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P00370 (DHE4_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 120. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
NADP-specific glutamate dehydrogenase

Short name=NADP-GDH
EC=1.4.1.4
Gene names
Name:gdhA
Ordered Locus Names:b1761, JW1750
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length447 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalyzes the reversible oxidative deamination of glutamate to alpha-ketoglutarate and ammonia. Ref.7 Ref.8

Catalytic activity

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

Enzyme regulation

Competitively inhibited by homoserine and by glutamine. Ref.7

Subunit structure

Homohexamer. Ref.8 Ref.12 Ref.13

Induction

Induced by growth on glucose and ammonia. Ref.7

Sequence similarities

Belongs to the Glu/Leu/Phe/Val dehydrogenases family.

Biophysicochemical properties

Kinetic parameters:

KM=40 µM for NADPH Ref.7 Ref.8

KM=42 µM for NADP

KM=640 µM for 2-oxoglutarate

KM=1100 µM for ammonia

pH dependence:

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.

Ontologies

Keywords
   LigandNADP
   Molecular functionOxidoreductase
   Technical term3D-structure
Complete proteome
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological_processglutamate biosynthetic process

Inferred from direct assay Ref.8. Source: EcoCyc

   Cellular_componentcytoplasm

Inferred from direct assay Ref.8. Source: EcoliWiki

   Molecular_functionglutamate dehydrogenase (NADP+) activity

Inferred from direct assay Ref.8. Source: EcoCyc

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 447447NADP-specific glutamate dehydrogenase
PRO_0000182769

Sites

Active site1281Proton donor By similarity
Binding site921Substrate By similarity
Binding site1131Substrate By similarity
Binding site1161Substrate By similarity
Binding site1671Substrate; via carbonyl oxygen By similarity
Binding site2111NADP By similarity
Binding site2421NADP By similarity
Binding site3801Substrate By similarity
Site1681Important for catalysis

Experimental info

Mutagenesis921K → S: Complete loss of dehydrogenase activity. Ref.10
Mutagenesis1281K → H: Reduces catalytic activity and increases pH optima for activity. Increases relative activity with amino acid substrates other than glutamate, especially L-norvaline. Ref.9
Mutagenesis1281K → R: Reduced catalytic activity and increases pH optima for activity. NADP-specific glutamate dehydrogenase. Ref.9
Sequence conflict3851A → P in AAA23868. Ref.2

Secondary structure

......................................................................... 447
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P00370 [UniParc].

Last modified July 21, 1986. Version 1.
Checksum: 7CB861D282C533C6

FASTA44748,581
        10         20         30         40         50         60 
MDQTYSLESF LNHVQKRDPN QTEFAQAVRE VMTTLWPFLE QNPKYRQMSL LERLVEPERV 

        70         80         90        100        110        120 
IQFRVVWVDD RNQIQVNRAW RVQFSSAIGP YKGGMRFHPS VNLSILKFLG FEQTFKNALT 

       130        140        150        160        170        180 
TLPMGGGKGG SDFDPKGKSE GEVMRFCQAL MTELYRHLGA DTDVPAGDIG VGGREVGFMA 

       190        200        210        220        230        240 
GMMKKLSNNT ACVFTGKGLS FGGSLIRPEA TGYGLVYFTE AMLKRHGMGF EGMRVSVSGS 

       250        260        270        280        290        300 
GNVAQYAIEK AMEFGARVIT ASDSSGTVVD ESGFTKEKLA RLIEIKASRD GRVADYAKEF 

       310        320        330        340        350        360 
GLVYLEGQQP WSLPVDIALP CATQNELDVD AAHQLIANGV KAVAEGANMP TTIEATELFQ 

       370        380        390        400        410        420 
QAGVLFAPGK AANAGGVATS GLEMAQNAAR LGWKAEKVDA RLHHIMLDIH HACVEHGGEG 

       430        440 
EQTNYVQGAN IAGFVKVADA MLAQGVI 

« Hide

References

« Hide 'large scale' references
[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]"A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 28.0-40.1 min region on the linkage map."
Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T., Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T., Mizobuchi K., Mori H., Mori T., Motomura K. expand/collapse author list , Nakade S., Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G., Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Takeuchi Y., Wada C., Yamamoto Y., Horiuchi T.
DNA Res. 3:363-377(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
J01615 Genomic DNA. Translation: AAA87979.1.
K02499 Genomic DNA. Translation: AAA23868.1.
U00096 Genomic DNA. Translation: AAC74831.1.
AP009048 Genomic DNA. Translation: BAA15550.1.
PIRDEECEN. A00382.
RefSeqNP_416275.1. NC_000913.3.
YP_490022.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2YFHX-ray2.70A/B/C/D/E/F87-90[»]
3SBOX-ray3.20A/B/C/D/E/F1-447[»]
4BHTX-ray2.50A/B/C/D/E/F1-447[»]
ProteinModelPortalP00370.
SMRP00370. Positions 6-447.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-9756N.
IntActP00370. 1 interaction.
STRING511145.b1761.

2D gel databases

SWISS-2DPAGEP00370.

Proteomic databases

PaxDbP00370.
PRIDEP00370.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC74831; AAC74831; b1761.
BAA15550; BAA15550; BAA15550.
GeneID12931328.
946802.
KEGGecj:Y75_p1736.
eco:b1761.
PATRIC32118833. VBIEscCol129921_1834.

Organism-specific databases

EchoBASEEB0367.
EcoGeneEG10372. gdhA.

Phylogenomic databases

eggNOGCOG0334.
HOGENOMHOG000243799.
KOK00262.
OMAVAIYTIE.
OrthoDBEOG65XN4D.
PhylomeDBP00370.
ProtClustDBPRK09414.

Enzyme and pathway databases

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

Gene expression databases

GenevestigatorP00370.

Family and domain databases

Gene3D3.40.50.720. 1 hit.
InterProIPR006095. 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]
PfamPF00208. ELFV_dehydrog. 1 hit.
PF02812. ELFV_dehydrog_N. 1 hit.
[Graphical view]
PIRSFPIRSF000185. Glu_DH. 1 hit.
PRINTSPR00082. GLFDHDRGNASE.
SMARTSM00839. ELFV_dehydrog. 1 hit.
[Graphical view]
PROSITEPS00074. GLFV_DEHYDROGENASE. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

PROP00370.

Entry information

Entry nameDHE4_ECOLI
AccessionPrimary (citable) accession number: P00370
Secondary accession number(s): P78173
Entry history
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: July 21, 1986
Last modified: April 16, 2014
This is version 120 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene