GME1_ORYSJ
ID GME1_ORYSJ Reviewed; 378 AA.
AC A3C4S4; B7EX80; Q0IXP2; Q0R4F5; Q109P5; Q338B5; Q5W7P1; Q8S862;
DT 10-JUL-2007, integrated into UniProtKB/Swiss-Prot.
DT 20-MAR-2007, sequence version 1.
DT 03-AUG-2022, entry version 102.
DE RecName: Full=GDP-mannose 3,5-epimerase 1;
DE Short=GDP-Man 3,5-epimerase 1;
DE EC=5.1.3.18 {ECO:0000269|PubMed:16413588};
DE AltName: Full=OsGME-1;
GN Name=GME-1; OrderedLocusNames=Os10g0417600, LOC_Os10g28200;
GN ORFNames=OsJ_030296, OSJNBa0061K21.15;
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 [MRNA], FUNCTION, CATALYTIC ACTIVITY, ACTIVITY
RP REGULATION, AND BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=cv. Nipponbare; TISSUE=Seed;
RX PubMed=16413588; DOI=10.1016/j.phytochem.2005.12.003;
RA Watanabe K., Suzuki K., Kitamura S.;
RT "Characterization of a GDP-d-mannose 3'',5''-epimerase from rice.";
RL Phytochemistry 67:338-346(2006).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12791992; DOI=10.1126/science.1083523;
RA Yu Y., Rambo T., Currie J., Saski C., Kim H.-R., Collura K., Thompson S.,
RA Simmons J., Yang T.-J., Nah G., Patel A.J., Thurmond S., Henry D.,
RA Oates R., Palmer M., Pries G., Gibson J., Anderson H., Paradkar M.,
RA Crane L., Dale J., Carver M.B., Wood T., Frisch D., Engler F.,
RA Soderlund C., Palmer L.E., Teytelman L., Nascimento L., De la Bastide M.,
RA Spiegel L., Ware D., O'Shaughnessy A., Dike S., Dedhia N., Preston R.,
RA Huang E., Ferraro K., Kuit K., Miller B., Zutavern T., Katzenberger F.,
RA Muller S., Balija V., Martienssen R.A., Stein L., Minx P., Johnson D.,
RA Cordum H., Mardis E., Cheng Z., Jiang J., Wilson R., McCombie W.R.,
RA Wing R.A., Yuan Q., Ouyang S., Liu J., Jones K.M., Gansberger K.,
RA Moffat K., Hill J., Tsitrin T., Overton L., Bera J., Kim M., Jin S.,
RA Tallon L., Ciecko A., Pai G., Van Aken S., Utterback T., Reidmuller S.,
RA Bormann J., Feldblyum T., Hsiao J., Zismann V., Blunt S., de Vazeille A.R.,
RA Shaffer T., Koo H., Suh B., Yang Q., Haas B., Peterson J., Pertea M.,
RA Volfovsky N., Wortman J., White O., Salzberg S.L., Fraser C.M., Buell C.R.,
RA Messing J., Song R., Fuks G., Llaca V., Kovchak S., Young S., Bowers J.E.,
RA Paterson A.H., Johns M.A., Mao L., Pan H., Dean R.A.;
RT "In-depth view of structure, activity, and evolution of rice chromosome
RT 10.";
RL Science 300:1566-1569(2003).
RN [3]
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 [4]
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 [5]
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 [6]
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 [7]
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 [8]
RP PATHWAY.
RX PubMed=9620799; DOI=10.1038/30728;
RA Wheeler G.L., Jones M.A., Smirnoff N.;
RT "The biosynthetic pathway of vitamin C in higher plants.";
RL Nature 393:365-369(1998).
CC -!- FUNCTION: Catalyzes a reversible epimerization of GDP-D-mannose that
CC precedes the committed step in the biosynthesis of vitamin C (L-
CC ascorbate), resulting in the hydrolysis of the highly energetic
CC glycosyl-pyrophosphoryl linkage. Able to catalyze 2 distinct
CC epimerization reactions and can release both GDP-L-galactose and GDP-L-
CC gulose from GDP-mannose. {ECO:0000269|PubMed:16413588}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=GDP-alpha-D-mannose = GDP-beta-L-gulose; Xref=Rhea:RHEA:63800,
CC ChEBI:CHEBI:57527, ChEBI:CHEBI:149550; EC=5.1.3.18;
CC Evidence={ECO:0000269|PubMed:16413588};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=GDP-beta-L-gulose = GDP-beta-L-galactose;
CC Xref=Rhea:RHEA:63804, ChEBI:CHEBI:61454, ChEBI:CHEBI:149550;
CC EC=5.1.3.18; Evidence={ECO:0000269|PubMed:16413588};
CC -!- COFACTOR:
CC Name=NAD(+); Xref=ChEBI:CHEBI:57540;
CC Evidence={ECO:0000250|UniProtKB:Q93VR3};
CC -!- ACTIVITY REGULATION: Strongly activated by NAD. Activated by NADP.
CC Slightly activated by NADH and NADPH. Inhibited by GDP.
CC {ECO:0000269|PubMed:16413588}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=7.12 uM for GDP-mannose {ECO:0000269|PubMed:16413588};
CC KM=12 uM for GDP-mannose (in the presence of 20 uM NAD(+))
CC {ECO:0000269|PubMed:16413588};
CC Note=The catalytic efficiency increases by 2-fold in the presence of
CC NAD(+).;
CC pH dependence:
CC Optimum pH is 7.5-8.0 at 20 degrees Celsius, and 8.0-8.5 at 25
CC degrees Celsius in the presence of NAD(+).
CC {ECO:0000269|PubMed:16413588};
CC -!- PATHWAY: Cofactor biosynthesis; L-ascorbate biosynthesis via GDP-alpha-
CC D-mannose pathway; L-ascorbate from GDP-alpha-D-mannose: step 1/5.
CC {ECO:0000269|PubMed:9620799}.
CC -!- SUBUNIT: Homodimer. {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the NAD(P)-dependent epimerase/dehydratase
CC family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=ABG66078.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AB193582; BAD66930.1; -; mRNA.
DR EMBL; AC016780; AAM08784.1; -; Genomic_DNA.
DR EMBL; DP000086; ABB47619.2; -; Genomic_DNA.
DR EMBL; DP000086; ABG66078.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP008216; BAF26523.1; -; Genomic_DNA.
DR EMBL; AP014966; BAT10866.1; -; Genomic_DNA.
DR EMBL; CM000147; EAZ16087.1; -; Genomic_DNA.
DR EMBL; AK104822; BAG96977.1; -; mRNA.
DR RefSeq; XP_015614669.1; XM_015759183.1.
DR AlphaFoldDB; A3C4S4; -.
DR SMR; A3C4S4; -.
DR BioGRID; 817673; 1.
DR STRING; 4530.OS10T0417600-01; -.
DR iPTMnet; A3C4S4; -.
DR PaxDb; A3C4S4; -.
DR PRIDE; A3C4S4; -.
DR EnsemblPlants; Os10t0417600-01; Os10t0417600-01; Os10g0417600.
DR GeneID; 4348636; -.
DR Gramene; Os10t0417600-01; Os10t0417600-01; Os10g0417600.
DR KEGG; osa:4348636; -.
DR eggNOG; KOG1429; Eukaryota.
DR HOGENOM; CLU_007383_4_2_1; -.
DR InParanoid; A3C4S4; -.
DR OMA; QTATDKF; -.
DR OrthoDB; 662484at2759; -.
DR BioCyc; MetaCyc:MON-11941; -.
DR BRENDA; 5.1.3.18; 4460.
DR PlantReactome; R-OSA-1119410; Ascorbate biosynthesis.
DR SABIO-RK; A3C4S4; -.
DR UniPathway; UPA00990; UER00931.
DR Proteomes; UP000000763; Chromosome 10.
DR Proteomes; UP000007752; Chromosome 10.
DR Proteomes; UP000059680; Chromosome 10.
DR Genevisible; A3C4S4; OS.
DR GO; GO:0047918; F:GDP-mannose 3,5-epimerase activity; IEA:UniProtKB-EC.
DR GO; GO:0051287; F:NAD binding; IEA:InterPro.
DR GO; GO:0019853; P:L-ascorbic acid biosynthetic process; IEA:UniProtKB-KW.
DR CDD; cd05273; GME-like_SDR_e; 1.
DR InterPro; IPR001509; Epimerase_deHydtase.
DR InterPro; IPR033890; GDP-Man_epi.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR Pfam; PF01370; Epimerase; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
PE 1: Evidence at protein level;
KW Ascorbate biosynthesis; Isomerase; NAD; Reference proteome.
FT CHAIN 1..378
FT /note="GDP-mannose 3,5-epimerase 1"
FT /id="PRO_0000233697"
FT ACT_SITE 175
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT BINDING 36..62
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 60
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 80
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 105
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 145..147
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 175
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 179
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 204
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 217..219
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 226
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 242..244
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 307
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 357
FT /ligand="substrate"
FT /evidence="ECO:0000250"
SQ SEQUENCE 378 AA; 42778 MW; 4BAE83BB932C321A CRC64;
MGSSEKNGTA YGEYTYAELE REQYWPSEKL RISITGAGGF IGSHIARRLK SEGHYIIASD
WKKNEHMTED MFCHEFHLVD LRVMDNCLKV TNGVDHVFNL AADMGGMGFI QSNHSVIMYN
NTMISFNMLE AARINGVKRF FYASSACIYP EFKQLETNVS LKESDAWPAE PQDAYGLEKL
ATEELCKHYT KDFGIECRVG RFHNIYGPFG TWKGGREKAP AAFCRKAQTS TDRFEMWGDG
LQTRSFTFID ECVEGVLRLT KSDFREPVNI GSDEMVSMNE MAEIILSFED RELPIHHIPG
PEGVRGRNSD NTLIKEKLGW APTMKLKDGL RFTYFWIKEQ IEKEKTQGVD IAGYGSSKVV
STQAPVQLGS LRAADGKE
