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Protein

Succinate-semialdehyde dehydrogenase [NADP(+)] GabD

Gene

gabD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the NADP+-dependent oxidation of succinate semialdehyde to succinate. It appears to be important for nitrogen metabolism under N limitation conditions.2 Publications

Catalytic activityi

Succinate semialdehyde + NADP+ + H2O = succinate + NADPH.1 Publication

Kineticsi

The enzyme activity measured in the presence of NADP+ is approximately 20-fold higher than that measured in the presence of NAD+.

  1. KM=16.94 µM for succinate semialdehyde1 Publication

    Pathwayi: 4-aminobutanoate degradation

    This protein is involved in the pathway 4-aminobutanoate degradation, which is part of Amino-acid degradation.
    View all proteins of this organism that are known to be involved in the pathway 4-aminobutanoate degradation and in Amino-acid degradation.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Active sitei255Proton acceptor1 Publication1
    Binding sitei256NADP; via carbonyl oxygen1 Publication1
    Active sitei289Nucleophile1 Publication1
    Binding sitei386NADP1 Publication1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi156 – 157NADP1 Publication2
    Nucleotide bindingi180 – 183NADP1 Publication4
    Nucleotide bindingi233 – 234NADP1 Publication2

    GO - Molecular functioni

    • aldehyde dehydrogenase (NAD) activity Source: GO_Central
    • succinate-semialdehyde dehydrogenase (NAD+) activity Source: UniProtKB
    • succinate-semialdehyde dehydrogenase [NAD(P)+] activity Source: UniProtKB

    GO - Biological processi

    • gamma-aminobutyric acid catabolic process Source: UniProtKB
    • nitrogen compound metabolic process Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Ligandi

    NADP

    Enzyme and pathway databases

    BioCyciEcoCyc:SUCCSEMIALDDEHYDROG-MONOMER.
    ECOL316407:JW2636-MONOMER.
    MetaCyc:SUCCSEMIALDDEHYDROG-MONOMER.
    BRENDAi1.2.1.79. 2026.
    UniPathwayiUPA00733.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Succinate-semialdehyde dehydrogenase [NADP(+)] GabD (EC:1.2.1.79)
    Short name:
    SSDH
    Gene namesi
    Name:gabD
    Ordered Locus Names:b2661, JW2636
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG11329. gabD.

    Subcellular locationi

    GO - Cellular componenti

    • cytoplasm Source: EcoliWiki
    Complete GO annotation...

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00000565721 – 482Succinate-semialdehyde dehydrogenase [NADP(+)] GabDAdd BLAST482

    Proteomic databases

    EPDiP25526.
    PaxDbiP25526.
    PRIDEiP25526.

    Expressioni

    Inductioni

    Induced by RpoS in response to multiple stress conditions, including shifts to acidic pH, nitrogen limitation or high osmolarity as well as starvation or stationary phase. Induced by gamma-aminobutyrate (GABA).2 Publications

    Interactioni

    Subunit structurei

    Homotetramer.1 Publication

    Protein-protein interaction databases

    BioGridi4259209. 15 interactors.
    DIPiDIP-9723N.
    IntActiP25526. 2 interactors.
    STRINGi511145.b2661.

    Structurei

    Secondary structure

    1482
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi6 – 8Combined sources3
    Beta strandi12 – 15Combined sources4
    Beta strandi18 – 20Combined sources3
    Beta strandi27 – 31Combined sources5
    Turni33 – 35Combined sources3
    Beta strandi38 – 43Combined sources6
    Helixi47 – 66Combined sources20
    Helixi69 – 85Combined sources17
    Helixi87 – 98Combined sources12
    Helixi102 – 122Combined sources21
    Helixi123 – 125Combined sources3
    Beta strandi128 – 131Combined sources4
    Beta strandi138 – 146Combined sources9
    Beta strandi149 – 153Combined sources5
    Beta strandi156 – 158Combined sources3
    Helixi161 – 173Combined sources13
    Beta strandi176 – 180Combined sources5
    Helixi187 – 199Combined sources13
    Turni203 – 205Combined sources3
    Beta strandi206 – 208Combined sources3
    Helixi214 – 222Combined sources9
    Beta strandi226 – 233Combined sources8
    Helixi235 – 245Combined sources11
    Turni246 – 249Combined sources4
    Beta strandi251 – 255Combined sources5
    Beta strandi260 – 264Combined sources5
    Helixi270 – 282Combined sources13
    Helixi283 – 286Combined sources4
    Beta strandi291 – 298Combined sources8
    Helixi299 – 301Combined sources3
    Helixi302 – 313Combined sources12
    Helixi334 – 349Combined sources16
    Beta strandi353 – 356Combined sources4
    Beta strandi371 – 375Combined sources5
    Helixi381 – 383Combined sources3
    Beta strandi389 – 397Combined sources9
    Helixi400 – 408Combined sources9
    Beta strandi414 – 419Combined sources6
    Helixi423 – 432Combined sources10
    Beta strandi436 – 441Combined sources6
    Beta strandi448 – 450Combined sources3
    Helixi456 – 458Combined sources3
    Beta strandi459 – 461Combined sources3
    Helixi465 – 470Combined sources6
    Beta strandi473 – 481Combined sources9

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3JZ4X-ray2.30A/B/C/D2-482[»]
    ProteinModelPortaliP25526.
    SMRiP25526.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the aldehyde dehydrogenase family.Curated

    Phylogenomic databases

    eggNOGiENOG4105C26. Bacteria.
    COG1012. LUCA.
    HOGENOMiHOG000271509.
    InParanoidiP25526.
    KOiK00135.
    OMAiCENPGVR.
    PhylomeDBiP25526.

    Family and domain databases

    Gene3Di3.40.309.10. 1 hit.
    3.40.605.10. 1 hit.
    InterProiIPR016161. Ald_DH/histidinol_DH.
    IPR016163. Ald_DH_C.
    IPR016160. Ald_DH_CS_CYS.
    IPR029510. Ald_DH_CS_GLU.
    IPR016162. Ald_DH_N.
    IPR015590. Aldehyde_DH_dom.
    IPR010102. Succ_semiAld_DH.
    [Graphical view]
    PfamiPF00171. Aldedh. 1 hit.
    [Graphical view]
    SUPFAMiSSF53720. SSF53720. 1 hit.
    TIGRFAMsiTIGR01780. SSADH. 1 hit.
    PROSITEiPS00070. ALDEHYDE_DEHYDR_CYS. 1 hit.
    PS00687. ALDEHYDE_DEHYDR_GLU. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P25526-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MKLNDSNLFR QQALINGEWL DANNGEAIDV TNPANGDKLG SVPKMGADET
    60 70 80 90 100
    RAAIDAANRA LPAWRALTAK ERATILRNWF NLMMEHQDDL ARLMTLEQGK
    110 120 130 140 150
    PLAEAKGEIS YAASFIEWFA EEGKRIYGDT IPGHQADKRL IVIKQPIGVT
    160 170 180 190 200
    AAITPWNFPA AMITRKAGPA LAAGCTMVLK PASQTPFSAL ALAELAIRAG
    210 220 230 240 250
    VPAGVFNVVT GSAGAVGNEL TSNPLVRKLS FTGSTEIGRQ LMEQCAKDIK
    260 270 280 290 300
    KVSLELGGNA PFIVFDDADL DKAVEGALAS KFRNAGQTCV CANRLYVQDG
    310 320 330 340 350
    VYDRFAEKLQ QAVSKLHIGD GLDNGVTIGP LIDEKAVAKV EEHIADALEK
    360 370 380 390 400
    GARVVCGGKA HERGGNFFQP TILVDVPANA KVSKEETFGP LAPLFRFKDE
    410 420 430 440 450
    ADVIAQANDT EFGLAAYFYA RDLSRVFRVG EALEYGIVGI NTGIISNEVA
    460 470 480
    PFGGIKASGL GREGSKYGIE DYLEIKYMCI GL
    Length:482
    Mass (Da):51,720
    Last modified:May 1, 1992 - v1
    Checksum:i091538F8741DB0CF
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M88334 Genomic DNA. Translation: AAC36831.1.
    U00096 Genomic DNA. Translation: AAC75708.1.
    AP009048 Genomic DNA. Translation: BAA16524.2.
    PIRiF65045.
    RefSeqiNP_417147.1. NC_000913.3.
    WP_000772831.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC75708; AAC75708; b2661.
    BAA16524; BAA16524; BAA16524.
    GeneIDi948060.
    KEGGiecj:JW2636.
    eco:b2661.
    PATRICi32120712. VBIEscCol129921_2753.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M88334 Genomic DNA. Translation: AAC36831.1.
    U00096 Genomic DNA. Translation: AAC75708.1.
    AP009048 Genomic DNA. Translation: BAA16524.2.
    PIRiF65045.
    RefSeqiNP_417147.1. NC_000913.3.
    WP_000772831.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3JZ4X-ray2.30A/B/C/D2-482[»]
    ProteinModelPortaliP25526.
    SMRiP25526.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4259209. 15 interactors.
    DIPiDIP-9723N.
    IntActiP25526. 2 interactors.
    STRINGi511145.b2661.

    Proteomic databases

    EPDiP25526.
    PaxDbiP25526.
    PRIDEiP25526.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC75708; AAC75708; b2661.
    BAA16524; BAA16524; BAA16524.
    GeneIDi948060.
    KEGGiecj:JW2636.
    eco:b2661.
    PATRICi32120712. VBIEscCol129921_2753.

    Organism-specific databases

    EchoBASEiEB1305.
    EcoGeneiEG11329. gabD.

    Phylogenomic databases

    eggNOGiENOG4105C26. Bacteria.
    COG1012. LUCA.
    HOGENOMiHOG000271509.
    InParanoidiP25526.
    KOiK00135.
    OMAiCENPGVR.
    PhylomeDBiP25526.

    Enzyme and pathway databases

    UniPathwayiUPA00733.
    BioCyciEcoCyc:SUCCSEMIALDDEHYDROG-MONOMER.
    ECOL316407:JW2636-MONOMER.
    MetaCyc:SUCCSEMIALDDEHYDROG-MONOMER.
    BRENDAi1.2.1.79. 2026.

    Miscellaneous databases

    PROiP25526.

    Family and domain databases

    Gene3Di3.40.309.10. 1 hit.
    3.40.605.10. 1 hit.
    InterProiIPR016161. Ald_DH/histidinol_DH.
    IPR016163. Ald_DH_C.
    IPR016160. Ald_DH_CS_CYS.
    IPR029510. Ald_DH_CS_GLU.
    IPR016162. Ald_DH_N.
    IPR015590. Aldehyde_DH_dom.
    IPR010102. Succ_semiAld_DH.
    [Graphical view]
    PfamiPF00171. Aldedh. 1 hit.
    [Graphical view]
    SUPFAMiSSF53720. SSF53720. 1 hit.
    TIGRFAMsiTIGR01780. SSADH. 1 hit.
    PROSITEiPS00070. ALDEHYDE_DEHYDR_CYS. 1 hit.
    PS00687. ALDEHYDE_DEHYDR_GLU. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiGABD_ECOLI
    AccessioniPrimary (citable) accession number: P25526
    Secondary accession number(s): P78207, P78208, P78209
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 1, 1992
    Last sequence update: May 1, 1992
    Last modified: November 30, 2016
    This is version 138 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. 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.