Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
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)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei128 – 1281Substrate; via amide nitrogenUniRule annotation
    Binding sitei152 – 1521SubstrateUniRule annotation
    Binding sitei227 – 2271NADUniRule annotation1 Publication
    Binding sitei288 – 2881NAD; via carbonyl oxygenUniRule annotation1 Publication
    Sitei290 – 2901Important for catalytic activityUniRule annotation
    Binding sitei314 – 3141NADUniRule annotation1 Publication
    Sitei338 – 3381Important for catalytic activityUniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi207 – 2082NADUniRule annotation1 Publication
    Nucleotide bindingi262 – 2665NADUniRule annotation1 Publication
    Nucleotide bindingi338 – 3414NADUniRule annotation1 Publication

    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)LengthDescriptionGraphical viewFeature identifierActions
    Transit peptidei1 – 2929Chloroplast and mitochondrion1 PublicationAdd
    BLAST
    Chaini30 – 384355Formate dehydrogenase, chloroplastic/mitochondrialPRO_0000007193Add
    BLAST

    Proteomic databases

    PaxDbiQ9S7E4.
    PRIDEiQ9S7E4.

    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 interaction.
    IntActiQ9S7E4. 1 interaction.
    STRINGi3702.AT5G14780.1.

    Structurei

    Secondary structure

    1
    384
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi37 – 415Combined sources
    Helixi47 – 515Combined sources
    Turni59 – 613Combined sources
    Helixi62 – 643Combined sources
    Helixi66 – 716Combined sources
    Beta strandi75 – 806Combined sources
    Helixi88 – 925Combined sources
    Turni93 – 953Combined sources
    Beta strandi97 – 1015Combined sources
    Helixi111 – 1166Combined sources
    Beta strandi122 – 1287Combined sources
    Helixi135 – 1406Combined sources
    Beta strandi144 – 1474Combined sources
    Turni149 – 1524Combined sources
    Helixi153 – 16917Combined sources
    Helixi171 – 1799Combined sources
    Helixi185 – 1895Combined sources
    Beta strandi199 – 2035Combined sources
    Helixi207 – 21610Combined sources
    Helixi217 – 2193Combined sources
    Beta strandi222 – 2265Combined sources
    Helixi233 – 2397Combined sources
    Helixi247 – 2504Combined sources
    Helixi251 – 2533Combined sources
    Beta strandi255 – 2595Combined sources
    Turni265 – 2695Combined sources
    Helixi273 – 2786Combined sources
    Beta strandi283 – 2875Combined sources
    Helixi291 – 2933Combined sources
    Helixi296 – 30510Combined sources
    Beta strandi306 – 3149Combined sources
    Beta strandi317 – 3204Combined sources
    Helixi326 – 3283Combined sources
    Helixi340 – 3423Combined sources
    Helixi344 – 36320Combined sources
    Helixi369 – 3713Combined sources
    Beta strandi372 – 3754Combined sources
    Helixi381 – 3833Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    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. Positions 34-384.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9S7E4.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni37 – 152116CatalyticUniRule annotationAdd
    BLAST
    Regioni153 – 339187Coenzyme-bindingUniRule annotationAdd
    BLAST
    Regioni340 – 38344CatalyticUniRule annotationAdd
    BLAST

    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.
    OMAiINCPLHD.
    PhylomeDBiQ9S7E4.

    Family and domain databases

    Gene3Di3.40.50.720. 2 hits.
    HAMAPiMF_03210. Formate_dehydrogenase.
    InterProiIPR006139. D-isomer_2_OHA_DH_cat_dom.
    IPR029753. D-isomer_DH_CS.
    IPR029752. D-isomer_DH_CS1.
    IPR006140. D-isomer_DH_NAD-bd.
    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_121482.3.
    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_121482.3.
    UniGeneiAt.23637.
    At.6781.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    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. Positions 34-384.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi16607. 1 interaction.
    IntActiQ9S7E4. 1 interaction.
    STRINGi3702.AT5G14780.1.

    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.
    OMAiINCPLHD.
    PhylomeDBiQ9S7E4.

    Enzyme and pathway databases

    BioCyciARA:AT5G14780-MONOMER.

    Miscellaneous databases

    EvolutionaryTraceiQ9S7E4.
    PROiQ9S7E4.

    Gene expression databases

    GenevisibleiQ9S7E4. AT.

    Family and domain databases

    Gene3Di3.40.50.720. 2 hits.
    HAMAPiMF_03210. Formate_dehydrogenase.
    InterProiIPR006139. D-isomer_2_OHA_DH_cat_dom.
    IPR029753. D-isomer_DH_CS.
    IPR029752. D-isomer_DH_CS1.
    IPR006140. D-isomer_DH_NAD-bd.
    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...

    Publicationsi

    « Hide 'large scale' publications
    1. "Formate dehydrogenase gene of Arabidopsis thaliana is induced by formaldehyde and not by formic acid."
      Fukusaki E., Ikeda T., Shiraishi T., Nishikawa T., Kobayashi A.
      J. Biosci. Bioeng. 90:691-693(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], INDUCTION.
    2. "Formate dehydrogenase in Arabidopsis thaliana: characterization and possible targeting to the chloroplast."
      Olson B.J., Skavdahl M., Ramberg H., Osterman J.C., Markwell J.
      Plant Sci. 159:205-212(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBCELLULAR LOCATION.
    3. "Molecular characterization and regulation of formate dehydrogenase in Arabidopsis thaliana."
      Li R., Bonham-Smith P.C., King J.
      Can. J. Bot. 79:796-804(2001)
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, INDUCTION.
    4. "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.
    5. The Arabidopsis Information Resource (TAIR)
      Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
      Cited for: GENOME REANNOTATION.
      Strain: cv. Columbia.
    6. "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.
    7. "Purification and characterization of formate dehydrogenase from Arabidopsis thaliana."
      Li R., Ziola B., King J.
      J. Plant Physiol. 157:161-167(2000)
      Cited for: PROTEIN SEQUENCE OF 30-54, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBCELLULAR LOCATION, SUBUNIT.
    8. "Experimental analysis of the Arabidopsis mitochondrial proteome highlights signaling and regulatory components, provides assessment of targeting prediction programs, and indicates plant-specific mitochondrial proteins."
      Heazlewood J.L., Tonti-Filippini J.S., Gout A.M., Day D.A., Whelan J., Millar A.H.
      Plant Cell 16:241-256(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
      Strain: cv. Landsberg erecta.
    9. "Structure of recombinant formate dehydrogenase from Arabidopsis thaliana."
      Timofeev V.I., Shabalin I.G., Serov A.E., Polyakov K.M., Popov V.O., Tishkov V.I., Kuranova I.P., Samigina V.R.
      Submitted (SEP-2009) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (1.30 ANGSTROMS) OF 34-384.
    10. "Structures of the apo and holo forms of NAD-dependent formate dehydrogenase from the higher-plant Arabidopsis thaliana."
      Shabalin I.G., Polyakov K.M., Skirgello O.E., Tishkov V.I., Popov V.O.
      Submitted (MAY-2010) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) OF 34-384 IN COMPLEX WITH NAD.

    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: February 17, 2016
    This is version 118 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.