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Protein

Glyoxylate/succinic semialdehyde reductase 1

Gene

GLYR1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the NADPH-dependent reduction of glyoxylate to glycolate as well as succinic semialdehyde (SSA) to gamma-hydroxybutyrate in vitro. May function in redox homeostasis and play a role in oxidative stress tolerance by detoxifying glyoxylate and SSA generated in glycolate metabolism and GABA metabolism, respectively.3 Publications

Catalytic activityi

Glycolate + NADP+ = glyoxylate + NADPH.2 Publications
4-hydroxybutanoate + NADP+ = succinate semialdehyde + NADPH.2 Publications

Enzyme regulationi

The ratio of NADPH/NADP+ may regulate enzymatic activity.

Kineticsi

  1. KM=4.5 µM for glyoxylate2 Publications
  2. KM=870 µM for succinate semialdehyde2 Publications
  3. KM=2.2 µM for NADPH (in the presence of glyoxylate as cosubstrate)2 Publications
  4. KM=2.6 µM for NADPH (in the presence of succinate semialdehyde as cosubstrate)2 Publications

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Active sitei170By similarity1
    Binding sitei238NADPBy similarity1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi4 – 18NADPBy similarityAdd BLAST15

    GO - Molecular functioni

    GO - Biological processi

    • response to oxidative stress Source: TAIR
    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Stress response

    Keywords - Ligandi

    NAD, NADP

    Enzyme and pathway databases

    BioCyciARA:AT3G25530-MONOMER.
    BRENDAi1.1.1.26. 399.
    1.1.1.61. 399.
    1.1.1.79. 399.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Glyoxylate/succinic semialdehyde reductase 1 (EC:1.1.1.792 Publications, EC:1.1.1.n112 Publications)
    Short name:
    AtGLYR1
    Short name:
    AtGR1
    Short name:
    SSA reductase 1
    Alternative name(s):
    Gamma-hydroxybutyrate dehydrogenase1 Publication
    Short name:
    AtGHBDH
    Gene namesi
    Name:GLYR1
    Synonyms:GR1
    Ordered Locus Names:At3g25530
    ORF Names:MWL2.18
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    Proteomesi
    • UP000006548 Componenti: Chromosome 3

    Organism-specific databases

    TAIRiAT3G25530.

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: TAIR
    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00004210321 – 289Glyoxylate/succinic semialdehyde reductase 1Add BLAST289

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei1N-acetylmethionineCombined sources1

    Keywords - PTMi

    Acetylation

    Proteomic databases

    PaxDbiQ9LSV0.
    PRIDEiQ9LSV0.
    ProMEXiQ9LSV0.

    Expressioni

    Inductioni

    By salinity, drought, submergence, cold and heat stresses, and ozone.2 Publications

    Gene expression databases

    GenevisibleiQ9LSV0. AT.

    Interactioni

    Protein-protein interaction databases

    BioGridi7470. 1 interactor.
    STRINGi3702.AT3G25530.1.

    Structurei

    Secondary structure

    1289
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi2 – 6Combined sources5
    Helixi10 – 21Combined sources12
    Beta strandi25 – 29Combined sources5
    Helixi33 – 36Combined sources4
    Helixi37 – 41Combined sources5
    Helixi50 – 56Combined sources7
    Beta strandi58 – 62Combined sources5
    Helixi67 – 75Combined sources9
    Helixi80 – 83Combined sources4
    Beta strandi89 – 92Combined sources4
    Helixi98 – 110Combined sources13
    Beta strandi114 – 117Combined sources4
    Helixi124 – 129Combined sources6
    Beta strandi132 – 138Combined sources7
    Helixi140 – 153Combined sources14
    Beta strandi154 – 159Combined sources6
    Helixi165 – 193Combined sources29
    Helixi198 – 207Combined sources10
    Helixi213 – 223Combined sources11
    Beta strandi230 – 232Combined sources3
    Helixi233 – 249Combined sources17
    Helixi255 – 269Combined sources15
    Helixi277 – 280Combined sources4
    Helixi281 – 285Combined sources5

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3DOJX-ray2.10A1-289[»]
    ProteinModelPortaliQ9LSV0.
    SMRiQ9LSV0.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9LSV0.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiKOG0409. Eukaryota.
    COG2084. LUCA.
    HOGENOMiHOG000219608.
    KOiK18121.
    OMAiMFKGKGP.
    OrthoDBiEOG09360IYA.
    PhylomeDBiQ9LSV0.

    Family and domain databases

    Gene3Di1.10.1040.10. 1 hit.
    3.40.50.720. 1 hit.
    InterProiIPR002204. 3-OH-isobutyrate_DH-rel_CS.
    IPR008927. 6-PGluconate_DH_C-like.
    IPR013328. 6PGD_dom_2.
    IPR006115. 6PGDH_NADP-bd.
    IPR015815. HIBADH-related.
    IPR016040. NAD(P)-bd_dom.
    IPR029154. NADP-bd.
    [Graphical view]
    PfamiPF14833. NAD_binding_11. 1 hit.
    PF03446. NAD_binding_2. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000103. HIBADH. 1 hit.
    SUPFAMiSSF48179. SSF48179. 1 hit.
    SSF51735. SSF51735. 1 hit.
    PROSITEiPS00895. 3_HYDROXYISOBUT_DH. 1 hit.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

    This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

    Isoform 1 (identifier: Q9LSV0-1) [UniParc]FASTAAdd to basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

            10         20         30         40         50
    MEVGFLGLGI MGKAMSMNLL KNGFKVTVWN RTLSKCDELV EHGASVCESP
    60 70 80 90 100
    AEVIKKCKYT IAMLSDPCAA LSVVFDKGGV LEQICEGKGY IDMSTVDAET
    110 120 130 140 150
    SLKINEAITG KGGRFVEGPV SGSKKPAEDG QLIILAAGDK ALFEESIPAF
    160 170 180 190 200
    DVLGKRSFYL GQVGNGAKMK LIVNMIMGSM MNAFSEGLVL ADKSGLSSDT
    210 220 230 240 250
    LLDILDLGAM TNPMFKGKGP SMNKSSYPPA FPLKHQQKDM RLALALGDEN
    260 270 280
    AVSMPVAAAA NEAFKKARSL GLGDLDFSAV IEAVKFSRE
    Length:289
    Mass (Da):30,692
    Last modified:October 1, 2000 - v1
    Checksum:i3E67002A19706636
    GO
    Isoform 2 (identifier: Q9LSV0-2) [UniParc]FASTAAdd to basket

    The sequence of this isoform differs from the canonical sequence as follows:
         73-83: Missing.

    Note: No experimental confirmation available.
    Show »
    Length:278
    Mass (Da):29,519
    Checksum:i6EC707EEE72E01B0
    GO

    Sequence cautioni

    The sequence AAK83640 differs from that shown. Reason: Frameshift at position 227.Curated

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti223N → T in AAK94781 (PubMed:12882961).Curated1
    Sequence conflicti263A → V in BAH19592 (PubMed:19423640).Curated1

    Alternative sequence

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Alternative sequenceiVSP_04505473 – 83Missing in isoform 2. 1 PublicationAdd BLAST11

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AY044183 mRNA. Translation: AAK94781.1.
    AB025639 Genomic DNA. Translation: BAB01322.1.
    CP002686 Genomic DNA. Translation: AEE77021.1.
    CP002686 Genomic DNA. Translation: AEE77022.1.
    AY049298 mRNA. Translation: AAK83640.1. Frameshift.
    AK316884 mRNA. Translation: BAH19592.1.
    BT025039 mRNA. Translation: ABE02414.1.
    RefSeqiNP_001030765.1. NM_001035688.1. [Q9LSV0-2]
    NP_566768.1. NM_113449.4. [Q9LSV0-1]
    UniGeneiAt.21370.

    Genome annotation databases

    EnsemblPlantsiAT3G25530.1; AT3G25530.1; AT3G25530. [Q9LSV0-1]
    GeneIDi822139.
    GrameneiAT3G25530.1; AT3G25530.1; AT3G25530.
    KEGGiath:AT3G25530.

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AY044183 mRNA. Translation: AAK94781.1.
    AB025639 Genomic DNA. Translation: BAB01322.1.
    CP002686 Genomic DNA. Translation: AEE77021.1.
    CP002686 Genomic DNA. Translation: AEE77022.1.
    AY049298 mRNA. Translation: AAK83640.1. Frameshift.
    AK316884 mRNA. Translation: BAH19592.1.
    BT025039 mRNA. Translation: ABE02414.1.
    RefSeqiNP_001030765.1. NM_001035688.1. [Q9LSV0-2]
    NP_566768.1. NM_113449.4. [Q9LSV0-1]
    UniGeneiAt.21370.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3DOJX-ray2.10A1-289[»]
    ProteinModelPortaliQ9LSV0.
    SMRiQ9LSV0.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi7470. 1 interactor.
    STRINGi3702.AT3G25530.1.

    Proteomic databases

    PaxDbiQ9LSV0.
    PRIDEiQ9LSV0.
    ProMEXiQ9LSV0.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblPlantsiAT3G25530.1; AT3G25530.1; AT3G25530. [Q9LSV0-1]
    GeneIDi822139.
    GrameneiAT3G25530.1; AT3G25530.1; AT3G25530.
    KEGGiath:AT3G25530.

    Organism-specific databases

    TAIRiAT3G25530.

    Phylogenomic databases

    eggNOGiKOG0409. Eukaryota.
    COG2084. LUCA.
    HOGENOMiHOG000219608.
    KOiK18121.
    OMAiMFKGKGP.
    OrthoDBiEOG09360IYA.
    PhylomeDBiQ9LSV0.

    Enzyme and pathway databases

    BioCyciARA:AT3G25530-MONOMER.
    BRENDAi1.1.1.26. 399.
    1.1.1.61. 399.
    1.1.1.79. 399.

    Miscellaneous databases

    EvolutionaryTraceiQ9LSV0.
    PROiQ9LSV0.

    Gene expression databases

    GenevisibleiQ9LSV0. AT.

    Family and domain databases

    Gene3Di1.10.1040.10. 1 hit.
    3.40.50.720. 1 hit.
    InterProiIPR002204. 3-OH-isobutyrate_DH-rel_CS.
    IPR008927. 6-PGluconate_DH_C-like.
    IPR013328. 6PGD_dom_2.
    IPR006115. 6PGDH_NADP-bd.
    IPR015815. HIBADH-related.
    IPR016040. NAD(P)-bd_dom.
    IPR029154. NADP-bd.
    [Graphical view]
    PfamiPF14833. NAD_binding_11. 1 hit.
    PF03446. NAD_binding_2. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000103. HIBADH. 1 hit.
    SUPFAMiSSF48179. SSF48179. 1 hit.
    SSF51735. SSF51735. 1 hit.
    PROSITEiPS00895. 3_HYDROXYISOBUT_DH. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiGLYR1_ARATH
    AccessioniPrimary (citable) accession number: Q9LSV0
    Secondary accession number(s): B9DFS5
    , F4J913, Q94A74, Q94B07
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 6, 2013
    Last sequence update: October 1, 2000
    Last modified: November 30, 2016
    This is version 119 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Follows a sequentially ordered Bi-Bi catalytic mechanism involving the complexation of NADPH to the enzyme before glyoxylate or SSA, and the release of NADP+ before glycolate or gamma-hydroxybutyrate, respectively. Although GLYR1 acts as an aldo/keto reductase, it has no significant homology with either mammalian and bacterial NADPH-dependent SSA reductases.

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Arabidopsis thaliana
      Arabidopsis thaliana: entries and gene names
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.