P00370 (DHE4_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
NADP-specific glutamate dehydrogenase
Short name=NADP-GDH
EC=1.4.1.4

Gene names

Name:	gdhA
Ordered Locus Names:	b1761, JW1750

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	447 AA.
Sequence status	Complete.
Protein existence	Evidence 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
Ligand	NADP
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	glutamate biosynthetic process Inferred from direct assay Ref.8. Source: EcoCyc
Cellular_component	cytoplasm Inferred from direct assay Ref.8. Source: EcoliWiki
Molecular_function	glutamate dehydrogenase (NADP+) activity Inferred from direct assay Ref.8. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 447

447

NADP-specific glutamate dehydrogenase

PRO_0000182769

Sites

Active site

128

1

Proton donor By similarity

Binding site

92

1

Substrate By similarity

Binding site

113

1

Substrate By similarity

Binding site

116

1

Substrate By similarity

Binding site

167

1

Substrate; via carbonyl oxygen By similarity

Binding site

211

1

NADP By similarity

Binding site

242

1

NADP By similarity

Binding site

380

1

Substrate By similarity

Site

168

1

Important for catalysis

Experimental info

Mutagenesis

92

1

K → S: Complete loss of dehydrogenase activity. Ref.10

Mutagenesis

128

1

K → 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

Mutagenesis

128

1

K → R: Reduced catalytic activity and increases pH optima for activity. NADP-specific glutamate dehydrogenase. Ref.9

Sequence conflict

385

1

A → P in AAA23868. Ref.2

Secondary structure

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447

Helix Strand Turn

Details...

Helix

7 – 15

9

Helix

22 – 41

20

Helix

43 – 49

7

Helix

50 – 54

5

Beta strand

58 – 68

11

Beta strand

74 – 85

12

Beta strand

87 – 97

11

Helix

103 – 119

17

Beta strand

121 – 123

3

Beta strand

126 – 132

7

Helix

140 – 154

15

Helix

155 – 157

3

Turn

160 – 162

3

Beta strand

163 – 166

4

Helix

173 – 187

15

Helix

199 – 201

3

Turn

205 – 209

5

Helix

210 – 225

16

Beta strand

235 – 238

4

Helix

243 – 253

11

Beta strand

259 – 263

5

Beta strand

265 – 269

5

Helix

276 – 286

11

Helix

293 – 299

7

Beta strand

303 – 306

4

Helix

310 – 312

3

Beta strand

316 – 320

5

Helix

329 – 337

9

Beta strand

342 – 344

3

Beta strand

346 – 349

4

Helix

353 – 361

9

Beta strand

365 – 367

3

Helix

369 – 372

4

Helix

375 – 389

15

Helix

395 – 415

21

Beta strand

419 – 422

4

Helix

425 – 443

19

Sequences

	Sequence		Length	Mass (Da)
	P00370 [UniParc]. Last modified July 21, 1986. Version 1. Checksum: 7CB861D282C533C6	FASTA	447	48,581
	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

References

	« Hide 'large scale' referencesShow '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. , 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 277:1453-1474(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 (APR-2011) to the PDB data bank Cited for: X-RAY CRYSTALLOGRAPHY (3.2 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.

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.

PIR

DEECEN. A00382.

RefSeq

NP_416275.1. NC_000913.2.
YP_490022.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2YFG	X-ray	2.50	A/B/C/D/E/F	1-447	[»]
3SBO	X-ray	3.20	A/B/C/D/E/F	1-447	[»]

ProteinModelPortal

P00370.

SMR

P00370. Positions 6-447.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-9756N.

IntAct

P00370. 1 interaction.

STRING

511145.b1761.

2D gel databases

SWISS-2DPAGE

P00370.

Proteomic databases

PaxDb

P00370.

PRIDE

P00370.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC74831; AAC74831; b1761.
BAA15550; BAA15550; BAA15550.

GeneID

12931328.
946802.

KEGG

ecj:Y75_p1736.
eco:b1761.

PATRIC

32118833. VBIEscCol129921_1834.

Organism-specific databases

EchoBASE

EB0367.

EcoGene

EG10372. gdhA.

Phylogenomic databases

eggNOG

COG0334.

HOGENOM

HOG000243799.

KO

K00262.

OMA

PCFAAFP.

ProtClustDB

PRK09414.

Enzyme and pathway databases

BioCyc

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

Gene expression databases

Genevestigator

P00370.

Family and domain databases

Gene3D

3.40.50.720. 1 hit.

InterPro

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]

Pfam

PF00208. ELFV_dehydrog. 1 hit.
PF02812. ELFV_dehydrog_N. 1 hit.
[Graphical view]

PIRSF

PIRSF000185. Glu_DH. 1 hit.

PRINTS

PR00082. GLFDHDRGNASE.

SMART

SM00839. ELFV_dehydrog. 1 hit.
[Graphical view]

PROSITE

PS00074. GLFV_DEHYDROGENASE. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

DHE4_ECOLI

Accession

Primary (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:	May 29, 2013
This is version 111 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program