EzCatDB: D00032
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DB codeD00032
CATH domainDomain 13.40.192.10 : Leucine Dehydrogenase; Chain A, domain 1Catalytic domain
Domain 23.40.50.720 : Rossmann fold
E.C.1.4.1.3

CATH domainRelated DB codes (homologues)
3.40.192.10 : Leucine Dehydrogenase; Chain A, domain 1D00458,D00033,D00035,D00605,D00845,D00857,D00858,M00210,T00010,T00011,T00414
3.40.50.720 : Rossmann foldS00543,S00551,S00552,S00553,S00602,S00604,S00605,S00608,S00610,S00625,S00319,S00328,S00329,S00330,S00331,S00332,D00456,D00457,D00458,S00324,S00320,S00325,S00326,S00327,D00459,S00335,S00336,S00334,T00219,S00339,D00513,D00001,D00002,D00003,D00005,D00007,D00008,D00010,D00012,D00017,D00018,D00023,D00027,D00028,D00031,D00033,D00034,D00035,D00037,D00048,D00071,D00476,D00481,D00482,D00490,D00492,D00494,D00545,D00601,D00603,D00604,D00605,D00615,D00845,D00857,D00858,M00161,M00171,M00210,T00002,T00010,T00011,T00015,T00227,T00247,T00408,T00414,D00827,D00262,D00274,D00275,M00035,T00109

Enzyme Name
UniProtKBKEGG

P80319P96110
Protein nameGlutamate dehydrogenaseGlutamate dehydrogenaseglutamate dehydrogenase [NAD(P)+]
glutamic dehydrogenase
glutamate dehydrogenase [NAD(P)+]
SynonymsGDH
EC 1.4.1.3
GDH
EC 1.4.1.3
RefSeqNP_579331.1 (Protein)
NC_003413.1 (DNA/RNA sequence)
NP_228821.1 (Protein)
NC_000853.1 (DNA/RNA sequence)
PfamPF00208 (ELFV_dehydrog)
PF02812 (ELFV_dehydrog_N)
[Graphical view]
PF00208 (ELFV_dehydrog)
PF02812 (ELFV_dehydrog_N)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00251Glutamate metabolism
MAP00330Arginine and proline metabolism
MAP00471D-Glutamine and D-glutamate metabolism
MAP00910Nitrogen metabolism

UniProtKB:Accession NumberP80319P96110
Entry nameDHE3_PYRFUDHE3_THEMA
ActivityL-glutamate + H(2)O + NAD(P)(+) = 2- oxoglutarate + NH(3) + NAD(P)H.L-glutamate + H(2)O + NAD(P)(+) = 2- oxoglutarate + NH(3) + NAD(P)H.
SubunitHomohexamer.Homohexamer.
Subcellular locationCytoplasm.
Cofactor


Compound table: links to PDB-related databases & PoSSuM

SubstratesProducts
KEGG-idC00003C00006C00025C00001C00004C00005C00026C00014C00080
CompoundNAD+NADP+L-GlutamateH2ONADHNADPH2-OxoglutarateNH3H+
Typeamide group,amine group,nucleotideamide group,amine group,nucleotideamino acids,carboxyl groupH2Oamide group,amine group,nucleotideamide group,amine group,nucleotidecarbohydrate,carboxyl groupamine group,organic ionothers
ChEBI15846
18009
16015
15377
16908
16474
30915
16134
15378
PubChem5893
5886
88747398
44272391
33032
962
22247451
439153
5884
51
222
1038
                 
1b26A01UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
1b26B01UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
1b26C01UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
1b26D01UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
1b26E01UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
1b26F01UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
1bvuA01UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
1bvuB01UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
1bvuC01UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
1bvuD01UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
1bvuE01UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
1bvuF01UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
1gtmA01UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
1gtmB01UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
1gtmC01UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
2tmgA01UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
2tmgB01UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
2tmgC01UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
2tmgD01UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
2tmgE01UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
2tmgF01UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
1b26A02UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
1b26B02UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
1b26C02UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
1b26D02UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
1b26E02UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
1b26F02UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
1bvuA02UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
1bvuB02UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
1bvuC02UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
1bvuD02UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
1bvuE02UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
1bvuF02UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
1gtmA02UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
1gtmB02UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
1gtmC02UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
2tmgA02UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
2tmgB02UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
2tmgC02UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
2tmgD02UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
2tmgE02UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
2tmgF02UnboundUnboundUnbound UnboundUnboundUnboundUnbound 

Active-site residues
resource
Swiss-prot; P80319, P96110
pdbCatalytic residuescomment
          
1b26A01LYS 104
 
1b26B01LYS 104
 
1b26C01LYS 104
 
1b26D01LYS 104
 
1b26E01LYS 104
 
1b26F01LYS 104
 
1bvuA01LYS 104
 
1bvuB01LYS 104
 
1bvuC01LYS 104
 
1bvuD01LYS 104
 
1bvuE01LYS 104
 
1bvuF01LYS 104
 
1gtmA01LYS 104
 
1gtmB01LYS 104
 
1gtmC01LYS 104
 
2tmgA01LYS 104
mutant N117R;S128R;T158E;S160E
2tmgB01LYS 104
mutant N117R;S128R;T158E;S160E
2tmgC01LYS 104
mutant N117R;S128R;T158E;S160E
2tmgD01LYS 104
mutant N117R;S128R;T158E;S160E
2tmgE01LYS 104
mutant N117R;S128R;T158E;S160E
2tmgF01LYS 104
mutant N117R;S128R;T158E;S160E
1b26A02 
 
1b26B02 
 
1b26C02 
 
1b26D02 
 
1b26E02 
 
1b26F02 
 
1bvuA02 
 
1bvuB02 
 
1bvuC02 
 
1bvuD02 
 
1bvuE02 
 
1bvuF02 
 
1gtmA02 
 
1gtmB02 
 
1gtmC02 
 
2tmgA02 
 
2tmgB02 
 
2tmgC02 
 
2tmgD02 
 
2tmgE02 
 
2tmgF02 
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[8]Fig.6, p.5243

references
[1]
PubMed ID1576153
JournalBiochim Biophys Acta
Year1992
Volume1120
Pages267-72
AuthorsRobb FT, Park JB, Adams MW
TitleCharacterization of an extremely thermostable glutamate dehydrogenase: a key enzyme in the primary metabolism of the hyperthermophilic archaebacterium, Pyrococcus furiosus.
[2]
PubMed ID7758464
JournalEur J Biochem
Year1995
Volume229
Pages688-95
AuthorsBritton KL, Baker PJ, Borges KM, Engel PC, Pasquo A, Rice DW, Robb FT, Scandurra R, Stillman TJ, Yip KS
TitleInsights into thermal stability from a comparison of the glutamate dehydrogenases from Pyrococcus furiosus and Thermococcus litoralis.
[3]
CommentsX-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS)
Medline ID96164432
PubMed ID8591026
JournalStructure
Year1995
Volume3
Pages1147-58
AuthorsYip KS, Stillman TJ, Britton KL, Artymiuk PJ, Baker PJ, Sedelnikova SE, Engel PC, Pasquo A, Chiaraluce R, Consalvi V
TitleThe structure of Pyrococcus furiosus glutamate dehydrogenase reveals a key role for ion-pair networks in maintaining enzyme stability at extreme temperatures.
Related PDB1gtm
Related UniProtKBP80319
[4]
PubMed ID9307012
JournalBiochem J
Year1997
Volume326
Pages649-55
AuthorsAghajanian S, Engel PC
TitleRe-activation of Clostridium symbiosum glutamate dehydrogenase from subunits denatured by urea.
[5]
CommentsX-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS)
Medline ID97280794
PubMed ID9135121
JournalJ Mol Biol
Year1997
Volume267
Pages916-32
AuthorsKnapp S, de Vos WM, Rice D, Ladenstein R
TitleCrystal structure of glutamate dehydrogenase from the hyperthermophilic eubacterium Thermotoga maritima at 3.0 A resolution.
Related PDB1b26
Related UniProtKBP96110
[6]
PubMed ID9788945
JournalBiophys J
Year1998
Volume75
Pages2504-7
AuthorsDaniel RM, Smith JC, Ferrand M, Hery S, Dunn R, Finney JL
TitleEnzyme activity below the dynamical transition at 220 K.
[7]
CommentsX-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS)
Medline ID98319860
PubMed ID9654452
JournalJ Mol Biol
Year1998
Volume280
Pages287-96
AuthorsLebbink JH, Knapp S, van der Oost J, Rice D, Ladenstein R, de Vos WM
TitleEngineering activity and stability of Thermotoga maritima glutamate dehydrogenase. I. Introduction of a six-residue ion-pair network in the hinge region.
Related UniProtKBP96110
[8]
PubMed ID10076069
JournalBiochim Biophys Acta
Year1999
Volume1426
Pages513-25
AuthorsPerez-Pomares F, Ferrer J, Camacho M, Pire C, LLorca F, Bonete MJ
TitleAmino acid residues involved in the catalytic mechanism of NAD-dependent glutamate dehydrogenase from Halobacterium salinarum.
[9]
CommentsX-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS)
Medline ID99296634
PubMed ID10366510
JournalJ Mol Biol
Year1999
Volume289
Pages357-69
AuthorsLebbink JH, Knapp S, van der Oost J, Rice D, Ladenstein R, de Vos WM
TitleEngineering activity and stability of Thermotoga maritima glutamate dehydrogenase. II: construction of a 16-residue ion-pair network at the subunit interface.
Related PDB2tmg
Related UniProtKBP96110
[10]
CommentsX-ray crystallography
PubMed ID10547290
JournalJ Mol Biol
Year1999
Volume293
Pages1121-32
AuthorsBritton KL, Yip KS, Sedelnikova SE, Stillman TJ, Adams MW, Ma K, Maeder DL, Robb FT, Tolliday N, Vetriani C, Rice DW, Baker PJ
TitleStructure determination of the glutamate dehydrogenase from the hyperthermophile Thermococcus litoralis and its comparison with that from Pyrococcus furiosus.
Related PDB1bvu
[11]
PubMed ID10924516
JournalJ Biol Chem
Year2000
Volume275
Pages39529-42
AuthorsMinambres B, Olivera ER, Jensen RA, Luengo JM
TitleA new class of glutamate dehydrogenases (GDH). Biochemical and genetic characterization of the first member, the AMP-requiring NAD-specific GDH of Streptomyces clavuligerus.

comments
This enzyme catalyzes three reactions, dehydrogenation, addition of hydroxyl group to double-bond and elimination accompanied by double-bond formation (see T00010; homologous enzyme).

createdupdated
2004-04-012009-02-26


Copyright: Nozomi Nagano, JST & CBRC-AIST
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Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
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Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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