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Protein

Formate dehydrogenase, chloroplastic/mitochondrial

Gene

FDH1

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

Functioni

Catalyzes the NAD+-dependent oxidation of formate to carbon dioxide. Involved in the cell stress response.UniRule annotation1 Publication

Catalytic activityi

Formate + NAD+ = CO2 + NADH.UniRule annotation2 Publications

Kineticsi

  1. KM=104 mM for formate(at pH 7 and 30 degrees Celsius)1 Publication
  2. KM=1.4 mM for formate (at pH 7.5 and 25 degrees Celsius)1 Publication
  3. KM=65 µM for NAD (at pH 7. and 30 degrees Celsius)1 Publication
  4. KM=34 µM for NAD (at pH 7.5 and 25 degrees Celsius)1 Publication

    pH dependencei

    Optimum pH is 6-8.1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei128Substrate; via amide nitrogenUniRule annotation1
    Binding sitei152SubstrateUniRule annotation1
    Binding sitei227NADUniRule annotation1 Publication1
    Binding sitei288NAD; via carbonyl oxygenUniRule annotation1 Publication1
    Sitei290Important for catalytic activityUniRule annotation1
    Binding sitei314NADUniRule annotation1 Publication1
    Sitei338Important for catalytic activityUniRule annotation1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi207 – 208NADUniRule annotation1 Publication2
    Nucleotide bindingi262 – 266NADUniRule annotation1 Publication5
    Nucleotide bindingi338 – 341NADUniRule annotation1 Publication4

    GO - Molecular functioni

    GO - Biological processi

    • response to cadmium ion Source: TAIR

    Keywordsi

    Molecular functionOxidoreductase
    LigandNAD

    Enzyme and pathway databases

    BioCyciARA:AT5G14780-MONOMER

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Formate dehydrogenase, chloroplastic/mitochondrialCurated (EC:1.17.1.9UniRule annotation2 Publications)
    Short name:
    FDHUniRule annotation
    Alternative name(s):
    NAD-dependent formate dehydrogenaseUniRule annotation
    Gene namesi
    Name:FDH1
    Synonyms:FDH1 Publication
    Ordered Locus Names:At5g14780
    ORF Names:T9L3_80
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    Proteomesi
    • UP000006548 Componenti: Chromosome 5

    Organism-specific databases

    AraportiAT5G14780
    TAIRilocus:2185500 AT5G14780

    Subcellular locationi

    Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Chloroplast Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertion Graphics by Christian Stolte; Source: COMPARTMENTS

    Keywords - Cellular componenti

    Chloroplast, Mitochondrion, Plastid

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Transit peptidei1 – 29Chloroplast and mitochondrion1 PublicationAdd BLAST29
    ChainiPRO_000000719330 – 384Formate dehydrogenase, chloroplastic/mitochondrialAdd BLAST355

    Proteomic databases

    PaxDbiQ9S7E4
    PRIDEiQ9S7E4

    PTM databases

    iPTMnetiQ9S7E4

    Expressioni

    Inductioni

    By one-carbon metabolites, such as methanol, formaldehyde, and formate (at protein level) (Ref. 3). Strongest induced by formaldehyde (PubMed:16232936).2 Publications

    Gene expression databases

    ExpressionAtlasiQ9S7E4 baseline and differential
    GenevisibleiQ9S7E4 AT

    Interactioni

    Subunit structurei

    Homodimer.UniRule annotation1 Publication

    Protein-protein interaction databases

    BioGridi16607, 1 interactor
    IntActiQ9S7E4, 1 interactor
    STRINGi3702.AT5G14780.1

    Structurei

    Secondary structure

    1384
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi37 – 41Combined sources5
    Helixi47 – 51Combined sources5
    Turni59 – 61Combined sources3
    Helixi62 – 64Combined sources3
    Helixi66 – 71Combined sources6
    Beta strandi75 – 80Combined sources6
    Helixi88 – 92Combined sources5
    Turni93 – 95Combined sources3
    Beta strandi97 – 101Combined sources5
    Helixi111 – 116Combined sources6
    Beta strandi122 – 128Combined sources7
    Helixi135 – 140Combined sources6
    Beta strandi144 – 147Combined sources4
    Turni149 – 152Combined sources4
    Helixi153 – 169Combined sources17
    Helixi171 – 179Combined sources9
    Helixi185 – 189Combined sources5
    Beta strandi199 – 203Combined sources5
    Helixi207 – 216Combined sources10
    Helixi217 – 219Combined sources3
    Beta strandi222 – 226Combined sources5
    Helixi233 – 239Combined sources7
    Helixi247 – 250Combined sources4
    Helixi251 – 253Combined sources3
    Beta strandi255 – 259Combined sources5
    Turni265 – 269Combined sources5
    Helixi273 – 278Combined sources6
    Beta strandi283 – 287Combined sources5
    Helixi291 – 293Combined sources3
    Helixi296 – 305Combined sources10
    Beta strandi306 – 314Combined sources9
    Beta strandi317 – 320Combined sources4
    Helixi326 – 328Combined sources3
    Helixi340 – 342Combined sources3
    Helixi344 – 363Combined sources20
    Helixi369 – 371Combined sources3
    Beta strandi372 – 375Combined sources4
    Helixi381 – 383Combined sources3

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3JTMX-ray1.30A34-384[»]
    3N7UX-ray2.00A/B/C/D/E/F/G/H/I/J/K/L34-384[»]
    3NAQX-ray1.70A/B28-384[»]
    ProteinModelPortaliQ9S7E4
    SMRiQ9S7E4
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9S7E4

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni37 – 152CatalyticUniRule annotationAdd BLAST116
    Regioni153 – 339Coenzyme-bindingUniRule annotationAdd BLAST187
    Regioni340 – 383CatalyticUniRule annotationAdd BLAST44

    Sequence similaritiesi

    Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family. FDH subfamily.UniRule annotation

    Keywords - Domaini

    Transit peptide

    Phylogenomic databases

    eggNOGiKOG0069 Eukaryota
    COG1052 LUCA
    HOGENOMiHOG000136703
    InParanoidiQ9S7E4
    KOiK00122
    OMAiEVTYCNS
    OrthoDBiEOG09360BWJ
    PhylomeDBiQ9S7E4

    Family and domain databases

    CDDicd05302 FDH, 1 hit
    HAMAPiMF_03210 Formate_dehydrogenase, 1 hit
    InterProiView protein in InterPro
    IPR006139 D-isomer_2_OHA_DH_cat_dom
    IPR029753 D-isomer_DH_CS
    IPR029752 D-isomer_DH_CS1
    IPR006140 D-isomer_DH_NAD-bd
    IPR033689 FDH_NAD-dep
    IPR036291 NAD(P)-bd_dom_sf
    PfamiView protein in Pfam
    PF00389 2-Hacid_dh, 1 hit
    PF02826 2-Hacid_dh_C, 1 hit
    SUPFAMiSSF51735 SSF51735, 1 hit
    PROSITEiView protein in PROSITE
    PS00065 D_2_HYDROXYACID_DH_1, 1 hit
    PS00670 D_2_HYDROXYACID_DH_2, 1 hit
    PS00671 D_2_HYDROXYACID_DH_3, 1 hit

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    Q9S7E4-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MAMRQAAKAT IRACSSSSSS GYFARRQFNA SSGDSKKIVG VFYKANEYAT
    60 70 80 90 100
    KNPNFLGCVE NALGIRDWLE SQGHQYIVTD DKEGPDCELE KHIPDLHVLI
    110 120 130 140 150
    STPFHPAYVT AERIKKAKNL KLLLTAGIGS DHIDLQAAAA AGLTVAEVTG
    160 170 180 190 200
    SNVVSVAEDE LMRILILMRN FVPGYNQVVK GEWNVAGIAY RAYDLEGKTI
    210 220 230 240 250
    GTVGAGRIGK LLLQRLKPFG CNLLYHDRLQ MAPELEKETG AKFVEDLNEM
    260 270 280 290 300
    LPKCDVIVIN MPLTEKTRGM FNKELIGKLK KGVLIVNNAR GAIMERQAVV
    310 320 330 340 350
    DAVESGHIGG YSGDVWDPQP APKDHPWRYM PNQAMTPHTS GTTIDAQLRY
    360 370 380
    AAGTKDMLER YFKGEDFPTE NYIVKDGELA PQYR
    Length:384
    Mass (Da):42,410
    Last modified:May 1, 2000 - v1
    Checksum:iA12BA423019D862B
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB023897 mRNA Translation: BAA88683.1
    AF217195 mRNA Translation: AAF67100.1
    AF208028 mRNA Translation: AAF19435.1
    AF208029 mRNA Translation: AAF19436.1
    AL391149 Genomic DNA Translation: CAC01877.1
    CP002688 Genomic DNA Translation: AED92076.1
    AY054285 mRNA Translation: AAL06944.1
    AY039609 mRNA Translation: AAK62664.1
    AY081734 mRNA Translation: AAL87387.1
    PIRiT51423
    RefSeqiNP_196982.1, NM_121482.4
    UniGeneiAt.23637
    At.6781

    Genome annotation databases

    EnsemblPlantsiAT5G14780.1; AT5G14780.1; AT5G14780
    GeneIDi831330
    GrameneiAT5G14780.1; AT5G14780.1; AT5G14780
    KEGGiath:AT5G14780

    Similar proteinsi

    Entry informationi

    Entry nameiFDH_ARATH
    AccessioniPrimary (citable) accession number: Q9S7E4
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 27, 2002
    Last sequence update: May 1, 2000
    Last modified: April 25, 2018
    This is version 132 of the entry and version 1 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, 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

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