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Information on EC 1.1.1.79 - glyoxylate reductase (NADP+) and Organism(s) Arabidopsis thaliana and UniProt Accession Q9LSV0

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IUBMB Comments
Also reduces hydroxypyruvate to glycerate; has some affinity for NAD+.
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This record set is specific for:
Arabidopsis thaliana
UNIPROT: Q9LSV0
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Word Map
The taxonomic range for the selected organisms is: Arabidopsis thaliana
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Synonyms
atgr1, atglyr1, d-2-hydroxy-acid dehydrogenase, glyoxylate reductase (nadp+), atgr2, glyoxylate reductase 1, atglyr2, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
glyoxylate reductase
-
glyoxylate reductase 1
-
glyoxylate reductase isoform 1
-
glyoxylate/succinic semialdehyde reductase
-
GLYR1
AtGR2
glycerate dehydrogenase
-
glyoxylate reductase 2
-
glyoxylate/succinic semialdehyde reductase
-
GLYR1
-
isoform
GLYR2
additional information
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
glycolate + NADP+ = glyoxylate + NADPH + H+
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
redox reaction
-
-
-
-
oxidation
-
-
-
-
reduction
-
-
-
-
SYSTEMATIC NAME
IUBMB Comments
glycolate:NADP+ oxidoreductase
Also reduces hydroxypyruvate to glycerate; has some affinity for NAD+.
CAS REGISTRY NUMBER
COMMENTARY hide
37250-17-2
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
glycolate + NAD+
glyoxylate + NADH + H+
show the reaction diagram
-
-
-
r
glycolate + NADP+
glyoxylate + NADPH + H+
show the reaction diagram
glyoxylate + NADH + H+
glycolate + NAD+
show the reaction diagram
NADH much less effective than NADPH
-
-
ir
glyoxylate + NADPH + H+
glycolate + NADP+
show the reaction diagram
succinic semialdehyde + NADH + H+
4-hydroxybutyrate + NAD+
show the reaction diagram
NADH much less effective than NADPH
-
-
?
succinic semialdehyde + NADPH + H+
4-hydroxybutyrate + NADP+
show the reaction diagram
glycolate + NADP+
glyoxylate + NADPH + H+
show the reaction diagram
-
-
-
r
glyoxylate + NADH
glycolate + NAD+
show the reaction diagram
NADH much less effective than NADPH
-
-
ir
glyoxylate + NADPH + H+
glycolate + NADP+
show the reaction diagram
succinic semialdehyde + NADH + H+
4-hydroxybutyrate + NAD+
show the reaction diagram
NADH much less effective than NADPH
-
-
?
succinic semialdehyde + NADPH + H+
4-hydroxybutyrate + NADP+
show the reaction diagram
additional information
?
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
glycolate + NAD+
glyoxylate + NADH + H+
show the reaction diagram
-
-
-
r
glycolate + NADP+
glyoxylate + NADPH + H+
show the reaction diagram
glyoxylate + NADPH + H+
glycolate + NADP+
show the reaction diagram
succinic semialdehyde + NADPH + H+
4-hydroxybutyrate + NADP+
show the reaction diagram
detoxification of succinic semialdehyde during stress
-
-
r
glycolate + NADP+
glyoxylate + NADPH + H+
show the reaction diagram
-
-
-
r
glyoxylate + NADPH + H+
glycolate + NADP+
show the reaction diagram
succinic semialdehyde + NADPH + H+
4-hydroxybutyrate + NADP+
show the reaction diagram
additional information
?
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
NADP+
NADPH
NADH
much less effective than NADPH
NADPH
additional information
-
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
4-hydroxybutyrate
glycolate
NADP+
NADP+
additional information
-
no inhibition by 4-hydroxybutyrate
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0045 - 12.4
glyoxylate
0.0009 - 0.0648
NADPH
0.87
Succinic semialdehyde
0.016 - 0.034
glyoxylate
0.0012 - 0.0014
NADPH
8.96
Succinic semialdehyde
additional information
additional information
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0052 - 3407
glyoxylate
8.1 - 93.7
NADPH
10.1
Succinic semialdehyde
isoform GLYR1, at pH 7.8 and 25°C
18.4 - 22.5
glyoxylate
10.7 - 12
NADPH
17
Succinic semialdehyde
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.19 - 3407
glyoxylate
779 - 51700
NADPH
11.6
Succinic semialdehyde
isoform GLYR1, at pH 7.8 and 25°C
906
glyoxylate
isoform GLYR2, at pH 7.8 and 25°C
660 - 9180
NADPH
1.9
Succinic semialdehyde
isoform GLYR2, at pH 7.8 and 25°C
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
79.9 - 93.5
4-hydroxybutyrate
22.1 - 23.7
glycolate
0.0031 - 0.147
NADP+
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.8 - 7.8
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.5 - 9
approximately 10% of activity at pH 5.5 and 9
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
8.5
calculated from amino acid sequence
8.54
calculated from the deduced amino acid sequence
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
additional information
GLYR1 is not relocalized from the cytosol to peroxisomes in response to abiotic stress
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
physiological function
GLYR1 scavenges succinic semialdehyde and glyoxylate that escape from mitochondria and peroxisomes, respectively
evolution
additional information
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
GLYR1_ARATH
289
0
30692
Swiss-Prot
other Location (Reliability: 3)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
35900
x * 35900, truncated enzyme from Escherichia coli including His-tag
36200
calculated from amino acid sequence
36287
x * 36287, calculated from the deduced amino acid sequence
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
x * 30700, isoform GLYR1, calculated from amino acid sequence
additional information
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified apo-enzyme, sitting drop vapor diffusion method, mixing of 0.002 ml of protein solution with 0.002 ml of reservoir solution containing 0.2 M calcium acetate hydrate, 20% PEG 3350, pH 6.5, 20°C, 6 weeks, X-ray diffraction structure determination and analysis at 2.1 A resolution, molecular replacement using a previously unrecognized member of the beta-HAD family, cytokine-like nuclear factor, structure
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D239A
site-directed mutagenesis
F231A
site-directed mutagenesis
K170A
site-directed mutagenesis, catalytically inactive mutant
K170E
site-directed mutagenesis, the mutant shows highly reduced kcat for glyoxylate compared to the wild-type
K170H
site-directed mutagenesis, the mutant shows highly reduced kcat for glyoxylate compared to the wild-type
K170R
site-directed mutagenesis, the mutant shows highly reduced kcat for glyoxylate compared to the wild-type
N174A
site-directed mutagenesis
R31L/T32K/K35D/C68R
site-directed mutagenesis of Rosmann fold (c.2.1.6) residues leading to a switch of cofactor preference of the enzyme from NADP(H) to NAD(H), altered cofactor kinetics of the mutant enzyme R31L/T32K/ K35D/C68R compared to the wild-type, overview
S121A
site-directed mutagenesis
T95A
site-directed mutagenesis
DELTA1-43
in contrast to the full length sequence yields a soluble protein when expressed in Escherichia coli
DELTA2-45
localizes in the cytosol instead of plastids
additional information
invertion of the cofactor specificity of the NADP+-dependent enzyme glyoxylate reductase by a structure-guided, semirational strategy, overview. The heuristic-based approach leverages the diversity and sensitivity of catalytically productive cofactor binding geometries to limit the problem to an experimentally tractable scale. Experimental validation of the CSR-SALAD method for switching cofactor preference to NAD while retaining catalytic activity
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-80°C, concentrated enzyme, can be stored for month
-80°C, concentrated protein eluate from the affinity column, for months, enzyme activity is reasonably stable
4°C, concentrated protein eluate from the affinity column, for hours, enzyme activity is reasonably stable
4°C, diluted enzyme, storage during assays, activity starts to decrease within 30 min
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
Ni-NTA Sepharose column chromatography
nickel affinity column chromatography
recombinant His6-tagged wild-type and mutant enzymes from Escherichia coli strain BL21 pLysS by precipitation with 10% PEG 8000, and nickel affinity chromatography
recombinant protein from Escherichia coli
nickel affinity column chromatography
recombinant His6-tagged truncated mutant enzyme from Escherichia coli strain BL21 pLysS by precipitation with 10% PEG 8000, and nickel affinity chromatography
recombinant truncated protein using His-tag
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
exclusive localization in the cytosol of transgenic Arabidopsis plants co-expressing GFP-GLYR1 and and Cherry-PTS1, a fusion protein consisting of the Cherry fluorescent protein linked to the PTS1 of the peroxisomal enzyme hydroxypyruvate reductase. Expression of N-terminal GFP-tagged or Myc-tagged GLYR1 in tobacco BY-2 cell cytosol. GFP- or Myc-tagged GLYR1 is competent, at least partially, for import into peroxisomes, since replacement of the C-terminal glutamate in GLYR1 with leucine, which yields a canonical PTS1 (i.e., a C-terminal small-basic-hydrophobic tripeptide motif), results in the modified fusion protein (GFPGLYR1-E to L and Myc-GLYR1-E to L) being dual localized to the cytosol and peroxisomes in BY-2 cells
expressed as GFP-fusion protein in tobacco BY-2 cells
expressed in Escherichia coli
expressed in Escherichia coli BL21(DE3) cells
gene GLYR1, sequence comparisons of GLYR genes and HPR genes, recombinant expression of His6-tagged wild-type and mutant enzymes in Escherichia coli strain BL21 pLysS
expressed as GFP-fusion protein in tobacco BY-2 cells
expressed as His-tag fusion protein in E. coli BL-21(DE3) Rosetta (pLysS), full-length and truncated GR2 sequences introduced into Escherichia coli, only the recombinant truncated GR2 is soluble, expression markedly improved by co-expression of the GroES/GroEL chaperone
expressed in Escherichia coli BL-21(DE3) Rosetta (pLysS) cells and in Nicotiana tabacum BY-2 cells
expressed in Escherichia coli BL21(DE3) cells
gene GLYR1, sequence comparisons of GLYR genes and HPR genes
gene GLYR2, sequence comparisons of GLYR genes and HPR genes, recombinant expression of a His6-tagged truncated AtGLYR2 cDNA sequence, lacking the N-terminal 58 amino acids, in Escherichia coli strain BL21 pLysS
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Hoover, G.J.; Prentice, G.A.; Merrill, A.R.; Shelp, B.J.
Kinetic mechanism of a recombinant Arabidopsis glyoxylate reductase: studies of initial velocity, dead-end inhibition and product inhibition
Can. J. Bot.
85
896-902
2007
Arabidopsis thaliana (Q9LSV0)
Manually annotated by BRENDA team
Simpson, J.P.; Di Leo, R.; Dhanoa, P.K.; Allan, W.L.; Makhmoudova, A.; Clark, S.M.; Hoover, G.J.; Mullen, R.T.; Shelp, B.J.
Identification and characterization of a plastid-localized Arabidopsis glyoxylate reductase isoform: comparison with a cytosolic isoform and implications for cellular redox homeostasis and aldehyde detoxification
J. Exp. Bot.
59
2545-2554
2008
Arabidopsis thaliana (F4I907), Arabidopsis thaliana (Q9LSV0), Arabidopsis thaliana
Manually annotated by BRENDA team
Allan, W.L.; Simpson, J.P.; Clark, S.M.; Shelp, B.J.
Gamma-hydroxybutyrate accumulation in Arabidopsis and tobacco plants is a general response to abiotic stress: putative regulation by redox balance and glyoxylate reductase isoforms
J. Exp. Bot.
59
2555-2564
2008
Arabidopsis thaliana, Nicotiana tabacum
Manually annotated by BRENDA team
Allan, W.L.; Clark, S.M.; Hoover, G.J.; Shelp, B.J.
Role of plant glyoxylate reductases during stress: a hypothesis
Biochem. J.
423
15-22
2009
Arabidopsis thaliana
Manually annotated by BRENDA team
Ching, S.L.; Gidda, S.K.; Rochon, A.; van Cauwenberghe, O.R.; Shelp, B.J.; Mullen, R.T.
Glyoxylate reductase isoform 1 is localized in the cytosol and not peroxisomes in plant cells
J. Integr. Plant Biol.
54
152-168
2012
Arabidopsis thaliana (Q9LSV0)
Manually annotated by BRENDA team
Hoover, G.J.; Jorgensen, R.; Rochon, A.; Bajwa, V.S.; Merrill, A.R.; Shelp, B.J.
Identification of catalytically important amino acid residues for enzymatic reduction of glyoxylate in plants
Biochim. Biophys. Acta
1834
2663-2671
2013
Arabidopsis thaliana (A0A178WMD4), Arabidopsis thaliana (F4I907), Arabidopsis thaliana (Q9CA90), Arabidopsis thaliana (Q9LSV0), Arabidopsis thaliana
Manually annotated by BRENDA team
Cahn, J.K.; Werlang, C.A.; Baumschlager, A.; Brinkmann-Chen, S.; Mayo, S.L.; Arnold, F.H.
A general tool for engineering the NAD/NADP cofactor preference of oxidoreductases
ACS Synth. Biol.
6
326-333
2016
Arabidopsis thaliana (Q9LSV0)
Manually annotated by BRENDA team
Cahn, J.K.; Werlang, C.A.; Baumschlager, A.; Brinkmann-Chen, S.; Mayo, S.L.; Arnold, F.H.
A general tool for engineering the NAD/NADP cofactor preference of oxidoreductases
ACS Synth. Biol.
6
326-333
2017
Arabidopsis thaliana (Q9LSV0)
Manually annotated by BRENDA team
Zarei, A.; Brikis, C.J.; Bajwa, V.S.; Chiu, G.Z.; Simpson, J.P.; DeEll, J.R.; Bozzo, G.G.; Shelp, B.J.
Plant glyoxylate/succinic semialdehyde reductases comparative biochemical properties, function during chilling stress, and subcellular localization
Front. Plant Sci.
8
1399
2017
Arabidopsis thaliana (F4I907), Arabidopsis thaliana (Q9LSV0), Malus domestica (A0A1C8M582), Malus domestica (A0A1C8M593), Oryza sativa
Manually annotated by BRENDA team