GLYR1_ARATH
ID GLYR1_ARATH Reviewed; 289 AA.
AC Q9LSV0; B9DFS5; F4J913; Q94A74; Q94B07;
DT 06-FEB-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 152.
DE RecName: Full=Glyoxylate/succinic semialdehyde reductase 1;
DE Short=AtGLYR1;
DE Short=AtGR1;
DE Short=SSA reductase 1;
DE EC=1.1.1.79 {ECO:0000269|Ref.7, ECO:0000269|Ref.8};
DE EC=1.1.1.n11 {ECO:0000269|Ref.7, ECO:0000269|Ref.8};
DE AltName: Full=Gamma-hydroxybutyrate dehydrogenase {ECO:0000303|PubMed:12882961};
DE Short=AtGHBDH;
GN Name=GLYR1; Synonyms=GR1; OrderedLocusNames=At3g25530; ORFNames=MWL2.18;
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 [MRNA] (ISOFORM 1), AND FUNCTION.
RC STRAIN=cv. Landsberg erecta;
RX PubMed=12882961; DOI=10.1074/jbc.m305717200;
RA Breitkreuz K.E., Allan W.L., Van Cauwenberghe O.R., Jakobs C., Talibi D.,
RA Andre B., Shelp B.J.;
RT "A novel gamma-hydroxybutyrate dehydrogenase: identification and expression
RT of an Arabidopsis cDNA and potential role under oxygen deficiency.";
RL J. Biol. Chem. 278:41552-41556(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10819329; DOI=10.1093/dnares/7.2.131;
RA Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence
RT features of the regions of 4,504,864 bp covered by sixty P1 and TAC
RT clones.";
RL DNA Res. 7:131-135(2000).
RN [3]
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 [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
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 [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC STRAIN=cv. Columbia;
RX PubMed=19423640; DOI=10.1093/dnares/dsp009;
RA Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M.,
RA Shinozaki K.;
RT "Analysis of multiple occurrences of alternative splicing events in
RT Arabidopsis thaliana using novel sequenced full-length cDNAs.";
RL DNA Res. 16:155-164(2009).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC STRAIN=cv. Columbia;
RA Shinn P., Chen H., Kim C.J., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (APR-2006) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RA Hoover G.J., Van Cauwenberghe O.R., Breitkreuz K.E., Clark S.M.,
RA Merrill A.R., Shelp B.J.;
RT "Characteristics of an Arabidopsis glyoxylate reductase: general
RT biochemical properties and substrate specificity for the recombinant
RT protein, and developmental expression and implications for glyoxylate and
RT succinic semialdehyde metabolism in planta.";
RL Can. J. Bot. 85:883-895(2007).
RN [8]
RP FUNCTION, CATALYTIC ACTIVITY, AND KINETIC PARAMETERS.
RA Hoover G.J., Prentice G.A., Merrill A.R., Shelp B.J.;
RT "Kinetic mechanism of a recombinant Arabidopsis glyoxylate reductase:
RT studies of initial velocity, dead-end inhibition and product inhibition.";
RL Can. J. Bot. 85:896-902(2007).
RN [9]
RP SUBCELLULAR LOCATION.
RX PubMed=18495639; DOI=10.1093/jxb/ern123;
RA Simpson J.P., Di Leo R., Dhanoa P.K., Allan W.L., Makhmoudova A.,
RA Clark S.M., Hoover G.J., Mullen R.T., Shelp B.J.;
RT "Identification and characterization of a plastid-localized Arabidopsis
RT glyoxylate reductase isoform: comparison with a cytosolic isoform and
RT implications for cellular redox homeostasis and aldehyde detoxification.";
RL J. Exp. Bot. 59:2545-2554(2008).
RN [10]
RP INDUCTION.
RX PubMed=18495640; DOI=10.1093/jxb/ern122;
RA Allan W.L., Simpson J.P., Clark S.M., Shelp B.J.;
RT "Gamma-hydroxybutyrate accumulation in Arabidopsis and tobacco plants is a
RT general response to abiotic stress: putative regulation by redox balance
RT and glyoxylate reductase isoforms.";
RL J. Exp. Bot. 59:2555-2564(2008).
RN [11]
RP INDUCTION BY OZONE.
RX PubMed=19453511; DOI=10.1111/j.1399-3054.2009.01220.x;
RA Yoshida S., Tamaoki M., Ioki M., Ogawa D., Sato Y., Aono M., Kubo A.,
RA Saji S., Saji H., Satoh S., Nakajima N.;
RT "Ethylene and salicylic acid control glutathione biosynthesis in ozone-
RT exposed Arabidopsis thaliana.";
RL Physiol. Plantarum 136:284-298(2009).
RN [12]
RP SUBCELLULAR LOCATION.
RX PubMed=22309191; DOI=10.1111/j.1744-7909.2012.01103.x;
RA Ching S.L., Gidda S.K., Rochon A., van Cauwenberghe O.R., Shelp B.J.,
RA Mullen R.T.;
RT "Glyoxylate reductase isoform 1 is localized in the cytosol and not
RT peroxisomes in plant cells.";
RL J. Integr. Plant Biol. 54:152-168(2012).
RN [13]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22223895; DOI=10.1074/mcp.m111.015131;
RA Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T.,
RA Giglione C.;
RT "Comparative large-scale characterisation of plant vs. mammal proteins
RT reveals similar and idiosyncratic N-alpha acetylation features.";
RL Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
RN [14]
RP X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS).
RA Hoover G., Jorgensen R., Merrill A.R., Shelp B.J.;
RT "Cytosolic NADPH-dependent glyoxylate reductase from Arabidopsis: crystal
RT structure and kinetic characterization of active site mutants.";
RL Submitted (JUL-2008) to the PDB data bank.
CC -!- FUNCTION: Catalyzes the NADPH-dependent reduction of glyoxylate to
CC glycolate as well as succinic semialdehyde (SSA) to gamma-
CC hydroxybutyrate in vitro. May function in redox homeostasis and play a
CC role in oxidative stress tolerance by detoxifying glyoxylate and SSA
CC generated in glycolate metabolism and GABA metabolism, respectively.
CC {ECO:0000269|PubMed:12882961, ECO:0000269|Ref.7, ECO:0000269|Ref.8}.
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|Ref.7, ECO:0000269|Ref.8};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=4-hydroxybutanoate + NADP(+) = H(+) + NADPH + succinate
CC semialdehyde; Xref=Rhea:RHEA:26381, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16724, ChEBI:CHEBI:57706, ChEBI:CHEBI:57783,
CC ChEBI:CHEBI:58349; EC=1.1.1.n11; Evidence={ECO:0000269|Ref.7,
CC ECO:0000269|Ref.8};
CC -!- ACTIVITY REGULATION: The ratio of NADPH/NADP(+) may regulate enzymatic
CC activity. {ECO:0000305}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=4.5 uM for glyoxylate {ECO:0000269|Ref.7, ECO:0000269|Ref.8};
CC KM=870 uM for succinate semialdehyde {ECO:0000269|Ref.7,
CC ECO:0000269|Ref.8};
CC KM=2.2 uM for NADPH (in the presence of glyoxylate as cosubstrate)
CC {ECO:0000269|Ref.7, ECO:0000269|Ref.8};
CC KM=2.6 uM for NADPH (in the presence of succinate semialdehyde as
CC cosubstrate) {ECO:0000269|Ref.7, ECO:0000269|Ref.8};
CC -!- SUBCELLULAR LOCATION: Cytoplasm, cytosol {ECO:0000269|PubMed:18495639,
CC ECO:0000269|PubMed:22309191}. Note=According to PubMed:22309191, GLYR1
CC does not localize in the peroxisome as initially described in
CC PubMed:18495639.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9LSV0-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9LSV0-2; Sequence=VSP_045054;
CC -!- INDUCTION: By salinity, drought, submergence, cold and heat stresses,
CC and ozone. {ECO:0000269|PubMed:18495640, ECO:0000269|PubMed:19453511}.
CC -!- MISCELLANEOUS: Follows a sequentially ordered Bi-Bi catalytic mechanism
CC involving the complexation of NADPH to the enzyme before glyoxylate or
CC SSA, and the release of NADP(+) before glycolate or gamma-
CC hydroxybutyrate, respectively. Although GLYR1 acts as an aldo/keto
CC reductase, it has no significant homology with either mammalian and
CC bacterial NADPH-dependent SSA reductases.
CC -!- SIMILARITY: Belongs to the HIBADH-related family. NP60 subfamily.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAK83640.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; AY044183; AAK94781.1; -; mRNA.
DR EMBL; AB025639; BAB01322.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE77021.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE77022.1; -; Genomic_DNA.
DR EMBL; AY049298; AAK83640.1; ALT_FRAME; mRNA.
DR EMBL; AK316884; BAH19592.1; -; mRNA.
DR EMBL; BT025039; ABE02414.1; -; mRNA.
DR RefSeq; NP_001030765.1; NM_001035688.1. [Q9LSV0-2]
DR RefSeq; NP_566768.1; NM_113449.4. [Q9LSV0-1]
DR PDB; 3DOJ; X-ray; 2.10 A; A=1-289.
DR PDBsum; 3DOJ; -.
DR AlphaFoldDB; Q9LSV0; -.
DR SMR; Q9LSV0; -.
DR BioGRID; 7470; 6.
DR STRING; 3702.AT3G25530.1; -.
DR iPTMnet; Q9LSV0; -.
DR PaxDb; Q9LSV0; -.
DR PRIDE; Q9LSV0; -.
DR ProMEX; Q9LSV0; -.
DR ProteomicsDB; 248530; -. [Q9LSV0-1]
DR EnsemblPlants; AT3G25530.1; AT3G25530.1; AT3G25530. [Q9LSV0-1]
DR EnsemblPlants; AT3G25530.2; AT3G25530.2; AT3G25530. [Q9LSV0-2]
DR GeneID; 822139; -.
DR Gramene; AT3G25530.1; AT3G25530.1; AT3G25530. [Q9LSV0-1]
DR Gramene; AT3G25530.2; AT3G25530.2; AT3G25530. [Q9LSV0-2]
DR KEGG; ath:AT3G25530; -.
DR Araport; AT3G25530; -.
DR TAIR; locus:2094518; AT3G25530.
DR eggNOG; KOG0409; Eukaryota.
DR OMA; AWVQSTT; -.
DR PhylomeDB; Q9LSV0; -.
DR BioCyc; ARA:AT3G25530-MON; -.
DR BioCyc; MetaCyc:MON-10405; -.
DR BRENDA; 1.1.1.26; 399.
DR BRENDA; 1.1.1.61; 399.
DR BRENDA; 1.1.1.79; 399.
DR BRENDA; 1.1.1.B47; 399.
DR EvolutionaryTrace; Q9LSV0; -.
DR PRO; PR:Q9LSV0; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9LSV0; baseline and differential.
DR Genevisible; Q9LSV0; AT.
DR GO; GO:0005829; C:cytosol; IDA:TAIR.
DR GO; GO:0003858; F:3-hydroxybutyrate dehydrogenase activity; IMP:TAIR.
DR GO; GO:0030267; F:glyoxylate reductase (NADP+) activity; IEA:UniProtKB-EC.
DR GO; GO:0051287; F:NAD binding; IEA:InterPro.
DR GO; GO:0050661; F:NADP binding; IEA:InterPro.
DR GO; GO:0016616; F:oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor; IBA:GO_Central.
DR GO; GO:0006979; P:response to oxidative stress; IMP:TAIR.
DR Gene3D; 1.10.1040.10; -; 1.
DR InterPro; IPR002204; 3-OH-isobutyrate_DH-rel_CS.
DR InterPro; IPR008927; 6-PGluconate_DH-like_C_sf.
DR InterPro; IPR013328; 6PGD_dom2.
DR InterPro; IPR006115; 6PGDH_NADP-bd.
DR InterPro; IPR015815; HIBADH-related.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR InterPro; IPR029154; NADP-bd.
DR Pfam; PF14833; NAD_binding_11; 1.
DR Pfam; PF03446; NAD_binding_2; 1.
DR PIRSF; PIRSF000103; HIBADH; 1.
DR SUPFAM; SSF48179; SSF48179; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
DR PROSITE; PS00895; 3_HYDROXYISOBUT_DH; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Alternative splicing; Cytoplasm; NAD; NADP;
KW Oxidoreductase; Reference proteome; Stress response.
FT CHAIN 1..289
FT /note="Glyoxylate/succinic semialdehyde reductase 1"
FT /id="PRO_0000421032"
FT ACT_SITE 170
FT /evidence="ECO:0000250"
FT BINDING 4..18
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250|UniProtKB:Q49A26"
FT BINDING 95
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250|UniProtKB:Q49A26"
FT BINDING 238
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250|UniProtKB:Q49A26"
FT MOD_RES 1
FT /note="N-acetylmethionine"
FT /evidence="ECO:0007744|PubMed:22223895"
FT VAR_SEQ 73..83
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:19423640"
FT /id="VSP_045054"
FT CONFLICT 223
FT /note="N -> T (in Ref. 1; AAK94781)"
FT /evidence="ECO:0000305"
FT CONFLICT 263
FT /note="A -> V (in Ref. 5; BAH19592)"
FT /evidence="ECO:0000305"
FT STRAND 2..6
FT /evidence="ECO:0007829|PDB:3DOJ"
FT HELIX 10..21
FT /evidence="ECO:0007829|PDB:3DOJ"
FT STRAND 25..29
FT /evidence="ECO:0007829|PDB:3DOJ"
FT HELIX 33..36
FT /evidence="ECO:0007829|PDB:3DOJ"
FT HELIX 37..41
FT /evidence="ECO:0007829|PDB:3DOJ"
FT HELIX 50..56
FT /evidence="ECO:0007829|PDB:3DOJ"
FT STRAND 58..62
FT /evidence="ECO:0007829|PDB:3DOJ"
FT HELIX 67..75
FT /evidence="ECO:0007829|PDB:3DOJ"
FT HELIX 80..83
FT /evidence="ECO:0007829|PDB:3DOJ"
FT STRAND 89..92
FT /evidence="ECO:0007829|PDB:3DOJ"
FT HELIX 98..110
FT /evidence="ECO:0007829|PDB:3DOJ"
FT STRAND 114..117
FT /evidence="ECO:0007829|PDB:3DOJ"
FT HELIX 124..129
FT /evidence="ECO:0007829|PDB:3DOJ"
FT STRAND 132..138
FT /evidence="ECO:0007829|PDB:3DOJ"
FT HELIX 140..153
FT /evidence="ECO:0007829|PDB:3DOJ"
FT STRAND 154..159
FT /evidence="ECO:0007829|PDB:3DOJ"
FT HELIX 165..193
FT /evidence="ECO:0007829|PDB:3DOJ"
FT HELIX 198..207
FT /evidence="ECO:0007829|PDB:3DOJ"
FT HELIX 213..223
FT /evidence="ECO:0007829|PDB:3DOJ"
FT STRAND 230..232
FT /evidence="ECO:0007829|PDB:3DOJ"
FT HELIX 233..249
FT /evidence="ECO:0007829|PDB:3DOJ"
FT HELIX 255..269
FT /evidence="ECO:0007829|PDB:3DOJ"
FT HELIX 277..280
FT /evidence="ECO:0007829|PDB:3DOJ"
FT HELIX 281..285
FT /evidence="ECO:0007829|PDB:3DOJ"
SQ SEQUENCE 289 AA; 30692 MW; 3E67002A19706636 CRC64;
MEVGFLGLGI MGKAMSMNLL KNGFKVTVWN RTLSKCDELV EHGASVCESP AEVIKKCKYT
IAMLSDPCAA LSVVFDKGGV LEQICEGKGY IDMSTVDAET SLKINEAITG KGGRFVEGPV
SGSKKPAEDG QLIILAAGDK ALFEESIPAF DVLGKRSFYL GQVGNGAKMK LIVNMIMGSM
MNAFSEGLVL ADKSGLSSDT LLDILDLGAM TNPMFKGKGP SMNKSSYPPA FPLKHQQKDM
RLALALGDEN AVSMPVAAAA NEAFKKARSL GLGDLDFSAV IEAVKFSRE
