2KGR_VITVI
ID 2KGR_VITVI Reviewed; 313 AA.
AC A5CAL1;
DT 17-JUN-2020, integrated into UniProtKB/Swiss-Prot.
DT 12-JUN-2007, sequence version 1.
DT 03-AUG-2022, entry version 100.
DE RecName: Full=Glyoxylate/hydroxypyruvate/pyruvate reductase 2KGR {ECO:0000305};
DE EC=1.1.1.26 {ECO:0000269|PubMed:31488549};
DE EC=1.1.1.28 {ECO:0000269|PubMed:31488549};
DE EC=1.1.1.79 {ECO:0000269|PubMed:31488549};
DE AltName: Full=2-keto-L-gulonate reductase {ECO:0000303|PubMed:31488549};
DE Short=Vv2KGR {ECO:0000303|PubMed:31488549};
DE EC=1.1.1.- {ECO:0000269|PubMed:31488549};
GN Name=2KGR {ECO:0000303|PubMed:31488549};
GN OrderedLocusNames=VIT_09s0002g04300 {ECO:0000312|EMBL:CCB59464.1};
GN ORFNames=VITISV_025327 {ECO:0000312|EMBL:CAN84153.1};
OS Vitis vinifera (Grape).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; Vitales; Vitaceae; Viteae; Vitis.
OX NCBI_TaxID=29760;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Pinot noir / PN40024;
RX PubMed=17721507; DOI=10.1038/nature06148;
RA Jaillon O., Aury J.-M., Noel B., Policriti A., Clepet C., Casagrande A.,
RA Choisne N., Aubourg S., Vitulo N., Jubin C., Vezzi A., Legeai F.,
RA Hugueney P., Dasilva C., Horner D., Mica E., Jublot D., Poulain J.,
RA Bruyere C., Billault A., Segurens B., Gouyvenoux M., Ugarte E.,
RA Cattonaro F., Anthouard V., Vico V., Del Fabbro C., Alaux M.,
RA Di Gaspero G., Dumas V., Felice N., Paillard S., Juman I., Moroldo M.,
RA Scalabrin S., Canaguier A., Le Clainche I., Malacrida G., Durand E.,
RA Pesole G., Laucou V., Chatelet P., Merdinoglu D., Delledonne M.,
RA Pezzotti M., Lecharny A., Scarpelli C., Artiguenave F., Pe M.E., Valle G.,
RA Morgante M., Caboche M., Adam-Blondon A.-F., Weissenbach J., Quetier F.,
RA Wincker P.;
RT "The grapevine genome sequence suggests ancestral hexaploidization in major
RT angiosperm phyla.";
RL Nature 449:463-467(2007).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Pinot noir;
RX PubMed=18094749; DOI=10.1371/journal.pone.0001326;
RA Velasco R., Zharkikh A., Troggio M., Cartwright D.A., Cestaro A., Pruss D.,
RA Pindo M., FitzGerald L.M., Vezzulli S., Reid J., Malacarne G., Iliev D.,
RA Coppola G., Wardell B., Micheletti D., Macalma T., Facci M., Mitchell J.T.,
RA Perazzolli M., Eldredge G., Gatto P., Oyzerski R., Moretto M., Gutin N.,
RA Stefanini M., Chen Y., Segala C., Davenport C., Dematte L., Mraz A.,
RA Battilana J., Stormo K., Costa F., Tao Q., Si-Ammour A., Harkins T.,
RA Lackey A., Perbost C., Taillon B., Stella A., Solovyev V., Fawcett J.A.,
RA Sterck L., Vandepoele K., Grando S.M., Toppo S., Moser C., Lanchbury J.,
RA Bogden R., Skolnick M., Sgaramella V., Bhatnagar S.K., Fontana P.,
RA Gutin A., Van de Peer Y., Salamini F., Viola R.;
RT "A high quality draft consensus sequence of the genome of a heterozygous
RT grapevine variety.";
RL PLoS ONE 2:E1326-E1326(2007).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.58 ANGSTROMS), CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, ACTIVE SITES, AND SUBUNIT.
RX PubMed=31488549; DOI=10.1074/jbc.ra119.010196;
RA Jia Y., Burbidge C.A., Sweetman C., Schutz E., Soole K., Jenkins C.,
RA Hancock R.D., Bruning J.B., Ford C.M.;
RT "An aldo-keto reductase with 2-keto-l-gulonate reductase activity functions
RT in l-tartaric acid biosynthesis from vitamin C in Vitis vinifera.";
RL J. Biol. Chem. 294:15932-15946(2019).
CC -!- FUNCTION: Involved in the biosynthesis of L-tartarate from L-ascorbate
CC (PubMed:31488549). Catalyzes the NAD(P)H-dependent reduction of 2-
CC dehydro-L-idonate (2-keto-L-gulonate) to L-idonate (PubMed:31488549).
CC Can also reduce hydroxypyruvate to glycerate, glyoxylate to glycolate
CC and pyruvate to D-lactate (PubMed:31488549). Prefers NADPH to NADH as
CC proton donor (PubMed:31488549). {ECO:0000269|PubMed:31488549}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-idonate + NADP(+) = 2-dehydro-L-idonate + H(+) + NADPH;
CC Xref=Rhea:RHEA:29839, ChEBI:CHEBI:15378, ChEBI:CHEBI:17796,
CC ChEBI:CHEBI:36602, ChEBI:CHEBI:57783, ChEBI:CHEBI:58349;
CC Evidence={ECO:0000269|PubMed:31488549};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:29840;
CC Evidence={ECO:0000269|PubMed:31488549};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-idonate + NAD(+) = 2-dehydro-L-idonate + H(+) + NADH;
CC Xref=Rhea:RHEA:27818, ChEBI:CHEBI:15378, ChEBI:CHEBI:17796,
CC ChEBI:CHEBI:36602, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945;
CC Evidence={ECO:0000269|PubMed:31488549};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:27819;
CC Evidence={ECO:0000269|PubMed:31488549};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(R)-glycerate + NADP(+) = 3-hydroxypyruvate + H(+) + NADPH;
CC Xref=Rhea:RHEA:18657, ChEBI:CHEBI:15378, ChEBI:CHEBI:16659,
CC ChEBI:CHEBI:17180, ChEBI:CHEBI:57783, ChEBI:CHEBI:58349;
CC Evidence={ECO:0000269|PubMed:31488549};
CC PhysiologicalDirection=right-to-left; Xref=Rhea:RHEA:18659;
CC Evidence={ECO:0000269|PubMed:31488549};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=glycolate + NADP(+) = glyoxylate + H(+) + NADPH;
CC Xref=Rhea:RHEA:10992, ChEBI:CHEBI:15378, ChEBI:CHEBI:29805,
CC ChEBI:CHEBI:36655, ChEBI:CHEBI:57783, ChEBI:CHEBI:58349; EC=1.1.1.79;
CC Evidence={ECO:0000269|PubMed:31488549};
CC PhysiologicalDirection=right-to-left; Xref=Rhea:RHEA:10994;
CC Evidence={ECO:0000269|PubMed:31488549};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=glycolate + NAD(+) = glyoxylate + H(+) + NADH;
CC Xref=Rhea:RHEA:18229, ChEBI:CHEBI:15378, ChEBI:CHEBI:29805,
CC ChEBI:CHEBI:36655, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945; EC=1.1.1.26;
CC Evidence={ECO:0000269|PubMed:31488549};
CC PhysiologicalDirection=right-to-left; Xref=Rhea:RHEA:18231;
CC Evidence={ECO:0000269|PubMed:31488549};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(R)-lactate + NADP(+) = H(+) + NADPH + pyruvate;
CC Xref=Rhea:RHEA:62968, ChEBI:CHEBI:15361, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16004, ChEBI:CHEBI:57783, ChEBI:CHEBI:58349;
CC Evidence={ECO:0000269|PubMed:31488549};
CC PhysiologicalDirection=right-to-left; Xref=Rhea:RHEA:62970;
CC Evidence={ECO:0000269|PubMed:31488549};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(R)-lactate + NAD(+) = H(+) + NADH + pyruvate;
CC Xref=Rhea:RHEA:16369, ChEBI:CHEBI:15361, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16004, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945; EC=1.1.1.28;
CC Evidence={ECO:0000269|PubMed:31488549};
CC PhysiologicalDirection=right-to-left; Xref=Rhea:RHEA:16371;
CC Evidence={ECO:0000269|PubMed:31488549};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.7 mM for 2-keto-L-gulonate (in presence of NADPH)
CC {ECO:0000269|PubMed:31488549};
CC KM=1.56 mM for 2-keto-L-gulonate (in presence of NADH)
CC {ECO:0000269|PubMed:31488549};
CC KM=0.096 mM for hydroxypyruvate (in presence of NADPH)
CC {ECO:0000269|PubMed:31488549};
CC KM=0.044 mM for glyoxylate (in presence of NADPH)
CC {ECO:0000269|PubMed:31488549};
CC KM=0.248 mM for glyoxylate (in presence of NADH)
CC {ECO:0000269|PubMed:31488549};
CC KM=1.37 mM for pyruvate (in presence of NADPH)
CC {ECO:0000269|PubMed:31488549};
CC KM=3.45 mM for pyruvate (in presence of NADH)
CC {ECO:0000269|PubMed:31488549};
CC Vmax=7.54 umol/min/mg enzyme with 2-keto-L-gulonate as substrate (in
CC presence of NADPH) {ECO:0000269|PubMed:31488549};
CC Vmax=17.19 umol/min/mg enzyme with 2-keto-L-gulonate as substrate (in
CC presence of NADH) {ECO:0000269|PubMed:31488549};
CC Vmax=6.29 umol/min/mg enzyme with hydroxypyruvate as substrate (in
CC presence of NADPH) {ECO:0000269|PubMed:31488549};
CC Vmax=13.82 umol/min/mg enzyme with glyoxylate as substrate (in
CC presence of NADPH) {ECO:0000269|PubMed:31488549};
CC Vmax=69.38 umol/min/mg enzyme with glyoxylate as substrate (in
CC presence of NADH) {ECO:0000269|PubMed:31488549};
CC Vmax=0.55 umol/min/mg enzyme with pyruvate as substrate (in presence
CC of NADPH) {ECO:0000269|PubMed:31488549};
CC Vmax=0.44 umol/min/mg enzyme with pyruvate as substrate (in presence
CC of NADH) {ECO:0000269|PubMed:31488549};
CC pH dependence:
CC Optimum pH is 7.5. {ECO:0000269|PubMed:31488549};
CC Temperature dependence:
CC Optimum temperature is 37 degrees Celsius.
CC {ECO:0000269|PubMed:31488549};
CC -!- SUBUNIT: Forms homodimers. {ECO:0000269|PubMed:31488549}.
CC -!- SIMILARITY: Belongs to the D-isomer specific 2-hydroxyacid
CC dehydrogenase family. {ECO:0000305}.
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DR EMBL; FN596494; CCB59464.1; -; Genomic_DNA.
DR EMBL; FN597028; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AM488308; CAN84153.1; -; Genomic_DNA.
DR RefSeq; XP_003632860.1; XM_003632812.3.
DR PDB; 6PEX; X-ray; 1.58 A; A/B/C/D=1-313.
DR PDBsum; 6PEX; -.
DR AlphaFoldDB; A5CAL1; -.
DR SMR; A5CAL1; -.
DR STRING; 29760.VIT_09s0002g04300.t01; -.
DR PRIDE; A5CAL1; -.
DR EnsemblPlants; Vitvi09g00358_t001; Vitvi09g00358_P001; Vitvi09g00358.
DR GeneID; 100251492; -.
DR Gramene; Vitvi09g00358_t001; Vitvi09g00358_P001; Vitvi09g00358.
DR KEGG; vvi:100251492; -.
DR eggNOG; KOG0069; Eukaryota.
DR HOGENOM; CLU_019796_1_2_1; -.
DR InParanoid; A5CAL1; -.
DR OrthoDB; 1378766at2759; -.
DR Proteomes; UP000009183; Chromosome 9.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0008720; F:D-lactate dehydrogenase activity; IEA:UniProtKB-EC.
DR GO; GO:0047964; F:glyoxylate reductase (NAD+) activity; IEA:UniProtKB-EC.
DR GO; GO:0030267; F:glyoxylate reductase (NADP+) activity; IBA:GO_Central.
DR GO; GO:0016618; F:hydroxypyruvate reductase activity; IBA:GO_Central.
DR GO; GO:0051287; F:NAD binding; IEA:InterPro.
DR InterPro; IPR006139; D-isomer_2_OHA_DH_cat_dom.
DR InterPro; IPR029752; D-isomer_DH_CS1.
DR InterPro; IPR006140; D-isomer_DH_NAD-bd.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR Pfam; PF00389; 2-Hacid_dh; 1.
DR Pfam; PF02826; 2-Hacid_dh_C; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
DR PROSITE; PS00065; D_2_HYDROXYACID_DH_1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; NAD; NADP; Oxidoreductase; Reference proteome.
FT CHAIN 1..313
FT /note="Glyoxylate/hydroxypyruvate/pyruvate reductase 2KGR"
FT /id="PRO_0000449838"
FT ACT_SITE 232
FT /evidence="ECO:0000305|PubMed:31488549"
FT ACT_SITE 261
FT /evidence="ECO:0000305|PubMed:31488549"
FT ACT_SITE 279
FT /note="Proton donor"
FT /evidence="ECO:0000305|PubMed:31488549"
FT BINDING 152..155
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250|UniProtKB:Q65CJ7"
FT BINDING 174..176
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250|UniProtKB:Q65CJ7"
FT BINDING 230
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250|UniProtKB:Q65CJ7"
FT BINDING 256
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250|UniProtKB:Q65CJ7"
FT STRAND 5..8
FT /evidence="ECO:0007829|PDB:6PEX"
FT HELIX 14..23
FT /evidence="ECO:0007829|PDB:6PEX"
FT STRAND 24..28
FT /evidence="ECO:0007829|PDB:6PEX"
FT HELIX 29..31
FT /evidence="ECO:0007829|PDB:6PEX"
FT STRAND 32..34
FT /evidence="ECO:0007829|PDB:6PEX"
FT HELIX 35..42
FT /evidence="ECO:0007829|PDB:6PEX"
FT TURN 43..45
FT /evidence="ECO:0007829|PDB:6PEX"
FT STRAND 47..51
FT /evidence="ECO:0007829|PDB:6PEX"
FT STRAND 53..55
FT /evidence="ECO:0007829|PDB:6PEX"
FT HELIX 59..64
FT /evidence="ECO:0007829|PDB:6PEX"
FT STRAND 70..76
FT /evidence="ECO:0007829|PDB:6PEX"
FT HELIX 83..88
FT /evidence="ECO:0007829|PDB:6PEX"
FT STRAND 92..94
FT /evidence="ECO:0007829|PDB:6PEX"
FT HELIX 101..116
FT /evidence="ECO:0007829|PDB:6PEX"
FT HELIX 119..127
FT /evidence="ECO:0007829|PDB:6PEX"
FT HELIX 130..132
FT /evidence="ECO:0007829|PDB:6PEX"
FT STRAND 147..150
FT /evidence="ECO:0007829|PDB:6PEX"
FT HELIX 154..164
FT /evidence="ECO:0007829|PDB:6PEX"
FT TURN 165..167
FT /evidence="ECO:0007829|PDB:6PEX"
FT STRAND 170..176
FT /evidence="ECO:0007829|PDB:6PEX"
FT STRAND 183..188
FT /evidence="ECO:0007829|PDB:6PEX"
FT HELIX 189..194
FT /evidence="ECO:0007829|PDB:6PEX"
FT STRAND 197..201
FT /evidence="ECO:0007829|PDB:6PEX"
FT TURN 207..211
FT /evidence="ECO:0007829|PDB:6PEX"
FT HELIX 215..221
FT /evidence="ECO:0007829|PDB:6PEX"
FT STRAND 226..229
FT /evidence="ECO:0007829|PDB:6PEX"
FT HELIX 233..235
FT /evidence="ECO:0007829|PDB:6PEX"
FT HELIX 238..246
FT /evidence="ECO:0007829|PDB:6PEX"
FT STRAND 252..256
FT /evidence="ECO:0007829|PDB:6PEX"
FT TURN 259..262
FT /evidence="ECO:0007829|PDB:6PEX"
FT HELIX 266..269
FT /evidence="ECO:0007829|PDB:6PEX"
FT STRAND 272..276
FT /evidence="ECO:0007829|PDB:6PEX"
FT HELIX 285..303
FT /evidence="ECO:0007829|PDB:6PEX"
FT STRAND 309..313
FT /evidence="ECO:0007829|PDB:6PEX"
SQ SEQUENCE 313 AA; 34304 MW; C924DA730B9A569C CRC64;
MESIGVLLTC PMNPYLEQEL DKRFKLFRFW DFPSANDLFR EHSNSIRAVV GNSFIGADAQ
MIEALPKMEI VSSFSVGLDK IDLVRCKEKG IRVTNTPDVL TEDVADLALA LILATLRRIC
ESDRYVRSGS WKKGDFKLTT KFTGKSVGII GLGRIGSAIA KRAEGFSCPI SYHSRTEKPG
TNYKYYPSVV ELASNCQILV VACALTPETR HIINREVINA LGPKGVVINI GRGLHVDEPE
LVSALVEGRL GGAGLDVFEN EPNVPEELLA MDNVVLLPHV GSGTVETRKD MADLVLGNLE
AHFLNKPLLT PVV
