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Protein

NADP-specific glutamate dehydrogenase

Gene

gdhA

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

Functioni

Catalyzes the reversible oxidative deamination of glutamate to alpha-ketoglutarate and ammonia.2 Publications

Catalytic activityi

L-glutamate + H2O + NADP+ = 2-oxoglutarate + NH3 + NADPH.

Enzyme regulationi

Competitively inhibited by homoserine and by glutamine.1 Publication

Kineticsi

  1. KM=40 µM for NADPH2 Publications
  2. KM=42 µM for NADP2 Publications
  3. KM=640 µM for 2-oxoglutarate2 Publications
  4. KM=1100 µM for ammonia2 Publications

    pH dependencei

    Optimum pH is 8 and 9 for the reductive amination and for the oxidative deamination, respectively. The enzyme remains active when heat treated or when left at room temperature for several months but is inactivated by freezing.2 Publications

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei92 – 921SubstrateBy similarity
    Binding sitei113 – 1131SubstrateBy similarity
    Binding sitei116 – 1161SubstrateBy similarity
    Active sitei128 – 1281Proton donorPROSITE-ProRule annotation
    Binding sitei167 – 1671Substrate; via carbonyl oxygenBy similarity
    Sitei168 – 1681Important for catalysis
    Binding sitei211 – 2111NADPBy similarity
    Binding sitei242 – 2421NADPBy similarity
    Binding sitei380 – 3801SubstrateBy similarity

    GO - Molecular functioni

    • glutamate dehydrogenase (NADP+) activity Source: EcoCyc

    GO - Biological processi

    • glutamate biosynthetic process Source: EcoCyc
    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Ligandi

    NADP

    Enzyme and pathway databases

    BioCyciEcoCyc:GDHA-MONOMER.
    ECOL316407:JW1750-MONOMER.
    MetaCyc:GDHA-MONOMER.
    BRENDAi1.4.1.4. 2026.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    NADP-specific glutamate dehydrogenase (EC:1.4.1.4)
    Short name:
    NADP-GDH
    Gene namesi
    Name:gdhA
    Ordered Locus Names:b1761, JW1750
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG10372. gdhA.

    Subcellular locationi

    GO - Cellular componenti

    • cytoplasm Source: EcoliWiki
    Complete GO annotation...

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi92 – 921K → S: Complete loss of dehydrogenase activity. 1 Publication
    Mutagenesisi128 – 1281K → H: Reduces catalytic activity and increases pH optima for activity. Increases relative activity with amino acid substrates other than glutamate, especially L-norvaline. 1 Publication
    Mutagenesisi128 – 1281K → R: Reduced catalytic activity and increases pH optima for activity. NADP-specific glutamate dehydrogenase. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 447447NADP-specific glutamate dehydrogenasePRO_0000182769Add
    BLAST

    Proteomic databases

    PaxDbiP00370.
    PRIDEiP00370.

    2D gel databases

    SWISS-2DPAGEP00370.

    Expressioni

    Inductioni

    Induced by growth on glucose and ammonia.

    Interactioni

    Subunit structurei

    Homohexamer.2 Publications

    Protein-protein interaction databases

    DIPiDIP-9756N.
    IntActiP00370. 1 interaction.
    STRINGi511145.b1761.

    Structurei

    Secondary structure

    1
    447
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi7 – 159Combined sources
    Helixi22 – 4120Combined sources
    Helixi43 – 497Combined sources
    Helixi50 – 545Combined sources
    Beta strandi58 – 6811Combined sources
    Beta strandi74 – 8512Combined sources
    Beta strandi87 – 9711Combined sources
    Helixi103 – 11917Combined sources
    Beta strandi121 – 1233Combined sources
    Beta strandi126 – 1327Combined sources
    Helixi140 – 15415Combined sources
    Helixi155 – 1573Combined sources
    Turni160 – 1623Combined sources
    Beta strandi163 – 1664Combined sources
    Helixi173 – 18715Combined sources
    Helixi199 – 2013Combined sources
    Turni205 – 2095Combined sources
    Helixi210 – 22516Combined sources
    Beta strandi234 – 2385Combined sources
    Helixi242 – 25312Combined sources
    Beta strandi260 – 2634Combined sources
    Beta strandi266 – 2694Combined sources
    Helixi276 – 28611Combined sources
    Beta strandi288 – 2903Combined sources
    Helixi293 – 3008Combined sources
    Beta strandi303 – 3064Combined sources
    Helixi310 – 3123Combined sources
    Beta strandi316 – 3205Combined sources
    Helixi329 – 3379Combined sources
    Beta strandi342 – 3443Combined sources
    Beta strandi346 – 3494Combined sources
    Helixi353 – 3619Combined sources
    Beta strandi365 – 3673Combined sources
    Helixi369 – 3724Combined sources
    Helixi375 – 38915Combined sources
    Helixi395 – 41521Combined sources
    Beta strandi419 – 4224Combined sources
    Helixi425 – 44319Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2YFHX-ray2.70A/B/C/D/E/F202-405[»]
    3SBOX-ray3.20A/B/C/D/E/F1-447[»]
    4BHTX-ray2.50A/B/C/D/E/F1-447[»]
    ProteinModelPortaliP00370.
    SMRiP00370. Positions 6-447.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0334.
    HOGENOMiHOG000243799.
    InParanoidiP00370.
    KOiK00262.
    OMAiEFNSAIG.
    OrthoDBiEOG65XN4D.
    PhylomeDBiP00370.

    Family and domain databases

    Gene3Di3.40.50.720. 1 hit.
    InterProiIPR006095. Glu/Leu/Phe/Val_DH.
    IPR006096. Glu/Leu/Phe/Val_DH_C.
    IPR006097. Glu/Leu/Phe/Val_DH_dimer_dom.
    IPR014362. Glu_DH.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view]
    PfamiPF00208. ELFV_dehydrog. 1 hit.
    PF02812. ELFV_dehydrog_N. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000185. Glu_DH. 1 hit.
    PRINTSiPR00082. GLFDHDRGNASE.
    SMARTiSM00839. ELFV_dehydrog. 1 hit.
    [Graphical view]
    PROSITEiPS00074. GLFV_DEHYDROGENASE. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P00370-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MDQTYSLESF LNHVQKRDPN QTEFAQAVRE VMTTLWPFLE QNPKYRQMSL
    60 70 80 90 100
    LERLVEPERV IQFRVVWVDD RNQIQVNRAW RVQFSSAIGP YKGGMRFHPS
    110 120 130 140 150
    VNLSILKFLG FEQTFKNALT TLPMGGGKGG SDFDPKGKSE GEVMRFCQAL
    160 170 180 190 200
    MTELYRHLGA DTDVPAGDIG VGGREVGFMA GMMKKLSNNT ACVFTGKGLS
    210 220 230 240 250
    FGGSLIRPEA TGYGLVYFTE AMLKRHGMGF EGMRVSVSGS GNVAQYAIEK
    260 270 280 290 300
    AMEFGARVIT ASDSSGTVVD ESGFTKEKLA RLIEIKASRD GRVADYAKEF
    310 320 330 340 350
    GLVYLEGQQP WSLPVDIALP CATQNELDVD AAHQLIANGV KAVAEGANMP
    360 370 380 390 400
    TTIEATELFQ QAGVLFAPGK AANAGGVATS GLEMAQNAAR LGWKAEKVDA
    410 420 430 440
    RLHHIMLDIH HACVEHGGEG EQTNYVQGAN IAGFVKVADA MLAQGVI
    Length:447
    Mass (Da):48,581
    Last modified:July 21, 1986 - v1
    Checksum:i7CB861D282C533C6
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti385 – 3851A → P in AAA23868 (PubMed:6373501).Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    J01615 Genomic DNA. Translation: AAA87979.1.
    K02499 Genomic DNA. Translation: AAA23868.1.
    U00096 Genomic DNA. Translation: AAC74831.1.
    AP009048 Genomic DNA. Translation: BAA15550.1.
    PIRiA00382. DEECEN.
    RefSeqiNP_416275.1. NC_000913.3.
    WP_000373021.1. NZ_CP010445.1.

    Genome annotation databases

    EnsemblBacteriaiAAC74831; AAC74831; b1761.
    BAA15550; BAA15550; BAA15550.
    GeneIDi946802.
    KEGGieco:b1761.
    PATRICi32118833. VBIEscCol129921_1834.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    J01615 Genomic DNA. Translation: AAA87979.1.
    K02499 Genomic DNA. Translation: AAA23868.1.
    U00096 Genomic DNA. Translation: AAC74831.1.
    AP009048 Genomic DNA. Translation: BAA15550.1.
    PIRiA00382. DEECEN.
    RefSeqiNP_416275.1. NC_000913.3.
    WP_000373021.1. NZ_CP010445.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2YFHX-ray2.70A/B/C/D/E/F202-405[»]
    3SBOX-ray3.20A/B/C/D/E/F1-447[»]
    4BHTX-ray2.50A/B/C/D/E/F1-447[»]
    ProteinModelPortaliP00370.
    SMRiP00370. Positions 6-447.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    DIPiDIP-9756N.
    IntActiP00370. 1 interaction.
    STRINGi511145.b1761.

    2D gel databases

    SWISS-2DPAGEP00370.

    Proteomic databases

    PaxDbiP00370.
    PRIDEiP00370.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC74831; AAC74831; b1761.
    BAA15550; BAA15550; BAA15550.
    GeneIDi946802.
    KEGGieco:b1761.
    PATRICi32118833. VBIEscCol129921_1834.

    Organism-specific databases

    EchoBASEiEB0367.
    EcoGeneiEG10372. gdhA.

    Phylogenomic databases

    eggNOGiCOG0334.
    HOGENOMiHOG000243799.
    InParanoidiP00370.
    KOiK00262.
    OMAiEFNSAIG.
    OrthoDBiEOG65XN4D.
    PhylomeDBiP00370.

    Enzyme and pathway databases

    BioCyciEcoCyc:GDHA-MONOMER.
    ECOL316407:JW1750-MONOMER.
    MetaCyc:GDHA-MONOMER.
    BRENDAi1.4.1.4. 2026.

    Miscellaneous databases

    PROiP00370.

    Family and domain databases

    Gene3Di3.40.50.720. 1 hit.
    InterProiIPR006095. Glu/Leu/Phe/Val_DH.
    IPR006096. Glu/Leu/Phe/Val_DH_C.
    IPR006097. Glu/Leu/Phe/Val_DH_dimer_dom.
    IPR014362. Glu_DH.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view]
    PfamiPF00208. ELFV_dehydrog. 1 hit.
    PF02812. ELFV_dehydrog_N. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000185. Glu_DH. 1 hit.
    PRINTSiPR00082. GLFDHDRGNASE.
    SMARTiSM00839. ELFV_dehydrog. 1 hit.
    [Graphical view]
    PROSITEiPS00074. GLFV_DEHYDROGENASE. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Complete nucleotide sequence of the Escherichia coli gdhA gene."
      McPherson M.J., Wootton J.C.
      Nucleic Acids Res. 11:5257-5266(1983) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-36.
      Strain: K12.
    2. "Complete nucleotide sequence of the glutamate dehydrogenase gene from Escherichia coli K-12."
      Valle F., Becerril B., Chen E., Seeburg P.H., Heyneker H., Bolivar F.
      Gene 27:193-199(1984) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    5. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    6. "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12."
      Link A.J., Robison K., Church G.M.
      Electrophoresis 18:1259-1313(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 1-12.
      Strain: K12 / EMG2.
    7. "Glutamate dehydrogenase from Escherichia coli: induction, purification and properties of the enzyme."
      Veronese F.M., Boccu E., Conventi L.
      Biochim. Biophys. Acta 377:217-228(1975) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION AS A GLUTAMATE DEHYDROGENASE, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES.
    8. "Glutamate dehydrogenase from Escherichia coli: purification and properties."
      Sakamoto N., Kotre A.M., Savageau M.A.
      J. Bacteriol. 124:775-783(1975) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION AS A GLUTAMATE DEHYDROGENASE, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.
    9. "Multiple interactions of lysine-128 of Escherichia coli glutamate dehydrogenase revealed by site-directed mutagenesis studies."
      McPherson M.J., Baron A.J., Jones K.M., Price G.J., Wootton J.C.
      Protein Eng. 2:147-152(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF LYS-128.
    10. "The gdhA1 point mutation in Escherichia coli K12 CLR207 alters a key lysine residue of glutamate dehydrogenase."
      Jones K.M., McPherson M.J., Baron A.J., Mattaj I.W., Riordan C.L., Wootton J.C.
      Mol. Gen. Genet. 240:286-289(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF LYS-92.
    11. "Escherichia coli proteome analysis using the gene-protein database."
      VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
      Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY 2D-GEL.
    12. "Structural determinants of cofactor specificity and domain flexibility in bacterial glutamate dehydrogenases."
      Oliveira T., Sharkey M.A., Hamza M., Engel P.C., Khan A.R.
      Submitted (MAR-2012) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS), SUBUNIT.
    13. "Macro-to-micro structural proteomics: native source proteins for high-throughput crystallization."
      Totir M., Echols N., Nanao M., Gee C.L., Moskaleva A., Gradia S., Iavarone A.T., Berger J.M., May A.P., Zubieta C., Alber T.
      PLoS ONE 7:E32498-E32498(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.2 ANGSTROMS) AND SUBUNIT.

    Entry informationi

    Entry nameiDHE4_ECOLI
    AccessioniPrimary (citable) accession number: P00370
    Secondary accession number(s): P78173
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 21, 1986
    Last sequence update: July 21, 1986
    Last modified: July 22, 2015
    This is version 132 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, Direct protein sequencing, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3

    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 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.