FDH_ARATH
ID FDH_ARATH Reviewed; 384 AA.
AC Q9S7E4;
DT 27-MAY-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 152.
DE RecName: Full=Formate dehydrogenase, chloroplastic/mitochondrial {ECO:0000305};
DE Short=FDH {ECO:0000255|HAMAP-Rule:MF_03210};
DE EC=1.17.1.9 {ECO:0000255|HAMAP-Rule:MF_03210, ECO:0000269|PubMed:11074273, ECO:0000269|Ref.7};
DE AltName: Full=NAD-dependent formate dehydrogenase {ECO:0000255|HAMAP-Rule:MF_03210};
DE Flags: Precursor;
GN Name=FDH1; Synonyms=FDH {ECO:0000303|Ref.7}; OrderedLocusNames=At5g14780;
GN ORFNames=T9L3_80;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], AND INDUCTION.
RX PubMed=16232936; DOI=10.1263/jbb.90.691;
RA Fukusaki E., Ikeda T., Shiraishi T., Nishikawa T., Kobayashi A.;
RT "Formate dehydrogenase gene of Arabidopsis thaliana is induced by
RT formaldehyde and not by formic acid.";
RL J. Biosci. Bioeng. 90:691-693(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA], CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, AND SUBCELLULAR LOCATION.
RX PubMed=11074273; DOI=10.1016/s0168-9452(00)00337-x;
RA Olson B.J., Skavdahl M., Ramberg H., Osterman J.C., Markwell J.;
RT "Formate dehydrogenase in Arabidopsis thaliana: characterization and
RT possible targeting to the chloroplast.";
RL Plant Sci. 159:205-212(2000).
RN [3]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, AND INDUCTION.
RX DOI=10.1139/b01-056;
RA Li R., Bonham-Smith P.C., King J.;
RT "Molecular characterization and regulation of formate dehydrogenase in
RT Arabidopsis thaliana.";
RL Can. J. Bot. 79:796-804(2001).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130714; DOI=10.1038/35048507;
RA Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
RA Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M.,
RA Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.,
RA Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M.,
RA Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L.,
RA O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D.,
RA Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M.,
RA Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L.,
RA Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B.,
RA Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P.,
RA Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M.,
RA Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D.,
RA Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
RA Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
RA Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
RA Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A.,
RA McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U.,
RA Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W.,
RA Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M.,
RA Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S.,
RA Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G.,
RA Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W.,
RA Bevan M., Fransz P.F.;
RT "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.";
RL Nature 408:823-826(2000).
RN [5]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [7]
RP PROTEIN SEQUENCE OF 30-54, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, SUBCELLULAR LOCATION, AND SUBUNIT.
RX DOI=10.1016/S0176-1617(00)80186-8;
RA Li R., Ziola B., King J.;
RT "Purification and characterization of formate dehydrogenase from
RT Arabidopsis thaliana.";
RL J. Plant Physiol. 157:161-167(2000).
RN [8]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND SUBCELLULAR LOCATION [LARGE SCALE
RP ANALYSIS].
RC STRAIN=cv. Landsberg erecta;
RX PubMed=14671022; DOI=10.1105/tpc.016055;
RA Heazlewood J.L., Tonti-Filippini J.S., Gout A.M., Day D.A., Whelan J.,
RA Millar A.H.;
RT "Experimental analysis of the Arabidopsis mitochondrial proteome highlights
RT signaling and regulatory components, provides assessment of targeting
RT prediction programs, and indicates plant-specific mitochondrial proteins.";
RL Plant Cell 16:241-256(2004).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (1.30 ANGSTROMS) OF 34-384.
RA Timofeev V.I., Shabalin I.G., Serov A.E., Polyakov K.M., Popov V.O.,
RA Tishkov V.I., Kuranova I.P., Samigina V.R.;
RT "Structure of recombinant formate dehydrogenase from Arabidopsis
RT thaliana.";
RL Submitted (SEP-2009) to the PDB data bank.
RN [10]
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) OF 34-384 IN COMPLEX WITH NAD.
RA Shabalin I.G., Polyakov K.M., Skirgello O.E., Tishkov V.I., Popov V.O.;
RT "Structures of the apo and holo forms of NAD-dependent formate
RT dehydrogenase from the higher-plant Arabidopsis thaliana.";
RL Submitted (MAY-2010) to the PDB data bank.
CC -!- FUNCTION: Catalyzes the NAD(+)-dependent oxidation of formate to carbon
CC dioxide. Involved in the cell stress response. {ECO:0000255|HAMAP-
CC Rule:MF_03210, ECO:0000269|Ref.3}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=formate + NAD(+) = CO2 + NADH; Xref=Rhea:RHEA:15985,
CC ChEBI:CHEBI:15740, ChEBI:CHEBI:16526, ChEBI:CHEBI:57540,
CC ChEBI:CHEBI:57945; EC=1.17.1.9; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_03210, ECO:0000269|PubMed:11074273, ECO:0000269|Ref.7};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=104 mM for formate(at pH 7 and 30 degrees Celsius)
CC {ECO:0000269|PubMed:11074273};
CC KM=1.4 mM for formate (at pH 7.5 and 25 degrees Celsius)
CC {ECO:0000269|Ref.7};
CC KM=65 uM for NAD (at pH 7. and 30 degrees Celsius)
CC {ECO:0000269|PubMed:11074273};
CC KM=34 uM for NAD (at pH 7.5 and 25 degrees Celsius)
CC {ECO:0000269|Ref.7};
CC pH dependence:
CC Optimum pH is 6-8. {ECO:0000269|Ref.7};
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_03210,
CC ECO:0000269|Ref.7}.
CC -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000255|HAMAP-Rule:MF_03210,
CC ECO:0000269|PubMed:14671022, ECO:0000269|Ref.7}. Plastid, chloroplast
CC {ECO:0000269|PubMed:11074273}.
CC -!- INDUCTION: By one-carbon metabolites, such as methanol, formaldehyde,
CC and formate (at protein level) (Ref.3). Strongest induced by
CC formaldehyde (PubMed:16232936). {ECO:0000269|PubMed:16232936,
CC ECO:0000269|Ref.3}.
CC -!- SIMILARITY: Belongs to the D-isomer specific 2-hydroxyacid
CC dehydrogenase family. FDH subfamily. {ECO:0000255|HAMAP-Rule:MF_03210}.
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DR EMBL; AB023897; BAA88683.1; -; mRNA.
DR EMBL; AF217195; AAF67100.1; -; mRNA.
DR EMBL; AF208028; AAF19435.1; -; mRNA.
DR EMBL; AF208029; AAF19436.1; -; mRNA.
DR EMBL; AL391149; CAC01877.1; -; Genomic_DNA.
DR EMBL; CP002688; AED92076.1; -; Genomic_DNA.
DR EMBL; AY054285; AAL06944.1; -; mRNA.
DR EMBL; AY039609; AAK62664.1; -; mRNA.
DR EMBL; AY081734; AAL87387.1; -; mRNA.
DR PIR; T51423; T51423.
DR RefSeq; NP_196982.1; NM_121482.4.
DR PDB; 3JTM; X-ray; 1.30 A; A=34-384.
DR PDB; 3N7U; X-ray; 2.00 A; A/B/C/D/E/F/G/H/I/J/K/L=34-384.
DR PDB; 3NAQ; X-ray; 1.70 A; A/B=28-384.
DR PDBsum; 3JTM; -.
DR PDBsum; 3N7U; -.
DR PDBsum; 3NAQ; -.
DR AlphaFoldDB; Q9S7E4; -.
DR SMR; Q9S7E4; -.
DR BioGRID; 16607; 8.
DR IntAct; Q9S7E4; 1.
DR STRING; 3702.AT5G14780.1; -.
DR iPTMnet; Q9S7E4; -.
DR PaxDb; Q9S7E4; -.
DR PRIDE; Q9S7E4; -.
DR ProteomicsDB; 232074; -.
DR EnsemblPlants; AT5G14780.1; AT5G14780.1; AT5G14780.
DR GeneID; 831330; -.
DR Gramene; AT5G14780.1; AT5G14780.1; AT5G14780.
DR KEGG; ath:AT5G14780; -.
DR Araport; AT5G14780; -.
DR TAIR; locus:2185500; AT5G14780.
DR eggNOG; KOG0069; Eukaryota.
DR HOGENOM; CLU_019796_0_0_1; -.
DR InParanoid; Q9S7E4; -.
DR OrthoDB; 700058at2759; -.
DR PhylomeDB; Q9S7E4; -.
DR BioCyc; ARA:AT5G14780-MON; -.
DR BioCyc; MetaCyc:AT5G14780-MON; -.
DR BRENDA; 1.17.1.9; 399.
DR EvolutionaryTrace; Q9S7E4; -.
DR PRO; PR:Q9S7E4; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9S7E4; baseline and differential.
DR Genevisible; Q9S7E4; AT.
DR GO; GO:0009507; C:chloroplast; IBA:GO_Central.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0009326; C:formate dehydrogenase complex; IEA:UniProtKB-EC.
DR GO; GO:0005739; C:mitochondrion; HDA:TAIR.
DR GO; GO:0009536; C:plastid; HDA:TAIR.
DR GO; GO:0009579; C:thylakoid; HDA:TAIR.
DR GO; GO:0008863; F:formate dehydrogenase (NAD+) activity; IBA:GO_Central.
DR GO; GO:0051287; F:NAD binding; IEA:InterPro.
DR GO; GO:0016616; F:oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor; IEA:InterPro.
DR GO; GO:0042183; P:formate catabolic process; IEA:UniProtKB-UniRule.
DR CDD; cd05302; FDH; 1.
DR HAMAP; MF_03210; Formate_dehydrogenase; 1.
DR InterPro; IPR006139; D-isomer_2_OHA_DH_cat_dom.
DR InterPro; IPR029753; D-isomer_DH_CS.
DR InterPro; IPR029752; D-isomer_DH_CS1.
DR InterPro; IPR006140; D-isomer_DH_NAD-bd.
DR InterPro; IPR033689; FDH_NAD-dep.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR Pfam; PF00389; 2-Hacid_dh; 1.
DR Pfam; PF02826; 2-Hacid_dh_C; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
DR PROSITE; PS00065; D_2_HYDROXYACID_DH_1; 1.
DR PROSITE; PS00670; D_2_HYDROXYACID_DH_2; 1.
DR PROSITE; PS00671; D_2_HYDROXYACID_DH_3; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Chloroplast; Direct protein sequencing; Mitochondrion; NAD;
KW Oxidoreductase; Plastid; Reference proteome; Transit peptide.
FT TRANSIT 1..29
FT /note="Chloroplast and mitochondrion"
FT /evidence="ECO:0000269|Ref.7"
FT CHAIN 30..384
FT /note="Formate dehydrogenase, chloroplastic/mitochondrial"
FT /id="PRO_0000007193"
FT BINDING 128
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03210"
FT BINDING 152
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03210"
FT BINDING 207..208
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03210,
FT ECO:0000269|Ref.10"
FT BINDING 227
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03210,
FT ECO:0000269|Ref.10"
FT BINDING 262..266
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03210,
FT ECO:0000269|Ref.10"
FT BINDING 288
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03210,
FT ECO:0000269|Ref.10"
FT BINDING 314
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03210,
FT ECO:0000269|Ref.10"
FT BINDING 338..341
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03210,
FT ECO:0000269|Ref.10"
FT SITE 290
FT /note="Important for catalytic activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03210"
FT SITE 338
FT /note="Important for catalytic activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03210"
FT STRAND 37..41
FT /evidence="ECO:0007829|PDB:3JTM"
FT HELIX 47..51
FT /evidence="ECO:0007829|PDB:3JTM"
FT TURN 59..61
FT /evidence="ECO:0007829|PDB:3JTM"
FT HELIX 62..64
FT /evidence="ECO:0007829|PDB:3JTM"
FT HELIX 66..71
FT /evidence="ECO:0007829|PDB:3JTM"
FT STRAND 75..80
FT /evidence="ECO:0007829|PDB:3JTM"
FT HELIX 88..92
FT /evidence="ECO:0007829|PDB:3JTM"
FT TURN 93..95
FT /evidence="ECO:0007829|PDB:3JTM"
FT STRAND 97..101
FT /evidence="ECO:0007829|PDB:3JTM"
FT HELIX 111..116
FT /evidence="ECO:0007829|PDB:3JTM"
FT STRAND 122..128
FT /evidence="ECO:0007829|PDB:3JTM"
FT HELIX 135..140
FT /evidence="ECO:0007829|PDB:3JTM"
FT STRAND 144..147
FT /evidence="ECO:0007829|PDB:3JTM"
FT TURN 149..152
FT /evidence="ECO:0007829|PDB:3JTM"
FT HELIX 153..169
FT /evidence="ECO:0007829|PDB:3JTM"
FT HELIX 171..179
FT /evidence="ECO:0007829|PDB:3JTM"
FT HELIX 185..189
FT /evidence="ECO:0007829|PDB:3JTM"
FT STRAND 199..203
FT /evidence="ECO:0007829|PDB:3JTM"
FT HELIX 207..216
FT /evidence="ECO:0007829|PDB:3JTM"
FT HELIX 217..219
FT /evidence="ECO:0007829|PDB:3JTM"
FT STRAND 222..226
FT /evidence="ECO:0007829|PDB:3JTM"
FT HELIX 233..239
FT /evidence="ECO:0007829|PDB:3JTM"
FT HELIX 247..250
FT /evidence="ECO:0007829|PDB:3JTM"
FT HELIX 251..253
FT /evidence="ECO:0007829|PDB:3JTM"
FT STRAND 255..259
FT /evidence="ECO:0007829|PDB:3JTM"
FT TURN 265..269
FT /evidence="ECO:0007829|PDB:3JTM"
FT HELIX 273..278
FT /evidence="ECO:0007829|PDB:3JTM"
FT STRAND 283..287
FT /evidence="ECO:0007829|PDB:3JTM"
FT HELIX 291..293
FT /evidence="ECO:0007829|PDB:3JTM"
FT HELIX 296..305
FT /evidence="ECO:0007829|PDB:3JTM"
FT STRAND 306..314
FT /evidence="ECO:0007829|PDB:3JTM"
FT STRAND 317..320
FT /evidence="ECO:0007829|PDB:3JTM"
FT HELIX 326..328
FT /evidence="ECO:0007829|PDB:3JTM"
FT HELIX 340..342
FT /evidence="ECO:0007829|PDB:3JTM"
FT HELIX 344..363
FT /evidence="ECO:0007829|PDB:3JTM"
FT HELIX 369..371
FT /evidence="ECO:0007829|PDB:3JTM"
FT STRAND 372..375
FT /evidence="ECO:0007829|PDB:3JTM"
FT HELIX 381..383
FT /evidence="ECO:0007829|PDB:3JTM"
SQ SEQUENCE 384 AA; 42410 MW; A12BA423019D862B CRC64;
MAMRQAAKAT IRACSSSSSS GYFARRQFNA SSGDSKKIVG VFYKANEYAT KNPNFLGCVE
NALGIRDWLE SQGHQYIVTD DKEGPDCELE KHIPDLHVLI STPFHPAYVT AERIKKAKNL
KLLLTAGIGS DHIDLQAAAA AGLTVAEVTG SNVVSVAEDE LMRILILMRN FVPGYNQVVK
GEWNVAGIAY RAYDLEGKTI GTVGAGRIGK LLLQRLKPFG CNLLYHDRLQ MAPELEKETG
AKFVEDLNEM LPKCDVIVIN MPLTEKTRGM FNKELIGKLK KGVLIVNNAR GAIMERQAVV
DAVESGHIGG YSGDVWDPQP APKDHPWRYM PNQAMTPHTS GTTIDAQLRY AAGTKDMLER
YFKGEDFPTE NYIVKDGELA PQYR
