GPDH2_ORYSJ
ID GPDH2_ORYSJ Reviewed; 467 AA.
AC Q8S2G5; A0A0N7KDX1; Q84VD0;
DT 28-NOV-2012, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2002, sequence version 1.
DT 03-AUG-2022, entry version 139.
DE RecName: Full=Probable glycerol-3-phosphate dehydrogenase [NAD(+)] 2, cytosolic;
DE EC=1.1.1.8;
GN OrderedLocusNames=Os01g0801600, LOC_Os01g58740;
GN ORFNames=OsJ_03778, P0003D09.23;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12447438; DOI=10.1038/nature01184;
RA Sasaki T., Matsumoto T., Yamamoto K., Sakata K., Baba T., Katayose Y.,
RA Wu J., Niimura Y., Cheng Z., Nagamura Y., Antonio B.A., Kanamori H.,
RA Hosokawa S., Masukawa M., Arikawa K., Chiden Y., Hayashi M., Okamoto M.,
RA Ando T., Aoki H., Arita K., Hamada M., Harada C., Hijishita S., Honda M.,
RA Ichikawa Y., Idonuma A., Iijima M., Ikeda M., Ikeno M., Ito S., Ito T.,
RA Ito Y., Ito Y., Iwabuchi A., Kamiya K., Karasawa W., Katagiri S.,
RA Kikuta A., Kobayashi N., Kono I., Machita K., Maehara T., Mizuno H.,
RA Mizubayashi T., Mukai Y., Nagasaki H., Nakashima M., Nakama Y.,
RA Nakamichi Y., Nakamura M., Namiki N., Negishi M., Ohta I., Ono N., Saji S.,
RA Sakai K., Shibata M., Shimokawa T., Shomura A., Song J., Takazaki Y.,
RA Terasawa K., Tsuji K., Waki K., Yamagata H., Yamane H., Yoshiki S.,
RA Yoshihara R., Yukawa K., Zhong H., Iwama H., Endo T., Ito H., Hahn J.H.,
RA Kim H.-I., Eun M.-Y., Yano M., Jiang J., Gojobori T.;
RT "The genome sequence and structure of rice chromosome 1.";
RL Nature 420:312-316(2002).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
RN [7]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 1-242.
RX PubMed=14750518; DOI=10.1023/b:plan.0000007001.30865.0f;
RA Cooper B., Hutchison D., Park S., Guimil S., Luginbuehl P., Ellero C.,
RA Goff S.A., Glazebrook J.;
RT "Identification of rice (Oryza sativa) proteins linked to the cyclin-
RT mediated regulation of the cell cycle.";
RL Plant Mol. Biol. 53:273-279(2003).
CC -!- FUNCTION: May be involved in cell redox homeostasis. {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=NAD(+) + sn-glycerol 3-phosphate = dihydroxyacetone phosphate
CC + H(+) + NADH; Xref=Rhea:RHEA:11092, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:57540, ChEBI:CHEBI:57597, ChEBI:CHEBI:57642,
CC ChEBI:CHEBI:57945; EC=1.1.1.8;
CC -!- SUBCELLULAR LOCATION: Cytoplasm, cytosol {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the NAD-dependent glycerol-3-phosphate
CC dehydrogenase family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAO72676.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AP003221; BAB86423.1; -; Genomic_DNA.
DR EMBL; AP008207; BAF06455.1; -; Genomic_DNA.
DR EMBL; AP014957; BAS74801.1; -; Genomic_DNA.
DR EMBL; CM000138; EAZ13855.1; -; Genomic_DNA.
DR EMBL; AK073318; -; NOT_ANNOTATED_CDS; mRNA.
DR EMBL; AY224556; AAO72676.1; ALT_INIT; mRNA.
DR RefSeq; XP_015617993.1; XM_015762507.1.
DR AlphaFoldDB; Q8S2G5; -.
DR SMR; Q8S2G5; -.
DR STRING; 4530.OS01T0801600-01; -.
DR PaxDb; Q8S2G5; -.
DR PRIDE; Q8S2G5; -.
DR EnsemblPlants; Os01t0801600-01; Os01t0801600-01; Os01g0801600.
DR GeneID; 4327964; -.
DR Gramene; Os01t0801600-01; Os01t0801600-01; Os01g0801600.
DR KEGG; osa:4327964; -.
DR eggNOG; KOG2711; Eukaryota.
DR HOGENOM; CLU_029303_2_0_1; -.
DR InParanoid; Q8S2G5; -.
DR OMA; LRHLMGK; -.
DR OrthoDB; 476066at2759; -.
DR PlantReactome; R-OSA-1119402; Phospholipid biosynthesis I.
DR Proteomes; UP000000763; Chromosome 1.
DR Proteomes; UP000007752; Chromosome 1.
DR Proteomes; UP000059680; Chromosome 1.
DR Genevisible; Q8S2G5; OS.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0009331; C:glycerol-3-phosphate dehydrogenase complex; IEA:InterPro.
DR GO; GO:0004367; F:glycerol-3-phosphate dehydrogenase [NAD+] activity; IBA:GO_Central.
DR GO; GO:0051287; F:NAD binding; IEA:InterPro.
DR GO; GO:0005975; P:carbohydrate metabolic process; IEA:InterPro.
DR GO; GO:0046168; P:glycerol-3-phosphate catabolic process; IEA:InterPro.
DR GO; GO:0006072; P:glycerol-3-phosphate metabolic process; IBA:GO_Central.
DR GO; GO:0006116; P:NADH oxidation; IBA:GO_Central.
DR Gene3D; 1.10.1040.10; -; 1.
DR InterPro; IPR008927; 6-PGluconate_DH-like_C_sf.
DR InterPro; IPR013328; 6PGD_dom2.
DR InterPro; IPR006168; G3P_DH_NAD-dep.
DR InterPro; IPR006109; G3P_DH_NAD-dep_C.
DR InterPro; IPR011128; G3P_DH_NAD-dep_N.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR Pfam; PF07479; NAD_Gly3P_dh_C; 1.
DR Pfam; PF01210; NAD_Gly3P_dh_N; 1.
DR PRINTS; PR00077; GPDHDRGNASE.
DR SUPFAM; SSF48179; SSF48179; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
PE 2: Evidence at transcript level;
KW Cytoplasm; NAD; Oxidoreductase; Reference proteome.
FT CHAIN 1..467
FT /note="Probable glycerol-3-phosphate dehydrogenase [NAD(+)]
FT 2, cytosolic"
FT /id="PRO_0000420178"
FT ACT_SITE 284
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT BINDING 47..52
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 195
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 195
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 234
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 346..347
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 346
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 374
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT CONFLICT 163..165
FT /note="NGL -> KRV (in Ref. 7; AAO72676)"
FT /evidence="ECO:0000305"
FT CONFLICT 394
FT /note="M -> V (in Ref. 6; AK073318)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 467 AA; 51583 MW; 7857AB03C7E6B051 CRC64;
MGGAEDAPRA AAANGHGNGA TVEEKLDELR RLLGKADGDP LRIVGVGAGA WGSVFCALMQ
DAYGHLRDKV QVRIWRRPGR AVDRATAEHL FEVINAREDV LRRLIRRCAY LKYVEGRLGD
RTLYADEILR DGFCLNMIDT PLCPLKVVTN LQEAVWDADI VINGLPSTDT REVFGEIGRY
WKERITAPII LSLAKGIEAS LDPLPRIITP TQMISNATGV PLENILYLGG PNIASEIYNK
EYANARICGA DKWRKPLAKF LRQPHFIVWD NSDLITHEVM GGLKNVYAIG AGMVAALTNE
SATSKSVYFA LCTSEMIYIT HLLEEEPEKL AGPLLADTYV TLLKGRNAWY GQKLAKGELT
LEMGDSIKGK GTIQGVSAVN AFYELLSQDS LSVMHPEANR SVAPVEMCPI LKALYKILIK
RELPPDSILQ AIRDETMYDP RERIEMAQGH SLYRPSLLGQ PKGDAKA
