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P00370

- DHE4_ECOLI

UniProt

P00370 - DHE4_ECOLI

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Protein
NADP-specific glutamate dehydrogenase
Gene
gdhA, b1761, JW1750
Organism
Escherichia coli (strain K12)
Status
Reviewed - 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 NADP
  3. KM=640 µM for 2-oxoglutarate
  4. KM=1100 µM for ammonia

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.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei92 – 921Substrate By similarity
Binding sitei113 – 1131Substrate By similarity
Binding sitei116 – 1161Substrate By similarity
Active sitei128 – 1281Proton donor By similarity
Binding sitei167 – 1671Substrate; via carbonyl oxygen By similarity
Sitei168 – 1681Important for catalysis
Binding sitei211 – 2111NADP By similarity
Binding sitei242 – 2421NADP By similarity
Binding sitei380 – 3801Substrate By similarity

GO - Molecular functioni

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

GO - Biological processi

  1. 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.

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
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 dehydrogenase
PRO_0000182769Add
BLAST

Proteomic databases

PaxDbiP00370.
PRIDEiP00370.

2D gel databases

SWISS-2DPAGEP00370.

Expressioni

Inductioni

Induced by growth on glucose and ammonia.1 Publication

Gene expression databases

GenevestigatoriP00370.

Interactioni

Subunit structurei

Homohexamer.3 Publications

Protein-protein interaction databases

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

Structurei

Secondary structure

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.

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

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti385 – 3851A → P in AAA23868. 1 Publication

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

« 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 9, 2014
This is version 122 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

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