DHE4_ECOLI
ID DHE4_ECOLI Reviewed; 447 AA.
AC P00370; P78173;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 21-JUL-1986, sequence version 1.
DT 03-AUG-2022, entry version 181.
DE RecName: Full=NADP-specific glutamate dehydrogenase;
DE Short=NADP-GDH;
DE EC=1.4.1.4 {ECO:0000269|PubMed:235298, ECO:0000269|PubMed:241744};
GN Name=gdhA {ECO:0000303|PubMed:6308576}; OrderedLocusNames=b1761, JW1750;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 1-36.
RC STRAIN=K12;
RX PubMed=6308576; DOI=10.1093/nar/11.15.5257;
RA McPherson M.J., Wootton J.C.;
RT "Complete nucleotide sequence of the Escherichia coli gdhA gene.";
RL Nucleic Acids Res. 11:5257-5266(1983).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=6373501; DOI=10.1016/0378-1119(84)90140-9;
RA Valle F., Becerril B., Chen E., Seeburg P.H., Heyneker H., Bolivar F.;
RT "Complete nucleotide sequence of the glutamate dehydrogenase gene from
RT Escherichia coli K-12.";
RL Gene 27:193-199(1984).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9097039; DOI=10.1093/dnares/3.6.363;
RA Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K.,
RA Miki T., Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S.,
RA Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G.,
RA Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Takeuchi Y.,
RA Wada C., Yamamoto Y., Horiuchi T.;
RT "A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 28.0-40.1 min region on the linkage map.";
RL DNA Res. 3:363-377(1996).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [6]
RP PROTEIN SEQUENCE OF 1-12.
RC STRAIN=K12 / EMG2;
RX PubMed=9298646; DOI=10.1002/elps.1150180807;
RA Link A.J., Robison K., Church G.M.;
RT "Comparing the predicted and observed properties of proteins encoded in the
RT genome of Escherichia coli K-12.";
RL Electrophoresis 18:1259-1313(1997).
RN [7]
RP FUNCTION AS A GLUTAMATE DEHYDROGENASE, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
RX PubMed=235298; DOI=10.1016/0005-2744(75)90304-6;
RA Veronese F.M., Boccu E., Conventi L.;
RT "Glutamate dehydrogenase from Escherichia coli: induction, purification and
RT properties of the enzyme.";
RL Biochim. Biophys. Acta 377:217-228(1975).
RN [8]
RP FUNCTION AS A GLUTAMATE DEHYDROGENASE, CATALYTIC ACTIVITY, ACTIVITY
RP REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
RX PubMed=241744; DOI=10.1128/jb.124.2.775-783.1975;
RA Sakamoto N., Kotre A.M., Savageau M.A.;
RT "Glutamate dehydrogenase from Escherichia coli: purification and
RT properties.";
RL J. Bacteriol. 124:775-783(1975).
RN [9]
RP MUTAGENESIS OF LYS-128.
RX PubMed=3149742; DOI=10.1093/protein/2.2.147;
RA McPherson M.J., Baron A.J., Jones K.M., Price G.J., Wootton J.C.;
RT "Multiple interactions of lysine-128 of Escherichia coli glutamate
RT dehydrogenase revealed by site-directed mutagenesis studies.";
RL Protein Eng. 2:147-152(1988).
RN [10]
RP MUTAGENESIS OF LYS-92.
RX PubMed=8355660; DOI=10.1007/bf00277068;
RA Jones K.M., McPherson M.J., Baron A.J., Mattaj I.W., Riordan C.L.,
RA Wootton J.C.;
RT "The gdhA1 point mutation in Escherichia coli K12 CLR207 alters a key
RT lysine residue of glutamate dehydrogenase.";
RL Mol. Gen. Genet. 240:286-289(1993).
RN [11]
RP IDENTIFICATION BY 2D-GEL.
RX PubMed=9298644; DOI=10.1002/elps.1150180805;
RA VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.;
RT "Escherichia coli proteome analysis using the gene-protein database.";
RL Electrophoresis 18:1243-1251(1997).
RN [12]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS), AND SUBUNIT.
RA Oliveira T., Sharkey M.A., Hamza M., Engel P.C., Khan A.R.;
RT "Structural determinants of cofactor specificity and domain flexibility in
RT bacterial glutamate dehydrogenases.";
RL Submitted (MAR-2012) to the PDB data bank.
RN [13]
RP X-RAY CRYSTALLOGRAPHY (3.2 ANGSTROMS) AND SUBUNIT.
RX PubMed=22393408; DOI=10.1371/journal.pone.0032498;
RA Totir M., Echols N., Nanao M., Gee C.L., Moskaleva A., Gradia S.,
RA Iavarone A.T., Berger J.M., May A.P., Zubieta C., Alber T.;
RT "Macro-to-micro structural proteomics: native source proteins for high-
RT throughput crystallization.";
RL PLoS ONE 7:E32498-E32498(2012).
CC -!- FUNCTION: Catalyzes the reversible oxidative deamination of glutamate
CC to alpha-ketoglutarate and ammonia. {ECO:0000269|PubMed:235298,
CC ECO:0000269|PubMed:241744}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + L-glutamate + NADP(+) = 2-oxoglutarate + H(+) + NADPH +
CC NH4(+); Xref=Rhea:RHEA:11612, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16810, ChEBI:CHEBI:28938, ChEBI:CHEBI:29985,
CC ChEBI:CHEBI:57783, ChEBI:CHEBI:58349; EC=1.4.1.4;
CC Evidence={ECO:0000269|PubMed:235298, ECO:0000269|PubMed:241744};
CC -!- ACTIVITY REGULATION: Competitively inhibited by homoserine and by
CC glutamine. {ECO:0000269|PubMed:241744}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=40 uM for NADPH {ECO:0000269|PubMed:241744};
CC KM=42 uM for NADP {ECO:0000269|PubMed:241744};
CC KM=640 uM for 2-oxoglutarate {ECO:0000269|PubMed:241744};
CC KM=1100 uM for ammonia {ECO:0000269|PubMed:241744};
CC pH dependence:
CC Optimum pH is 8 and 9 for the reductive amination and for the
CC oxidative deamination, respectively. {ECO:0000269|PubMed:235298};
CC Temperature dependence:
CC The enzyme remains active when heat treated or when left at room
CC temperature for several months but is inactivated by freezing.
CC {ECO:0000269|PubMed:241744};
CC -!- SUBUNIT: Homohexamer. {ECO:0000269|PubMed:235298,
CC ECO:0000269|PubMed:241744, ECO:0000269|Ref.12}.
CC -!- INDUCTION: Induced by growth on glucose and ammonia.
CC -!- SIMILARITY: Belongs to the Glu/Leu/Phe/Val dehydrogenases family.
CC {ECO:0000305}.
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DR EMBL; J01615; AAA87979.1; -; Genomic_DNA.
DR EMBL; K02499; AAA23868.1; -; Genomic_DNA.
DR EMBL; U00096; AAC74831.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA15550.1; -; Genomic_DNA.
DR PIR; A00382; DEECEN.
DR RefSeq; NP_416275.1; NC_000913.3.
DR RefSeq; WP_000373021.1; NZ_SSZK01000001.1.
DR PDB; 2YFH; X-ray; 2.69 A; A/B/C/D/E/F=202-405.
DR PDB; 3SBO; X-ray; 3.20 A; A/B/C/D/E/F=1-447.
DR PDB; 4BHT; X-ray; 2.50 A; A/B/C/D/E/F=1-447.
DR PDBsum; 2YFH; -.
DR PDBsum; 3SBO; -.
DR PDBsum; 4BHT; -.
DR AlphaFoldDB; P00370; -.
DR SMR; P00370; -.
DR BioGRID; 4260322; 628.
DR ComplexPortal; CPX-1976; Glutamate dehydrogenase complex.
DR DIP; DIP-9756N; -.
DR IntAct; P00370; 1.
DR MINT; P00370; -.
DR STRING; 511145.b1761; -.
DR SWISS-2DPAGE; P00370; -.
DR jPOST; P00370; -.
DR PaxDb; P00370; -.
DR PRIDE; P00370; -.
DR EnsemblBacteria; AAC74831; AAC74831; b1761.
DR EnsemblBacteria; BAA15550; BAA15550; BAA15550.
DR GeneID; 946802; -.
DR KEGG; ecj:JW1750; -.
DR KEGG; eco:b1761; -.
DR PATRIC; fig|1411691.4.peg.493; -.
DR EchoBASE; EB0367; -.
DR eggNOG; COG0334; Bacteria.
DR HOGENOM; CLU_025763_2_1_6; -.
DR InParanoid; P00370; -.
DR OMA; PCFAAFP; -.
DR PhylomeDB; P00370; -.
DR BioCyc; EcoCyc:GDHA-MON; -.
DR BioCyc; MetaCyc:GDHA-MON; -.
DR BRENDA; 1.4.1.4; 2026.
DR SABIO-RK; P00370; -.
DR PRO; PR:P00370; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IDA:EcoliWiki.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:1990148; C:glutamate dehydrogenase complex; IPI:ComplexPortal.
DR GO; GO:0004354; F:glutamate dehydrogenase (NADP+) activity; IDA:EcoCyc.
DR GO; GO:0097216; F:guanosine tetraphosphate binding; IDA:EcoCyc.
DR GO; GO:0006537; P:glutamate biosynthetic process; IDA:EcoCyc.
DR GO; GO:0006536; P:glutamate metabolic process; IDA:ComplexPortal.
DR CDD; cd05313; NAD_bind_2_Glu_DH; 1.
DR InterPro; IPR046346; Aminiacid_DH-like_N_sf.
DR InterPro; IPR006095; Glu/Leu/Phe/Val_DH.
DR InterPro; IPR033524; Glu/Leu/Phe/Val_DH_AS.
DR InterPro; IPR006096; Glu/Leu/Phe/Val_DH_C.
DR InterPro; IPR006097; Glu/Leu/Phe/Val_DH_dimer_dom.
DR InterPro; IPR014362; Glu_DH.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR InterPro; IPR033922; NAD_bind_Glu_DH.
DR Pfam; PF00208; ELFV_dehydrog; 1.
DR Pfam; PF02812; ELFV_dehydrog_N; 1.
DR PIRSF; PIRSF000185; Glu_DH; 1.
DR PRINTS; PR00082; GLFDHDRGNASE.
DR SMART; SM00839; ELFV_dehydrog; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
DR SUPFAM; SSF53223; SSF53223; 1.
DR PROSITE; PS00074; GLFV_DEHYDROGENASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; NADP; Oxidoreductase;
KW Reference proteome.
FT CHAIN 1..447
FT /note="NADP-specific glutamate dehydrogenase"
FT /id="PRO_0000182769"
FT ACT_SITE 128
FT /note="Proton donor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10011"
FT BINDING 92
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 113
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 116
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 167
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 211
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250"
FT BINDING 242
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250"
FT BINDING 380
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT SITE 168
FT /note="Important for catalysis"
FT MUTAGEN 92
FT /note="K->S: Complete loss of dehydrogenase activity."
FT /evidence="ECO:0000269|PubMed:8355660"
FT MUTAGEN 128
FT /note="K->H: Reduces catalytic activity and increases pH
FT optima for activity. Increases relative activity with amino
FT acid substrates other than glutamate, especially L-
FT norvaline."
FT /evidence="ECO:0000269|PubMed:3149742"
FT MUTAGEN 128
FT /note="K->R: Reduced catalytic activity and increases pH
FT optima for activity. NADP-specific glutamate
FT dehydrogenase."
FT /evidence="ECO:0000269|PubMed:3149742"
FT CONFLICT 385
FT /note="A -> P (in Ref. 2; AAA23868)"
FT /evidence="ECO:0000305"
FT HELIX 7..15
FT /evidence="ECO:0007829|PDB:4BHT"
FT HELIX 22..41
FT /evidence="ECO:0007829|PDB:4BHT"
FT HELIX 43..49
FT /evidence="ECO:0007829|PDB:4BHT"
FT HELIX 50..54
FT /evidence="ECO:0007829|PDB:4BHT"
FT STRAND 58..68
FT /evidence="ECO:0007829|PDB:4BHT"
FT STRAND 74..85
FT /evidence="ECO:0007829|PDB:4BHT"
FT STRAND 87..97
FT /evidence="ECO:0007829|PDB:4BHT"
FT HELIX 103..119
FT /evidence="ECO:0007829|PDB:4BHT"
FT STRAND 121..123
FT /evidence="ECO:0007829|PDB:3SBO"
FT STRAND 126..132
FT /evidence="ECO:0007829|PDB:4BHT"
FT HELIX 140..154
FT /evidence="ECO:0007829|PDB:4BHT"
FT HELIX 155..157
FT /evidence="ECO:0007829|PDB:4BHT"
FT TURN 160..162
FT /evidence="ECO:0007829|PDB:4BHT"
FT STRAND 163..166
FT /evidence="ECO:0007829|PDB:4BHT"
FT HELIX 173..187
FT /evidence="ECO:0007829|PDB:4BHT"
FT HELIX 199..201
FT /evidence="ECO:0007829|PDB:4BHT"
FT TURN 205..209
FT /evidence="ECO:0007829|PDB:4BHT"
FT HELIX 210..225
FT /evidence="ECO:0007829|PDB:4BHT"
FT STRAND 234..238
FT /evidence="ECO:0007829|PDB:4BHT"
FT HELIX 242..253
FT /evidence="ECO:0007829|PDB:4BHT"
FT STRAND 260..263
FT /evidence="ECO:0007829|PDB:4BHT"
FT STRAND 266..269
FT /evidence="ECO:0007829|PDB:4BHT"
FT HELIX 276..286
FT /evidence="ECO:0007829|PDB:4BHT"
FT STRAND 288..290
FT /evidence="ECO:0007829|PDB:4BHT"
FT HELIX 293..300
FT /evidence="ECO:0007829|PDB:4BHT"
FT STRAND 303..306
FT /evidence="ECO:0007829|PDB:4BHT"
FT HELIX 310..312
FT /evidence="ECO:0007829|PDB:4BHT"
FT STRAND 316..320
FT /evidence="ECO:0007829|PDB:4BHT"
FT HELIX 329..337
FT /evidence="ECO:0007829|PDB:4BHT"
FT STRAND 342..344
FT /evidence="ECO:0007829|PDB:4BHT"
FT STRAND 346..349
FT /evidence="ECO:0007829|PDB:4BHT"
FT HELIX 353..361
FT /evidence="ECO:0007829|PDB:4BHT"
FT STRAND 365..367
FT /evidence="ECO:0007829|PDB:4BHT"
FT HELIX 369..372
FT /evidence="ECO:0007829|PDB:4BHT"
FT HELIX 375..389
FT /evidence="ECO:0007829|PDB:4BHT"
FT HELIX 395..415
FT /evidence="ECO:0007829|PDB:4BHT"
FT STRAND 419..422
FT /evidence="ECO:0007829|PDB:4BHT"
FT HELIX 425..443
FT /evidence="ECO:0007829|PDB:4BHT"
SQ SEQUENCE 447 AA; 48581 MW; 7CB861D282C533C6 CRC64;
MDQTYSLESF LNHVQKRDPN QTEFAQAVRE VMTTLWPFLE QNPKYRQMSL LERLVEPERV
IQFRVVWVDD RNQIQVNRAW RVQFSSAIGP YKGGMRFHPS VNLSILKFLG FEQTFKNALT
TLPMGGGKGG SDFDPKGKSE GEVMRFCQAL MTELYRHLGA DTDVPAGDIG VGGREVGFMA
GMMKKLSNNT ACVFTGKGLS FGGSLIRPEA TGYGLVYFTE AMLKRHGMGF EGMRVSVSGS
GNVAQYAIEK AMEFGARVIT ASDSSGTVVD ESGFTKEKLA RLIEIKASRD GRVADYAKEF
GLVYLEGQQP WSLPVDIALP CATQNELDVD AAHQLIANGV KAVAEGANMP TTIEATELFQ
QAGVLFAPGK AANAGGVATS GLEMAQNAAR LGWKAEKVDA RLHHIMLDIH HACVEHGGEG
EQTNYVQGAN IAGFVKVADA MLAQGVI
