548[»]
3GDPX-ray1.57A/B28-548[»]
ProteinModelPortaliQ945K2.
SMRiQ945K2.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiQ945K2.

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 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: November 2, 2016
This is version 70 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.