ID MAOP3_ARATH Reviewed; 588 AA.
AC Q9XGZ0;
DT 31-OCT-2012, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1999, sequence version 1.
DT 27-MAR-2024, entry version 148.
DE RecName: Full=NADP-dependent malic enzyme 3;
DE Short=AtNADP-ME3;
DE Short=NADP-malic enzyme 3;
DE EC=1.1.1.40;
GN Name=NADP-ME3; OrderedLocusNames=At5g25880; ORFNames=T1N24.25;
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=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 [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 DEVELOPMENTAL STAGE, TISSUE SPECIFICITY, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, GENE FAMILY, AND NOMENCLATURE.
RC STRAIN=cv. Columbia;
RX PubMed=16113210; DOI=10.1104/pp.105.065953;
RA Wheeler M.C., Tronconi M.A., Drincovich M.F., Andreo C.S., Fluegge U.-I.,
RA Maurino V.G.;
RT "A comprehensive analysis of the NADP-malic enzyme gene family of
RT Arabidopsis.";
RL Plant Physiol. 139:39-51(2005).
RN [4]
RP SUBCELLULAR LOCATION, ACTIVITY REGULATION, AND BIOPHYSICOCHEMICAL
RP PROPERTIES.
RX PubMed=19725876; DOI=10.1111/j.1742-4658.2009.07258.x;
RA Gerrard Wheeler M.C., Arias C.L., Maurino V.G., Andreo C.S.,
RA Drincovich M.F.;
RT "Identification of domains involved in the allosteric regulation of
RT cytosolic Arabidopsis thaliana NADP-malic enzymes.";
RL FEBS J. 276:5665-5677(2009).
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(S)-malate + NADP(+) = CO2 + NADPH + pyruvate;
CC Xref=Rhea:RHEA:18253, ChEBI:CHEBI:15361, ChEBI:CHEBI:15589,
CC ChEBI:CHEBI:16526, ChEBI:CHEBI:57783, ChEBI:CHEBI:58349; EC=1.1.1.40;
CC Evidence={ECO:0000269|PubMed:16113210};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H(+) + oxaloacetate = CO2 + pyruvate; Xref=Rhea:RHEA:15641,
CC ChEBI:CHEBI:15361, ChEBI:CHEBI:15378, ChEBI:CHEBI:16452,
CC ChEBI:CHEBI:16526; EC=1.1.1.40;
CC Evidence={ECO:0000269|PubMed:16113210};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
CC Note=Divalent metal cations. Prefers magnesium or manganese.
CC {ECO:0000250};
CC -!- ACTIVITY REGULATION: Slightly activated by succinate and aspartate.
CC Repressed by fumarate, malate, oxaloacetate and glucose.
CC {ECO:0000269|PubMed:19725876}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=6.5 uM for NADP (at pH 7.5) {ECO:0000269|PubMed:16113210,
CC ECO:0000269|PubMed:19725876};
CC KM=0.83 mM for malate (at pH 7.5) {ECO:0000269|PubMed:16113210,
CC ECO:0000269|PubMed:19725876};
CC KM=5 mM for pyruvate (at pH 7) {ECO:0000269|PubMed:16113210,
CC ECO:0000269|PubMed:19725876};
CC Note=kcat is 268.1 sec(-1) with NADP and malate as substrates (at pH
CC 7.5). kcat is 237 sec(-1) with pyruvate as substrate (at pH 7).;
CC pH dependence:
CC Optimum pH is 7.7. {ECO:0000269|PubMed:16113210,
CC ECO:0000269|PubMed:19725876};
CC -!- SUBUNIT: Homohexamers and homooctamers. {ECO:0000269|PubMed:16113210}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:19725876}.
CC -!- TISSUE SPECIFICITY: Mostly expressed in flowers, and, to a lower
CC extent, in stems. In leaves and stems, restricted to the trichomes and
CC trichome basal cells. Also present in the stipules flanking the base of
CC the inflorescence bract leaves and in the meristematic zone of
CC developing lateral roots. In flowers, present in pollen and the
CC abscission zone of developing siliques. {ECO:0000269|PubMed:16113210}.
CC -!- DEVELOPMENTAL STAGE: During embryogenesis, present in the embryo at the
CC globular and heart stages. Detected in the central vasculature of the
CC siliques. During germination, only observed in stipules at the shoot
CC apex and restricted to trichomes of the primary leaves.
CC {ECO:0000269|PubMed:16113210}.
CC -!- SIMILARITY: Belongs to the malic enzymes family. {ECO:0000305}.
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DR EMBL; AF149413; AAD40139.1; -; Genomic_DNA.
DR EMBL; CP002688; AED93497.1; -; Genomic_DNA.
DR RefSeq; NP_197960.1; NM_122489.3.
DR AlphaFoldDB; Q9XGZ0; -.
DR SMR; Q9XGZ0; -.
DR BioGRID; 17932; 1.
DR STRING; 3702.Q9XGZ0; -.
DR PaxDb; 3702-AT5G25880-1; -.
DR ProteomicsDB; 232209; -.
DR EnsemblPlants; AT5G25880.1; AT5G25880.1; AT5G25880.
DR GeneID; 832657; -.
DR Gramene; AT5G25880.1; AT5G25880.1; AT5G25880.
DR KEGG; ath:AT5G25880; -.
DR Araport; AT5G25880; -.
DR TAIR; AT5G25880; NADP-ME3.
DR eggNOG; KOG1257; Eukaryota.
DR HOGENOM; CLU_011405_5_1_1; -.
DR InParanoid; Q9XGZ0; -.
DR OrthoDB; 1069499at2759; -.
DR PhylomeDB; Q9XGZ0; -.
DR BioCyc; ARA:AT5G25880-MONOMER; -.
DR BRENDA; 1.1.1.40; 399.
DR SABIO-RK; Q9XGZ0; -.
DR PRO; PR:Q9XGZ0; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9XGZ0; baseline and differential.
DR Genevisible; Q9XGZ0; AT.
DR GO; GO:0005829; C:cytosol; IDA:TAIR.
DR GO; GO:0009536; C:plastid; HDA:TAIR.
DR GO; GO:0004473; F:malate dehydrogenase (decarboxylating) (NADP+) activity; IDA:TAIR.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0051287; F:NAD binding; IEA:InterPro.
DR GO; GO:0008948; F:oxaloacetate decarboxylase activity; IEA:UniProtKB-EC.
DR GO; GO:0006108; P:malate metabolic process; IDA:TAIR.
DR CDD; cd05312; NAD_bind_1_malic_enz; 1.
DR Gene3D; 3.40.50.10380; Malic enzyme, N-terminal domain; 1.
DR Gene3D; 3.40.50.720; NAD(P)-binding Rossmann-like Domain; 1.
DR InterPro; IPR046346; Aminoacid_DH-like_N_sf.
DR InterPro; IPR015884; Malic_enzyme_CS.
DR InterPro; IPR012301; Malic_N_dom.
DR InterPro; IPR037062; Malic_N_dom_sf.
DR InterPro; IPR012302; Malic_NAD-bd.
DR InterPro; IPR001891; Malic_OxRdtase.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR PANTHER; PTHR23406; MALIC ENZYME-RELATED; 1.
DR PANTHER; PTHR23406:SF64; NADP-DEPENDENT MALIC ENZYME 3; 1.
DR Pfam; PF00390; malic; 1.
DR Pfam; PF03949; Malic_M; 1.
DR PIRSF; PIRSF000106; ME; 1.
DR PRINTS; PR00072; MALOXRDTASE.
DR SMART; SM01274; malic; 1.
DR SMART; SM00919; Malic_M; 1.
DR SUPFAM; SSF53223; Aminoacid dehydrogenase-like, N-terminal domain; 1.
DR SUPFAM; SSF51735; NAD(P)-binding Rossmann-fold domains; 1.
DR PROSITE; PS00331; MALIC_ENZYMES; 1.
PE 1: Evidence at protein level;
KW Acetylation; Cytoplasm; Metal-binding; NADP; Oxidoreductase;
KW Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000250|UniProtKB:Q9LYG3"
FT CHAIN 2..588
FT /note="NADP-dependent malic enzyme 3"
FT /id="PRO_0000420151"
FT ACT_SITE 136
FT /note="Proton donor"
FT /evidence="ECO:0000250"
FT ACT_SITE 207
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT BINDING 189
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250"
FT BINDING 279
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250"
FT BINDING 280
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250"
FT BINDING 303
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250"
FT BINDING 303
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250"
FT BINDING 332..348
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250"
FT BINDING 444
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250"
FT SITE 303
FT /note="Important for activity"
FT /evidence="ECO:0000250"
FT MOD_RES 2
FT /note="N-acetylglycine"
FT /evidence="ECO:0000250|UniProtKB:Q9LYG3"
SQ SEQUENCE 588 AA; 64610 MW; C27EE353F29417A5 CRC64;
MGTNQTQISD EYVTGNSSGV GGGISDVYGE DSATLDQLVT PWVTSVASGY TLMRDPRYNK
GLAFTDKERD AHYITGLLPP VVLSQDVQER KVMHNLRQYT VPLQRYMALM DLQERNERLF
YKLLIDNVEE LLPVVYTPTV GEACQKYGSI YRRPQGLYIS LKEKGKILEV LKNWPQRGIQ
VIVVTDGERI LGLGDLGCQG MGIPVGKLSL YTALGGIRPS ACLPITIDVG TNNEKLLNNE
FYIGLKQKRA NGEEYAEFLQ EFMCAVKQNY GEKVLVQFED FANHHAFELL SKYCSSHLVF
NDDIQGTASV VLAGLIAAQK VLGKSLADHT FLFLGAGEAG TGIAELIALK ISKETGKPID
ETRKKIWLVD SKGLIVSERK ESLQHFKQPW AHDHKPVKEL LAAVNAIKPT VLIGTSGVGK
TFTKEVVEAM ATLNEKPLIL ALSNPTSQAE CTAEEAYTWT KGRAIFASGS PFDPVQYDGK
KFTPGQANNC YIFPGLGLGL IMSGAIRVRD DMLLAASEAL ASQVTEENFA NGLIYPPFAN
IRKISANIAA SVGAKTYELG LASNLPRPKD LVKMAESCMY SPVYRNFR
//
