NDB1_ARATH
ID NDB1_ARATH Reviewed; 571 AA.
AC Q1JPL4; Q8LDE7; Q9M0I5;
DT 03-OCT-2012, integrated into UniProtKB/Swiss-Prot.
DT 13-JUN-2006, sequence version 1.
DT 03-AUG-2022, entry version 120.
DE RecName: Full=External alternative NAD(P)H-ubiquinone oxidoreductase B1, mitochondrial;
DE EC=1.6.5.9;
DE AltName: Full=External alternative NADH dehydrogenase NDB1;
DE AltName: Full=NADH:ubiquinone reductase (non-electrogenic) NDB1;
DE Flags: Precursor;
GN Name=NDB1; OrderedLocusNames=At4g28220; ORFNames=F26K10.100;
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
RN [2]
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 [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Shinn P., Chen H., Kim C.J., Quinitio C., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (MAY-2006) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP SUBCELLULAR LOCATION, AND TISSUE SPECIFICITY.
RX PubMed=12972666; DOI=10.1104/pp.103.024208;
RA Michalecka A.M., Svensson A.S., Johansson F.I., Agius S.C., Johanson U.,
RA Brennicke A., Binder S., Rasmusson A.G.;
RT "Arabidopsis genes encoding mitochondrial type II NAD(P)H dehydrogenases
RT have different evolutionary origin and show distinct responses to light.";
RL Plant Physiol. 133:642-652(2003).
RN [6]
RP REVIEW.
RX PubMed=15725055; DOI=10.1146/annurev.arplant.55.031903.141720;
RA Rasmusson A.G., Soole K.L., Elthon T.E.;
RT "Alternative NAD(P)H dehydrogenases of plant mitochondria.";
RL Annu. Rev. Plant Biol. 55:23-39(2004).
RN [7]
RP SUBCELLULAR LOCATION, AND TISSUE SPECIFICITY.
RC STRAIN=cv. Columbia;
RX PubMed=16258072; DOI=10.1093/pcp/pci221;
RA Elhafez D., Murcha M.W., Clifton R., Soole K.L., Day D.A., Whelan J.;
RT "Characterization of mitochondrial alternative NAD(P)H dehydrogenases in
RT Arabidopsis: intraorganelle location and expression.";
RL Plant Cell Physiol. 47:43-54(2006).
RN [8]
RP FUNCTION, MUTAGENESIS OF ASP-387, ACTIVITY REGULATION, CALCIUM-BINDING, AND
RP BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=17673460; DOI=10.1074/jbc.m704674200;
RA Geisler D.A., Broselid C., Hederstedt L., Rasmusson A.G.;
RT "Ca2+-binding and Ca2+-independent respiratory NADH and NADPH
RT dehydrogenases of Arabidopsis thaliana.";
RL J. Biol. Chem. 282:28455-28464(2007).
RN [9]
RP SUBCELLULAR LOCATION, AND MICROBODY TARGETING SIGNAL.
RX PubMed=18703057; DOI=10.1016/j.febslet.2008.07.061;
RA Carrie C., Murcha M.W., Kuehn K., Duncan O., Barthet M., Smith P.M.,
RA Eubel H., Meyer E., Day D.A., Millar A.H., Whelan J.;
RT "Type II NAD(P)H dehydrogenases are targeted to mitochondria and
RT chloroplasts or peroxisomes in Arabidopsis thaliana.";
RL FEBS Lett. 582:3073-3079(2008).
CC -!- FUNCTION: Alternative NADH-ubiquinone oxidoreductase which catalyzes
CC the oxidation of mitochondrial NADH does not translocate protons across
CC the inner mitochondrial membrane (By similarity). Calcium-dependent
CC NAD(P)H dehydrogenase. Binds calcium ions. {ECO:0000250,
CC ECO:0000269|PubMed:17673460}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a quinone + H(+) + NADH = a quinol + NAD(+);
CC Xref=Rhea:RHEA:46160, ChEBI:CHEBI:15378, ChEBI:CHEBI:24646,
CC ChEBI:CHEBI:57540, ChEBI:CHEBI:57945, ChEBI:CHEBI:132124; EC=1.6.5.9;
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a ubiquinone + H(+) + NADH = a ubiquinol + NAD(+);
CC Xref=Rhea:RHEA:23152, Rhea:RHEA-COMP:9565, Rhea:RHEA-COMP:9566,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:16389, ChEBI:CHEBI:17976,
CC ChEBI:CHEBI:57540, ChEBI:CHEBI:57945;
CC -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692; Evidence={ECO:0000250};
CC Note=Binds 1 FAD per subunit. {ECO:0000250};
CC -!- ACTIVITY REGULATION: Activity is calcium-dependent with a more
CC pronounced effect at higher pH. {ECO:0000269|PubMed:17673460}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 6.8-7.2 with NADPH as substrate and 6.8 with NADH as
CC substrate. {ECO:0000269|PubMed:17673460};
CC -!- SUBCELLULAR LOCATION: Mitochondrion inner membrane; Peripheral membrane
CC protein; Intermembrane side. Peroxisome.
CC -!- TISSUE SPECIFICITY: Expressed in seedlings, roots, cotyledons, leaves,
CC stems, buds and flowers. {ECO:0000269|PubMed:12972666,
CC ECO:0000269|PubMed:16258072}.
CC -!- SIMILARITY: Belongs to the NADH dehydrogenase family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB79624.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AL161572; CAB79624.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE85455.1; -; Genomic_DNA.
DR EMBL; BT025339; ABF57295.1; -; mRNA.
DR EMBL; AY086046; AAM63256.1; -; mRNA.
DR PIR; T09038; T09038.
DR RefSeq; NP_567801.1; NM_118962.5.
DR AlphaFoldDB; Q1JPL4; -.
DR SMR; Q1JPL4; -.
DR STRING; 3702.AT4G28220.1; -.
DR SwissPalm; Q1JPL4; -.
DR PaxDb; Q1JPL4; -.
DR PRIDE; Q1JPL4; -.
DR ProteomicsDB; 236817; -.
DR EnsemblPlants; AT4G28220.1; AT4G28220.1; AT4G28220.
DR GeneID; 828937; -.
DR Gramene; AT4G28220.1; AT4G28220.1; AT4G28220.
DR KEGG; ath:AT4G28220; -.
DR Araport; AT4G28220; -.
DR TAIR; locus:2123713; AT4G28220.
DR eggNOG; KOG2495; Eukaryota.
DR HOGENOM; CLU_021377_1_0_1; -.
DR InParanoid; Q1JPL4; -.
DR OrthoDB; 487337at2759; -.
DR PhylomeDB; Q1JPL4; -.
DR BioCyc; ARA:AT4G28220-MON; -.
DR PRO; PR:Q1JPL4; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q1JPL4; baseline and differential.
DR Genevisible; Q1JPL4; AT.
DR GO; GO:0031314; C:extrinsic component of mitochondrial inner membrane; IDA:TAIR.
DR GO; GO:0005758; C:mitochondrial intermembrane space; ISS:UniProtKB.
DR GO; GO:0005739; C:mitochondrion; IDA:UniProtKB.
DR GO; GO:0005777; C:peroxisome; IDA:UniProtKB.
DR GO; GO:0005509; F:calcium ion binding; IEA:InterPro.
DR GO; GO:0050136; F:NADH dehydrogenase (quinone) activity; IEA:RHEA.
DR GO; GO:0003959; F:NADPH dehydrogenase activity; IMP:TAIR.
DR GO; GO:0016491; F:oxidoreductase activity; ISS:UniProtKB.
DR GO; GO:0006116; P:NADH oxidation; IEA:InterPro.
DR GO; GO:0070995; P:NADPH oxidation; IMP:TAIR.
DR InterPro; IPR011992; EF-hand-dom_pair.
DR InterPro; IPR018247; EF_Hand_1_Ca_BS.
DR InterPro; IPR002048; EF_hand_dom.
DR InterPro; IPR036188; FAD/NAD-bd_sf.
DR InterPro; IPR023753; FAD/NAD-binding_dom.
DR InterPro; IPR045024; NDH-2.
DR PANTHER; PTHR43706; PTHR43706; 1.
DR Pfam; PF07992; Pyr_redox_2; 1.
DR SUPFAM; SSF47473; SSF47473; 1.
DR SUPFAM; SSF51905; SSF51905; 2.
DR PROSITE; PS00018; EF_HAND_1; 1.
DR PROSITE; PS50222; EF_HAND_2; 1.
PE 1: Evidence at protein level;
KW Calcium; FAD; Flavoprotein; Membrane; Metal-binding; Mitochondrion;
KW Mitochondrion inner membrane; NAD; NADP; Oxidoreductase; Peroxisome;
KW Reference proteome; Transit peptide.
FT TRANSIT 1..35
FT /note="Mitochondrion"
FT /evidence="ECO:0000255"
FT CHAIN 36..571
FT /note="External alternative NAD(P)H-ubiquinone
FT oxidoreductase B1, mitochondrial"
FT /id="PRO_0000419505"
FT DOMAIN 372..407
FT /note="EF-hand"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00448"
FT MOTIF 562..571
FT /note="Microbody targeting signal"
FT BINDING 51..81
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 215..251
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 385
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00448"
FT BINDING 387
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00448"
FT BINDING 389
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00448"
FT BINDING 391
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00448"
FT BINDING 396
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00448"
FT MUTAGEN 387
FT /note="D->A: Impaired calcium binding and loss of NADH
FT oxidase activity."
FT /evidence="ECO:0000269|PubMed:17673460"
FT CONFLICT 39
FT /note="E -> A (in Ref. 4; AAM63256)"
FT /evidence="ECO:0000305"
FT CONFLICT 175
FT /note="L -> I (in Ref. 4; AAM63256)"
FT /evidence="ECO:0000305"
FT CONFLICT 386
FT /note="A -> V (in Ref. 4; AAM63256)"
FT /evidence="ECO:0000305"
FT CONFLICT 540
FT /note="V -> I (in Ref. 4; AAM63256)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 571 AA; 63314 MW; 5B8B7925B95A2D91 CRC64;
MTLLSSLGRA SRSAPLASKL LLLGTLSGGS IVAYADANEE ANKKEEHKKK KVVVLGTGWA
GISFLKDLDI TSYDVQVVSP QNYFAFTPLL PSVTCGTVEA RSIVESVRNI TKKKNGEIEL
WEADCFKIDH VNQKVHCRPV FKDDPEASQE FSLGYDYLIV AVGAQVNTFG TPGVLENCHF
LKEVEDAQRI RRGVIDCFEK AILPGLTEEQ RRRKLHFVIV GGGPTGVEFA AELHDFIIED
ITKIYPSVKE LVKITLIQSG DHILNTFDER ISSFAEQKFT RDGIDVQTGM RVMSVTDKDI
TVKVKSSGEL VSIPHGLILW STGVGTRPVI SDFMEQVGQG GRRAVATNEW LQVTGCENVY
AVGDCASIAQ RKILGDIANI FKAADADNSG TLTMEELEGV VDDIIVRYPQ VELYLKSKHM
RHINDLLADS EGNARKEVDI EAFKLALSEA DSQMKTLPAT AQVAAQQGAY LAKCFNRMEQ
CKELPEGPKR FRTGGHHQFR PFQYKHFGQF APLGGDQAAA ELPGDWVSAG KSAQWLWYSV
YASKQVSWRT RALVVSDWTR RYIFGRDSSR I
