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Protein

Formate dehydrogenase, chloroplastic/mitochondrial

Gene

FDH1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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 annotation1 Publication

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

    • formate catabolic process Source: GO_Central
    • response to cadmium ion Source: TAIR
    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Ligandi

    NAD

    Enzyme and pathway databases

    BioCyciARA:AT5G14780-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Formate dehydrogenase, chloroplastic/mitochondrialCurated (EC:1.2.1.2UniRule 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

    TAIRiAT5G14780.

    Subcellular locationi

    • Mitochondrion UniRule annotation2 Publications
    • Plastidchloroplast 1 Publication

    GO - Cellular componenti

    • chloroplast Source: TAIR
    • mitochondrion Source: TAIR
    • thylakoid Source: TAIR
    Complete GO annotation...

    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

    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.
    OMAiHAKEEPR.
    OrthoDBiEOG09360BWJ.
    PhylomeDBiQ9S7E4.

    Family and domain databases

    CDDicd05302. FDH. 1 hit.
    Gene3Di3.40.50.720. 2 hits.
    HAMAPiMF_03210. Formate_dehydrogenase. 1 hit.
    InterProiIPR006139. 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.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view]
    PfamiPF00389. 2-Hacid_dh. 1 hit.
    PF02826. 2-Hacid_dh_C. 1 hit.
    [Graphical view]
    SUPFAMiSSF51735. SSF51735. 1 hit.
    PROSITEiPS00065. D_2_HYDROXYACID_DH_1. 1 hit.
    PS00670. D_2_HYDROXYACID_DH_2. 1 hit.
    PS00671. D_2_HYDROXYACID_DH_3. 1 hit.
    [Graphical view]

    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.

    Cross-referencesi

    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.

    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...

    Protein-protein interaction databases

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

    PTM databases

    iPTMnetiQ9S7E4.

    Proteomic databases

    PaxDbiQ9S7E4.
    PRIDEiQ9S7E4.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

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

    Organism-specific databases

    TAIRiAT5G14780.

    Phylogenomic databases

    eggNOGiKOG0069. Eukaryota.
    COG1052. LUCA.
    HOGENOMiHOG000136703.
    InParanoidiQ9S7E4.
    KOiK00122.
    OMAiHAKEEPR.
    OrthoDBiEOG09360BWJ.
    PhylomeDBiQ9S7E4.

    Enzyme and pathway databases

    BioCyciARA:AT5G14780-MONOMER.

    Miscellaneous databases

    EvolutionaryTraceiQ9S7E4.
    PROiQ9S7E4.

    Gene expression databases

    GenevisibleiQ9S7E4. AT.

    Family and domain databases

    CDDicd05302. FDH. 1 hit.
    Gene3Di3.40.50.720. 2 hits.
    HAMAPiMF_03210. Formate_dehydrogenase. 1 hit.
    InterProiIPR006139. 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.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view]
    PfamiPF00389. 2-Hacid_dh. 1 hit.
    PF02826. 2-Hacid_dh_C. 1 hit.
    [Graphical view]
    SUPFAMiSSF51735. SSF51735. 1 hit.
    PROSITEiPS00065. D_2_HYDROXYACID_DH_1. 1 hit.
    PS00670. D_2_HYDROXYACID_DH_2. 1 hit.
    PS00671. D_2_HYDROXYACID_DH_3. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiFDH_ARATH
    AccessioniPrimary (citable) accession number: Q9S7E4
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 27, 2002
    Last sequence update: May 1, 2000
    Last modified: November 30, 2016
    This is version 123 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, 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

    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.