DB code: T00010

CATH domain 3.40.50.720 : Rossmann fold
3.40.192.10 : Leucine Dehydrogenase; Chain A, domain 1 Catalytic domain
1.10.285.10 : Glutamate Dehydrogenase; Chain A, domain 3
E.C. 1.4.1.2
CSA 1hrd
M-CSA 1hrd
MACiE

CATH domain Related DB codes (homologues)
3.40.192.10 : Leucine Dehydrogenase; Chain A, domain 1 D00458 D00032 D00033 D00035 D00605 D00845 D00857 D00858 M00210 T00011 T00414
3.40.50.720 : Rossmann fold S00543 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 D00032 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 T00011 T00015 T00227 T00247 T00408 T00414 D00827 D00262 D00274 D00275 M00035 T00109

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam
P24295 NAD-specific glutamate dehydrogenase
NAD-GDH
EC 1.4.1.2
PF00208 (ELFV_dehydrog)
PF02812 (ELFV_dehydrog_N)
[Graphical View]

KEGG enzyme name
glutamate dehydrogenase
glutamic dehydrogenase
glutamate dehydrogenase (NAD+)
glutamate oxidoreductase
glutamic acid dehydrogenase
L-glutamate dehydrogenase
NAD+-dependent glutamate dehydrogenase
NAD+-dependent glutamic dehydrogenase
NAD+-glutamate dehydrogenase
NAD+-linked glutamate dehydrogenase
NAD+-linked glutamic dehydrogenase
NAD+-specific glutamic dehydrogenase
NAD+-specific glutamate dehydrogenase
NAD+:glutamate oxidoreductase
NADH-linked glutamate dehydrogenase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P24295 DHE2_CLOSY L-glutamate + H(2)O + NAD(+) = 2-oxoglutarate + NH(3) + NADH. Homohexamer.

KEGG Pathways
Map code Pathways E.C.
MAP00910 Nitrogen metabolism
MAP00251 Glutamate metabolism

Compound table
Substrates Products Intermediates
KEGG-id C00025 C00001 C00003 C00026 C00014 C00004 C00080
E.C.
Compound L-Glutamate H2O NAD+ 2-Oxoglutarate NH3 NADH H+
Type amino acids,carboxyl group H2O amide group,amine group,nucleotide carbohydrate,carboxyl group amine group,organic ion amide group,amine group,nucleotide others
ChEBI 16015
15377
15846
30915
16134
16908
15378
PubChem 88747398
44272391
33032
962
22247451
5893
51
222
439153
1038
1aupA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1bgvA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1hrdA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1hrdB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1hrdC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1k89A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1aupA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1bgvA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:GLU Unbound Unbound Unbound Unbound
1hrdA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1hrdB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1hrdC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1k89A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1aupA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1bgvA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1hrdA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1hrdB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1hrdC03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1k89A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot;P24295

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1aupA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1bgvA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1hrdA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1hrdB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1hrdC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1k89A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1aupA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 125;ASP 165 mutant K89I
1bgvA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 125;ASP 165
1hrdA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 125;ASP 165
1hrdB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 125;ASP 165
1hrdC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 125;ASP 165
1k89A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 125;ASP 165 mutant K89I
1aupA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1bgvA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1hrdA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1hrdB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1hrdC03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1k89A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[7]
Fig.5, p.1136-1138 3
[15]
Fig.6, p.524
[21]

References
[1]
Resource
Comments
Medline ID
PubMed ID 3981633
Journal J Mol Biol
Year 1985
Volume 181
Pages 147-9
Authors Rice DW, Hornby DP, Engel PC
Title Crystallization of an NAD+-dependent glutamate dehydrogenase from Clostridium symbiosum.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 3593276
Journal Biochem J
Year 1987
Volume 242
Pages 789-95
Authors Rice DW, Baker PJ, Farrants GW, Hornby DP
Title The crystal structure of glutamate dehydrogenase from Clostridium symbiosum at 0.6 nm resolution.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 1764463
Journal Biochim Biophys Acta
Year 1991
Volume 1115
Pages 123-30
Authors Syed SE, Engel PC, Parker DM
Title Functional studies of a glutamate dehydrogenase with known three-dimensional structure: steady-state kinetics of the forward and reverse reactions catalysed by the NAD(+)-dependent glutamate dehydrogenase of Clostridium symbiosum.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 1633808
Journal Eur J Biochem
Year 1992
Volume 207
Pages 533-40
Authors Lilley KS, Engel PC
Title The essential active-site lysines of clostridial glutamate dehydrogenase. A study with pyridoxal-5'-phosphate.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 1349042
Journal J Mol Biol
Year 1992
Volume 224
Pages 1181-4
Authors Stillman TJ, Baker PJ, Britton KL, Rice DW, Rodgers HF
Title Effect of additives on the crystallization of glutamate dehydrogenase from Clostridium symbiosum. Evidence for a ligand-induced conformational change.
Related PDB
Related UniProtKB
[6]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.96 ANGSTROMS).
Medline ID 92204934
PubMed ID 1553382
Journal Proteins
Year 1992
Volume 12
Pages 75-86
Authors Baker PJ, Britton KL, Engel PC, Farrants GW, Lilley KS, Rice DW, Stillman TJ
Title Subunit assembly and active site location in the structure of glutamate dehydrogenase.
Related PDB
Related UniProtKB P24295
[7]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
Medline ID 94087726
PubMed ID 8263917
Journal J Mol Biol
Year 1993
Volume 234
Pages 1131-9
Authors Stillman TJ, Baker PJ, Britton KL, Rice DW
Title Conformational flexibility in glutamate dehydrogenase. Role of water in substrate recognition and catalysis.
Related PDB 1bgv
Related UniProtKB P24295
[8]
Resource
Comments
Medline ID
PubMed ID 8263939
Journal J Mol Biol
Year 1993
Volume 234
Pages 938-45
Authors Britton KL, Baker PJ, Engel PC, Rice DW, Stillman TJ
Title Evolution of substrate diversity in the superfamily of amino acid dehydrogenases. Prospects for rational chiral synthesis.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 8129708
Journal Biochem J
Year 1994
Volume 298
Pages 107-13
Authors Syed SE, Hornby DP, Brown PE, Fitton JE, Engel PC
Title Site and significance of chemically modifiable cysteine residues in glutamate dehydrogenase of Clostridium symbiosum and the use of protection studies to measure coenzyme binding.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 8037659
Journal Biochem J
Year 1994
Volume 301
Pages 13-6
Authors Dean JL, Wang XG, Teller JK, Waugh ML, Britton KL, Baker PJ, Stillman TJ, Martin SR, Rice DW, Engel PC
Title The catalytic role of aspartate in the active site of glutamate dehydrogenase.
Related PDB
Related UniProtKB
[11]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 8591026
Journal Structure
Year 1995
Volume 3
Pages 1147-58
Authors Yip KS, Stillman TJ, Britton KL, Artymiuk PJ, Baker PJ, Sedelnikova SE, Engel PC, Pasquo A, Chiaraluce R, Consalvi V
Title The structure of Pyrococcus furiosus glutamate dehydrogenase reveals a key role for ion-pair networks in maintaining enzyme stability at extreme temperatures.
Related PDB 1hrd
Related UniProtKB
[12]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
Medline ID 98070235
PubMed ID 9405044
Journal Biochemistry
Year 1997
Volume 36
Pages 16109-15
Authors Baker PJ, Waugh ML, Wang XG, Stillman TJ, Turnbull AP, Engel PC, Rice DW
Title Determinants of substrate specificity in the superfamily of amino acid dehydrogenases.
Related PDB 1aup
Related UniProtKB P24295
[13]
Resource
Comments
Medline ID
PubMed ID 9188163
Journal Eur Biophys J
Year 1997
Volume 25
Pages 417-22
Authors Dean JL, Colfen H, Harding SE, Rice DW, Engel PC
Title Alteration of the quaternary structure of glutamate dehydrogenase from Clostridium symbiosum by a single mutation distant from the subunit interfaces.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 10333502
Journal Biochem J
Year 1999
Volume 340
Pages 555-60
Authors Hayden BM, Dean JL, Martin SR, Engel PC
Title Chemical rescue of the catalytically disabled clostridial glutamate dehydrogenase mutant D165S by fluoride ion.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 10076069
Journal Biochim Biophys Acta
Year 1999
Volume 1426
Pages 513-25
Authors Perez-Pomares F, Ferrer J, Camacho M, Pire C, LLorca F, Bonete MJ
Title Amino acid residues involved in the catalytic mechanism of NAD-dependent glutamate dehydrogenase from Halobacterium salinarum.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 10607407
Journal Biochimie
Year 1999
Volume 81
Pages 1123-9
Authors Ahn JY, Choi S, Cho SW
Title Identification of lysine residue involved in inactivation of brain glutamate dehydrogenase isoproteins by o-phthalaldehyde.
Related PDB
Related UniProtKB
[17]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 9878450
Journal J Mol Biol
Year 1999
Volume 285
Pages 875-85
Authors Stillman TJ, Migueis AM, Wang XG, Baker PJ, Britton KL, Engel PC, Rice DW
Title Insights into the mechanism of domain closure and substrate specificity of glutamate dehydrogenase from Clostridium symbiosum.
Related PDB 1k89
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 10790778
Journal Bioelectrochemistry
Year 2000
Volume 51
Pages 35-9
Authors Dai HC, Zhuang QK, Li NQ, Luo HX, Gao XX
Title Electrochemical study of the effect of ADP and AMP on the kinetics of glutamate dehydrogenase.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 10924516
Journal J Biol Chem
Year 2000
Volume 275
Pages 39529-42
Authors Minambres B, Olivera ER, Jensen RA, Luengo JM
Title A new class of glutamate dehydrogenases (GDH). Biochemical and genetic characterization of the first member, the AMP-requiring NAD-specific GDH of Streptomyces clavuligerus.
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 11231268
Journal Eur J Biochem
Year 2001
Volume 268
Pages 1173-80
Authors Hayden BM, Engel PC
Title Construction, separation and properties of hybrid hexamers of glutamate dehydrogenase in which five of the six subunits are contributed by the catalytically inert D165S.
Related PDB
Related UniProtKB
[21]
Resource
Comments
Medline ID
PubMed ID 12220195
Journal Biochemistry
Year 2002
Volume 41
Pages 11284-93
Authors Tally JF, Maniscalco SJ, Saha SK, Fisher HF
Title Detection of multiple active site domain motions in transient-state component time courses of the Clostridium symbiosum L-glutamate dehydrogenase-catalyzed oxidative deamination reaction.
Related PDB
Related UniProtKB

Comments
This enzyme catalyzes three reactions, dehydrogenation, addition of hydroxyl group to double-bond and elimination accompanied by double-bond formation (see [7]).

Created Updated
2003-10-30 2009-02-26