NDB2_ARATH
ID NDB2_ARATH Reviewed; 582 AA.
AC Q94BV7; Q9S9T5;
DT 03-OCT-2012, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 137.
DE RecName: Full=External alternative NAD(P)H-ubiquinone oxidoreductase B2, mitochondrial;
DE EC=1.6.5.9;
DE AltName: Full=External alternative NADH dehydrogenase NDB2;
DE AltName: Full=NADH:ubiquinone reductase (non-electrogenic) NDB2;
DE Flags: Precursor;
GN Name=NDB2; OrderedLocusNames=At4g05020; ORFNames=T32N4.4;
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].
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 [4]
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 [5]
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 [6]
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 [7]
RP INDUCTION BY ABIOTIC STRESSES.
RX PubMed=16027974; DOI=10.1007/s11103-005-5514-7;
RA Clifton R., Lister R., Parker K.L., Sappl P.G., Elhafez D., Millar A.H.,
RA Day D.A., Whelan J.;
RT "Stress-induced co-expression of alternative respiratory chain components
RT in Arabidopsis thaliana.";
RL Plant Mol. Biol. 58:193-212(2005).
RN [8]
RP SUBCELLULAR LOCATION, TISSUE SPECIFICITY, AND INDUCTION BY LIGHT.
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 [9]
RP FUNCTION, CALCIUM-BINDING, ACTIVITY REGULATION, AND BIOPHYSICOCHEMICAL
RP 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 [10]
RP SUBCELLULAR LOCATION.
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).
RN [11]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND SUBCELLULAR LOCATION [LARGE SCALE
RP ANALYSIS].
RX PubMed=21841088; DOI=10.1104/pp.111.182352;
RA Klodmann J., Senkler M., Rode C., Braun H.-P.;
RT "Defining the protein complex proteome of plant mitochondria.";
RL Plant Physiol. 157:587-598(2011).
RN [12]
RP INDUCTION BY AMMONIUM AND NITRATE.
RX PubMed=22732219; DOI=10.5483/bmbrep.2012.45.6.010;
RA Park B.S., Kim S.-I., Song J.T., Seo H.S.;
RT "Arabidopsis SIZ1 positively regulates alternative respiratory bypass
RT pathways.";
RL BMB Rep. 45:342-347(2012).
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; more efficient on NADH. Binds calcium ions.
CC {ECO:0000250, 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: NADPH oxidase activity is stimulated by calcium
CC ions. {ECO:0000269|PubMed:17673460}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 6.8 with NADPH as substrate and 6.8-7.8 with NADH as
CC substrate. {ECO:0000269|PubMed:17673460};
CC -!- SUBCELLULAR LOCATION: Mitochondrion inner membrane; Peripheral membrane
CC protein; Intermembrane side {ECO:0000269|PubMed:21841088}. Peroxisome
CC {ECO:0000250}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=1;
CC Comment=A number of isoforms are produced. According to EST
CC sequences.;
CC Name=1;
CC IsoId=Q94BV7-1; Sequence=Displayed;
CC -!- TISSUE SPECIFICITY: Mostly expressed in seedlings and roots and, to a
CC lower extent, in cotyledons, leaves, stems, buds and flowers.
CC {ECO:0000269|PubMed:12972666, ECO:0000269|PubMed:16258072}.
CC -!- INDUCTION: Follows a circadian regulation; up-regulated in a diurnal
CC manner. Accumulates in response to ammonium but repressed by nitrate.
CC Induced by chloramphenicol (Chl), paraquat (Par), rotenone (Rot) and
CC salicylic acid (SA). {ECO:0000269|PubMed:16027974,
CC ECO:0000269|PubMed:16258072, ECO:0000269|PubMed:22732219}.
CC -!- SIMILARITY: Belongs to the NADH dehydrogenase family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAD48975.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB81044.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AF162444; AAD48975.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161502; CAB81044.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE82460.1; -; Genomic_DNA.
DR EMBL; AY039856; AAK63960.1; -; mRNA.
DR EMBL; BT002241; AAN72252.1; -; mRNA.
DR PIR; B85063; B85063.
DR RefSeq; NP_567283.1; NM_116741.4. [Q94BV7-1]
DR AlphaFoldDB; Q94BV7; -.
DR SMR; Q94BV7; -.
DR STRING; 3702.AT4G05020.2; -.
DR SwissPalm; Q94BV7; -.
DR PRIDE; Q94BV7; -.
DR ProteomicsDB; 251099; -. [Q94BV7-1]
DR EnsemblPlants; AT4G05020.1; AT4G05020.1; AT4G05020. [Q94BV7-1]
DR GeneID; 825844; -.
DR Gramene; AT4G05020.1; AT4G05020.1; AT4G05020. [Q94BV7-1]
DR KEGG; ath:AT4G05020; -.
DR Araport; AT4G05020; -.
DR eggNOG; KOG2495; Eukaryota.
DR HOGENOM; CLU_021377_1_0_1; -.
DR InParanoid; Q94BV7; -.
DR OMA; VYLWRSI; -.
DR PhylomeDB; Q94BV7; -.
DR BioCyc; ARA:AT4G05020-MON; -.
DR PRO; PR:Q94BV7; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q94BV7; baseline and differential.
DR Genevisible; Q94BV7; AT.
DR GO; GO:0005743; C:mitochondrial inner membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005758; C:mitochondrial intermembrane space; ISS:UniProtKB.
DR GO; GO:0005739; C:mitochondrion; IDA:UniProtKB.
DR GO; GO:0005777; C:peroxisome; IEA:UniProtKB-SubCell.
DR GO; GO:0005509; F:calcium ion binding; IEA:InterPro.
DR GO; GO:0050136; F:NADH dehydrogenase (quinone) activity; IEA:RHEA.
DR GO; GO:0016491; F:oxidoreductase activity; ISS:UniProtKB.
DR GO; GO:0006116; P:NADH oxidation; IEA:InterPro.
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; PF00036; EF-hand_1; 1.
DR Pfam; PF07992; Pyr_redox_2; 1.
DR SMART; SM00054; EFh; 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 Alternative splicing; Calcium; FAD; Flavoprotein; Membrane; Metal-binding;
KW Mitochondrion; Mitochondrion inner membrane; NAD; NADP; Oxidoreductase;
KW Peroxisome; Reference proteome; Transit peptide.
FT TRANSIT 1..38
FT /note="Mitochondrion"
FT /evidence="ECO:0000255"
FT CHAIN 39..582
FT /note="External alternative NAD(P)H-ubiquinone
FT oxidoreductase B2, mitochondrial"
FT /id="PRO_0000419506"
FT DOMAIN 379..414
FT /note="EF-hand"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00448"
FT MOTIF 573..582
FT /note="Microbody targeting signal"
FT /evidence="ECO:0000250"
FT BINDING 60..90
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 223..259
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 392
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00448"
FT BINDING 394
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 BINDING 398
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00448"
FT BINDING 403
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00448"
SQ SEQUENCE 582 AA; 65059 MW; D9A1EF2B9C84BF5F CRC64;
MRNFSVFERF SKAFKDHPSL TRILVVSTIS GGGLIAYSEA NASYGANGGA VVETGTKKKK
VVLLGTGWAG TSFLKNLNNS QYEVQIISPR NYFAFTPLLP SVTCGTVEAR SVVEPIRNIG
RKNVDTSYLE AECFKIDPAS KKVYCRSKQG LSSNGKKEFS VDYDYLVIAT GAQSNTFNIP
GVEENCHFLK EVEDAQRIRK TVIDSFEKAS LPELSDEERK RILHFVVVGG GPTGVEFAAE
LHDFVTEDLV SLYPRAKGSV RITLLEAADH ILTMFDKRIT EFAEEKFSRD GIDVKLGSMV
TKVNEKDISA KTKGGEVSSI PYGMIVWSTG IGTRPVIKDF MKQIGQGNRR ALATDEWLRV
EGTDNIYALG DCATINQRKV MEDVSAIFSK ADKDKSGTLT LKEFQEAMDD ICVRYPQVEL
YLKSKRMRGI ADLLKEAETD DVSKNNIELK IEEFKSALSQ VDSQVKFLPA TAQVAAQQGA
YLAKCFDRME ECEKSPEGPI RMRGEGRHRF RPFRYRHLGQ FAPLGGEQTA AQLPGDWVSI
GHSSQWLWYS VYASKQVSWR TRVLVVSDWM RRFIFGRDSS SI
