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P00370

- DHE4_ECOLI

UniProt

P00370 - DHE4_ECOLI

Protein

NADP-specific glutamate dehydrogenase

Gene

gdhA

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 123 (01 Oct 2014)
      Sequence version 1 (21 Jul 1986)
      Previous versions | rss
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    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

    1. glutamate dehydrogenase (NADP+) activity Source: EcoCyc

    GO - Biological processi

    1. glutamate biosynthetic process Source: EcoCyc

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Ligandi

    NADP

    Enzyme and pathway databases

    BioCyciEcoCyc:GDHA-MONOMER.
    ECOL316407:JW1750-MONOMER.
    MetaCyc:GDHA-MONOMER.

    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: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG10372. gdhA.

    Subcellular locationi

    GO - Cellular componenti

    1. cytoplasm Source: EcoliWiki

    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.

    Gene expression databases

    GenevestigatoriP00370.

    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 – 159
    Helixi22 – 4120
    Helixi43 – 497
    Helixi50 – 545
    Beta strandi58 – 6811
    Beta strandi74 – 8512
    Beta strandi87 – 9711
    Helixi103 – 11917
    Beta strandi121 – 1233
    Beta strandi126 – 1327
    Helixi140 – 15415
    Helixi155 – 1573
    Turni160 – 1623
    Beta strandi163 – 1664
    Helixi173 – 18715
    Helixi199 – 2013
    Turni205 – 2095
    Helixi210 – 22516
    Beta strandi234 – 2385
    Helixi242 – 25312
    Beta strandi260 – 2634
    Beta strandi266 – 2694
    Helixi276 – 28611
    Beta strandi288 – 2903
    Helixi293 – 3008
    Beta strandi303 – 3064
    Helixi310 – 3123
    Beta strandi316 – 3205
    Helixi329 – 3379
    Beta strandi342 – 3443
    Beta strandi346 – 3494
    Helixi353 – 3619
    Beta strandi365 – 3673
    Helixi369 – 3724
    Helixi375 – 38915
    Helixi395 – 41521
    Beta strandi419 – 4224
    Helixi425 – 44319

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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.
    KOiK00262.
    OMAiIMLDIHA.
    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

    MDQTYSLESF LNHVQKRDPN QTEFAQAVRE VMTTLWPFLE QNPKYRQMSL    50
    LERLVEPERV IQFRVVWVDD RNQIQVNRAW RVQFSSAIGP YKGGMRFHPS 100
    VNLSILKFLG FEQTFKNALT TLPMGGGKGG SDFDPKGKSE GEVMRFCQAL 150
    MTELYRHLGA DTDVPAGDIG VGGREVGFMA GMMKKLSNNT ACVFTGKGLS 200
    FGGSLIRPEA TGYGLVYFTE AMLKRHGMGF EGMRVSVSGS GNVAQYAIEK 250
    AMEFGARVIT ASDSSGTVVD ESGFTKEKLA RLIEIKASRD GRVADYAKEF 300
    GLVYLEGQQP WSLPVDIALP CATQNELDVD AAHQLIANGV KAVAEGANMP 350
    TTIEATELFQ QAGVLFAPGK AANAGGVATS GLEMAQNAAR LGWKAEKVDA 400
    RLHHIMLDIH HACVEHGGEG EQTNYVQGAN IAGFVKVADA MLAQGVI 447
    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:
    EMBL
    GenBank
    DDBJ
    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.
    YP_490022.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC74831; AAC74831; b1761.
    BAA15550; BAA15550; BAA15550.
    GeneIDi12931328.
    946802.
    KEGGiecj:Y75_p1736.
    eco:b1761.
    PATRICi32118833. VBIEscCol129921_1834.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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 .
    PIRi A00382. DEECEN.
    RefSeqi NP_416275.1. NC_000913.3.
    YP_490022.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2YFH X-ray 2.70 A/B/C/D/E/F 202-405 [» ]
    3SBO X-ray 3.20 A/B/C/D/E/F 1-447 [» ]
    4BHT X-ray 2.50 A/B/C/D/E/F 1-447 [» ]
    ProteinModelPortali P00370.
    SMRi P00370. Positions 6-447.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-9756N.
    IntActi P00370. 1 interaction.
    STRINGi 511145.b1761.

    2D gel databases

    SWISS-2DPAGE P00370.

    Proteomic databases

    PaxDbi P00370.
    PRIDEi P00370.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC74831 ; AAC74831 ; b1761 .
    BAA15550 ; BAA15550 ; BAA15550 .
    GeneIDi 12931328.
    946802.
    KEGGi ecj:Y75_p1736.
    eco:b1761.
    PATRICi 32118833. VBIEscCol129921_1834.

    Organism-specific databases

    EchoBASEi EB0367.
    EcoGenei EG10372. gdhA.

    Phylogenomic databases

    eggNOGi COG0334.
    HOGENOMi HOG000243799.
    KOi K00262.
    OMAi IMLDIHA.
    OrthoDBi EOG65XN4D.
    PhylomeDBi P00370.

    Enzyme and pathway databases

    BioCyci EcoCyc:GDHA-MONOMER.
    ECOL316407:JW1750-MONOMER.
    MetaCyc:GDHA-MONOMER.

    Miscellaneous databases

    PROi P00370.

    Gene expression databases

    Genevestigatori P00370.

    Family and domain databases

    Gene3Di 3.40.50.720. 1 hit.
    InterProi IPR006095. 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 ]
    Pfami PF00208. ELFV_dehydrog. 1 hit.
    PF02812. ELFV_dehydrog_N. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF000185. Glu_DH. 1 hit.
    PRINTSi PR00082. GLFDHDRGNASE.
    SMARTi SM00839. ELFV_dehydrog. 1 hit.
    [Graphical view ]
    PROSITEi PS00074. GLFV_DEHYDROGENASE. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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: October 1, 2014
    This is version 123 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