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Protein

Alpha-hydroxynitrile lyase

Gene

HNL

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Involved in cyanogenesis, the release of HCN from injured tissues (By similarity). Displays R-selective hydroxynitrile lyase activity. Also accepts nitromethane (MeNO2) as a donor in a reaction with aromatic aldehydes to yield (R)-beta-nitro alcohols.By similarity4 Publications

Catalytic activityi

(R)-mandelonitrile = cyanide + benzaldehyde.1 Publication

Kineticsi

  1. KM=1.4 mM for mandelonitrile1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei81 – 811
    Active sitei208 – 2081
    Active sitei236 – 2361

    GO - Molecular functioni

    • mandelonitrile lyase activity Source: TAIR

    GO - Biological processi

    • glycoside catabolic process Source: TAIR
    • response to wounding Source: TAIR
    Complete GO annotation...

    Keywords - Molecular functioni

    Lyase

    Enzyme and pathway databases

    BioCyciARA:AT5G10300-MONOMER.
    BRENDAi4.1.2.10. 399.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Alpha-hydroxynitrile lyase (EC:4.1.2.10)
    Short name:
    AtHNL
    Alternative name(s):
    (R)-hydroxynitrile lyase
    (R)-oxynitrilase
    Methylesterase 5
    Short name:
    AtMES5
    Gene namesi
    Name:HNL
    Synonyms:MES5
    Ordered Locus Names:At5g10300
    ORF Names:F18D22_70
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548 Componenti: Chromosome 5

    Organism-specific databases

    TAIRiAT5G10300.

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi81 – 811S → A: Loss of activity. 1 Publication
    Mutagenesisi208 – 2081D → N: Loss of activity. 1 Publication
    Mutagenesisi236 – 2361H → F: Loss of activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 258258Alpha-hydroxynitrile lyasePRO_0000418174Add
    BLAST

    Proteomic databases

    PRIDEiQ9LFT6.

    Expressioni

    Gene expression databases

    GenevestigatoriQ9LFT6.

    Interactioni

    Subunit structurei

    Homodimer.By similarity

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    MES9O231713EBI-4453194,EBI-4446268

    Protein-protein interaction databases

    IntActiQ9LFT6. 1 interaction.
    STRINGi3702.AT5G10300.1-P.

    Structurei

    Secondary structure

    1
    258
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi6 – 105Combined sources
    Helixi17 – 204Combined sources
    Helixi23 – 297Combined sources
    Beta strandi33 – 375Combined sources
    Helixi49 – 513Combined sources
    Helixi55 – 6713Combined sources
    Beta strandi75 – 806Combined sources
    Helixi83 – 919Combined sources
    Helixi95 – 973Combined sources
    Beta strandi98 – 1058Combined sources
    Beta strandi111 – 1133Combined sources
    Helixi117 – 1237Combined sources
    Beta strandi133 – 1397Combined sources
    Beta strandi142 – 1487Combined sources
    Helixi151 – 1577Combined sources
    Helixi164 – 17310Combined sources
    Helixi181 – 1855Combined sources
    Turni192 – 1943Combined sources
    Helixi195 – 1973Combined sources
    Beta strandi200 – 2056Combined sources
    Beta strandi209 – 2113Combined sources
    Helixi213 – 22210Combined sources
    Beta strandi228 – 2314Combined sources
    Helixi238 – 2414Combined sources
    Helixi243 – 25614Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3DQZX-ray2.50A/B/C/D1-258[»]
    ProteinModelPortaliQ9LFT6.
    SMRiQ9LFT6. Positions 3-258.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9LFT6.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiNOG252413.
    HOGENOMiHOG000133452.
    InParanoidiQ9LFT6.
    OMAiDCEFSSH.
    PhylomeDBiQ9LFT6.

    Family and domain databases

    Gene3Di3.40.50.1820. 1 hit.
    InterProiIPR029058. AB_hydrolase.
    IPR000073. AB_hydrolase_1.
    [Graphical view]
    PfamiPF12697. Abhydrolase_6. 1 hit.
    [Graphical view]
    SUPFAMiSSF53474. SSF53474. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q9LFT6-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MERKHHFVLV HNAYHGAWIW YKLKPLLESA GHRVTAVELA ASGIDPRPIQ
    60 70 80 90 100
    AVETVDEYSK PLIETLKSLP ENEEVILVGF SFGGINIALA ADIFPAKIKV
    110 120 130 140 150
    LVFLNAFLPD TTHVPSHVLD KYMEMPGGLG DCEFSSHETR NGTMSLLKMG
    160 170 180 190 200
    PKFMKARLYQ NCPIEDYELA KMLHRQGSFF TEDLSKKEKF SEEGYGSVQR
    210 220 230 240 250
    VYVMSSEDKA IPCDFIRWMI DNFNVSKVYE IDGGDHMVML SKPQKLFDSL

    SAIATDYM
    Length:258
    Mass (Da):29,217
    Last modified:October 1, 2000 - v1
    Checksum:i0CFA965320F1FD2E
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti70 – 701P → Q in AAL25532 (PubMed:14593172).Curated
    Sequence conflicti75 – 751V → G in AAL25532 (PubMed:14593172).Curated
    Sequence conflicti177 – 1771G → R in AAK76689 (PubMed:14593172).Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AL360334 Genomic DNA. Translation: CAB96686.1.
    CP002688 Genomic DNA. Translation: AED91518.1.
    AY046015 mRNA. Translation: AAK76689.1.
    AY058115 mRNA. Translation: AAL25532.1.
    AY093714 mRNA. Translation: AAM10338.1.
    AY142490 mRNA. Translation: AAN13041.1.
    AK226255 mRNA. Translation: BAE98416.1.
    PIRiT50818.
    RefSeqiNP_196592.1. NM_121068.3.
    UniGeneiAt.19934.

    Genome annotation databases

    EnsemblPlantsiAT5G10300.1; AT5G10300.1; AT5G10300.
    GeneIDi830894.
    KEGGiath:AT5G10300.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AL360334 Genomic DNA. Translation: CAB96686.1.
    CP002688 Genomic DNA. Translation: AED91518.1.
    AY046015 mRNA. Translation: AAK76689.1.
    AY058115 mRNA. Translation: AAL25532.1.
    AY093714 mRNA. Translation: AAM10338.1.
    AY142490 mRNA. Translation: AAN13041.1.
    AK226255 mRNA. Translation: BAE98416.1.
    PIRiT50818.
    RefSeqiNP_196592.1. NM_121068.3.
    UniGeneiAt.19934.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3DQZX-ray2.50A/B/C/D1-258[»]
    ProteinModelPortaliQ9LFT6.
    SMRiQ9LFT6. Positions 3-258.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    IntActiQ9LFT6. 1 interaction.
    STRINGi3702.AT5G10300.1-P.

    Proteomic databases

    PRIDEiQ9LFT6.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblPlantsiAT5G10300.1; AT5G10300.1; AT5G10300.
    GeneIDi830894.
    KEGGiath:AT5G10300.

    Organism-specific databases

    TAIRiAT5G10300.

    Phylogenomic databases

    eggNOGiNOG252413.
    HOGENOMiHOG000133452.
    InParanoidiQ9LFT6.
    OMAiDCEFSSH.
    PhylomeDBiQ9LFT6.

    Enzyme and pathway databases

    BioCyciARA:AT5G10300-MONOMER.
    BRENDAi4.1.2.10. 399.

    Miscellaneous databases

    EvolutionaryTraceiQ9LFT6.
    PROiQ9LFT6.

    Gene expression databases

    GenevestigatoriQ9LFT6.

    Family and domain databases

    Gene3Di3.40.50.1820. 1 hit.
    InterProiIPR029058. AB_hydrolase.
    IPR000073. AB_hydrolase_1.
    [Graphical view]
    PfamiPF12697. Abhydrolase_6. 1 hit.
    [Graphical view]
    SUPFAMiSSF53474. SSF53474. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana."
      Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E., Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.
      , Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L., O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D., Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M., Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L., Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B., Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P., Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M., Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D., Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A., Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I., Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T., Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A., McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U., Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M., Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G., Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W., Bevan M., Fransz P.F.
      Nature 408:823-826(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Columbia.
    2. The Arabidopsis Information Resource (TAIR)
      Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
      Cited for: GENOME REANNOTATION.
      Strain: cv. Columbia.
    3. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
      Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
      , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
      Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: cv. Columbia.
    4. "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs."
      Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A., Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y., Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.
      , Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y., Shinozaki K.
      Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: cv. Columbia.
    5. "Inactive methyl indole-3-acetic acid ester can be hydrolyzed and activated by several esterases belonging to the AtMES esterase family of Arabidopsis."
      Yang Y., Xu R., Ma C.J., Vlot A.C., Klessig D.F., Pichersky E.
      Plant Physiol. 147:1034-1045(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: GENE FAMILY, FUNCTION.
    6. "Uneven twins: comparison of two enantiocomplementary hydroxynitrile lyases with alpha/beta-hydrolase fold."
      Guterl J.K., Andexer J.N., Sehl T., von Langermann J., Frindi-Wosch I., Rosenkranz T., Fitter J., Gruber K., Kragl U., Eggert T., Pohl M.
      J. Biotechnol. 141:166-173(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES.
    7. "Synthesis of (R)-?-nitro alcohols catalyzed by R-selective hydroxynitrile lyase from Arabidopsis thaliana in the aqueous-organic biphasic system."
      Fuhshuku K., Asano Y.
      J. Biotechnol. 153:153-159(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    8. "An R-selective hydroxynitrile lyase from Arabidopsis thaliana with an alpha/beta-hydrolase fold."
      Andexer J., von Langermann J., Mell A., Bocola M., Kragl U., Eggert T., Pohl M.
      Angew. Chem. Int. Ed. Engl. 46:8679-8681(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.50 ANGSTROMS), FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF SER-81; ASP-208 AND HIS-236.

    Entry informationi

    Entry nameiHNL_ARATH
    AccessioniPrimary (citable) accession number: Q9LFT6
    Secondary accession number(s): Q93Z57, Q94AI5
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 11, 2012
    Last sequence update: October 1, 2000
    Last modified: April 29, 2015
    This is version 93 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Caution

    Was originally thought to belong to the methylesterase (MES) family.1 Publication

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Arabidopsis thaliana
      Arabidopsis thaliana: entries and gene names
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3

    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 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.