T00010
type: Enzyme
cath: Rossmann fold
cath: Leucine Dehydrogenase; Chain A, domain 1
cath: Glutamate Dehydrogenase; Chain A, domain 3
ec: https://purl.uniprot.org/enzyme/1.4.1.2
csa: 1hrd
uniprot: P24295
kegg enzyme: glutamate dehydrogenase
kegg enzyme: glutamic dehydrogenase
kegg enzyme: glutamate dehydrogenase (NAD+)
kegg enzyme: glutamate oxidoreductase
kegg enzyme: glutamic acid dehydrogenase
kegg enzyme: L-glutamate dehydrogenase
kegg enzyme: NAD+-dependent glutamate dehydrogenase
kegg enzyme: NAD+-dependent glutamic dehydrogenase
kegg enzyme: NAD+-glutamate dehydrogenase
kegg enzyme: NAD+-linked glutamate dehydrogenase
kegg enzyme: NAD+-linked glutamic dehydrogenase
kegg enzyme: NAD+-specific glutamic dehydrogenase
kegg enzyme: NAD+-specific glutamate dehydrogenase
kegg enzyme: NAD+:glutamate oxidoreductase
kegg enzyme: NADH-linked glutamate dehydrogenase
kegg pathway: Glutamate metabolism
kegg pathway: Nitrogen metabolism
kegg substrate: L-Glutamate
kegg substrate: H2O
kegg substrate: NAD+
kegg product: 2-Oxoglutarate
kegg product: NH3
kegg product: NADH
kegg product: H+
pdb: 1aupA01
pdb: 1bgvA01
pdb: 1hrdA01
pdb: 1hrdB01
pdb: 1hrdC01
pdb: 1k89A01
pdb: 1aupA02
pdb: 1bgvA02
pdb: 1hrdA02
pdb: 1hrdB02
pdb: 1hrdC02
pdb: 1k89A02
pdb: 1aupA03
pdb: 1bgvA03
pdb: 1hrdA03
pdb: 1hrdB03
pdb: 1hrdC03
pdb: 1k89A03
pdb bound state: Unbound
  compound: L-Glutamate
  pdb: 1aupA01
pdb bound state: Unbound
  compound: L-Glutamate
  pdb: 1bgvA01
pdb bound state: Unbound
  compound: L-Glutamate
  pdb: 1hrdA01
pdb bound state: Unbound
  compound: L-Glutamate
  pdb: 1hrdB01
pdb bound state: Unbound
  compound: L-Glutamate
  pdb: 1hrdC01
pdb bound state: Unbound
  compound: L-Glutamate
  pdb: 1k89A01
pdb bound state: Unbound
  compound: L-Glutamate
  pdb: 1aupA02
pdb bound state: Unbound
  compound: L-Glutamate
  pdb: 1hrdA02
active site residues resources: P24295
references: Crystallization of an NAD+-dependent glutamate dehydrogenase from Clostridium symbiosum.
references: The crystal structure of glutamate dehydrogenase from Clostridium symbiosum at 0.6 nm resolution.
references: http://ezcatdb.cbrc.jp/EzCatDB/reference/T00010#3
references: The essential active-site lysines of clostridial glutamate dehydrogenase. A study with pyridoxal-5'-phosphate.
references: Effect of additives on the crystallization of glutamate dehydrogenase from Clostridium symbiosum. Evidence for a ligand-induced conformational change.
references: Subunit assembly and active site location in the structure of glutamate dehydrogenase.
references: Conformational flexibility in glutamate dehydrogenase. Role of water in substrate recognition and catalysis.
references: Evolution of substrate diversity in the superfamily of amino acid dehydrogenases. Prospects for rational chiral synthesis.
references: Site and significance of chemically modifiable cysteine residues in glutamate dehydrogenase of Clostridium symbiosum and the use of protection studies to measure coenzyme binding.
references: The catalytic role of aspartate in the active site of glutamate dehydrogenase.
references: The structure of Pyrococcus furiosus glutamate dehydrogenase reveals a key role for ion-pair networks in maintaining enzyme stability at extreme temperatures.
references: Determinants of substrate specificity in the superfamily of amino acid dehydrogenases.
references: Alteration of the quaternary structure of glutamate dehydrogenase from Clostridium symbiosum by a single mutation distant from the subunit interfaces.
references: Chemical rescue of the catalytically disabled clostridial glutamate dehydrogenase mutant D165S by fluoride ion.
references: Amino acid residues involved in the catalytic mechanism of NAD-dependent glutamate dehydrogenase from Halobacterium salinarum.
references: Identification of lysine residue involved in inactivation of brain glutamate dehydrogenase isoproteins by o-phthalaldehyde.
references: Insights into the mechanism of domain closure and substrate specificity of glutamate dehydrogenase from Clostridium symbiosum.
references: Electrochemical study of the effect of ADP and AMP on the kinetics of glutamate dehydrogenase.
references: A new class of glutamate dehydrogenases (GDH). Biochemical and genetic characterization of the first member, the AMP-requiring NAD-specific GDH of Streptomyces clavuligerus.
references: Construction, separation and properties of hybrid hexamers of glutamate dehydrogenase in which five of the six subunits are contributed by the catalytically inert D165S.
references: Detection of multiple active site domain motions in transient-state component time courses of the Clostridium symbiosum L-glutamate dehydrogenase-catalyzed oxidative deamination reaction.
comment: This enzyme catalyzes three reactions, dehydrogenation, addition of hydroxyl group to double-bond and elimination accompanied by double-bond formation (see [7]).

Rossmann fold
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/3.40.50.720

Leucine Dehydrogenase; Chain A, domain 1
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/3.40.192.10
catalytic domain: index.html

Glutamate Dehydrogenase; Chain A, domain 3
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/1.10.285.10

Glutamate metabolism
type: KeggPathway
references: KEGG:MAP00251

Nitrogen metabolism
type: KeggPathway
references: KEGG:MAP00910

L-Glutamate
type: KeggSubstrate
references: KEGG:C00025
compound type: amino acids
compound type: carboxyl group
references: CHEBI:16015
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

H2O
type: KeggSubstrate
references: KEGG:C00001
compound type: H2O
references: CHEBI:15377
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

NAD+
type: KeggSubstrate
references: KEGG:C00003
compound type: amide group
compound type: amine group
compound type: nucleotide
references: CHEBI:15846
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

2-Oxoglutarate
type: KeggProduct
references: KEGG:C00026
compound type: carbohydrate
compound type: carboxyl group
references: CHEBI:30915
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

NH3
type: KeggProduct
references: KEGG:C00014
compound type: amine group
compound type: organic ion
references: CHEBI:16134
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

NADH
type: KeggProduct
references: KEGG:C00004
compound type: amide group
compound type: amine group
compound type: nucleotide
references: CHEBI:16908
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

H+
type: KeggProduct
references: KEGG:C00080
compound type: others
references: CHEBI:15378
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

1aupA02
type: Pdb
references: 1aup
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1aup
catalytic residue: LYS 125;ASP 165
comment: mutant K89I

1bgvA02
type: Pdb
references: 1bgv
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1bgv
catalytic residue: LYS 125;ASP 165

1hrdA02
type: Pdb
references: 1hrd
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1hrd
catalytic residue: LYS 125;ASP 165

1hrdB02
type: Pdb
references: 1hrd
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1hrd
catalytic residue: LYS 125;ASP 165

1hrdC02
type: Pdb
references: 1hrd
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1hrd
catalytic residue: LYS 125;ASP 165

1k89A02
type: Pdb
references: 1k89
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1k89
catalytic residue: LYS 125;ASP 165
comment: mutant K89I

Crystallization of an NAD+-dependent glutamate dehydrogenase from Clostridium symbiosum.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/3981633
journal: J Mol Biol
volume: 181
pages: 147-9
published year: 1985
authors:
  item: Rice DW
  item: Hornby DP
  item: Engel PC

The crystal structure of glutamate dehydrogenase from Clostridium symbiosum at 0.6 nm resolution.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/3593276
journal: Biochem J
volume: 242
pages: 789-95
published year: 1987
authors:
  item: Rice DW
  item: Baker PJ
  item: Farrants GW
  item: Hornby DP

http://ezcatdb.cbrc.jp/EzCatDB/reference/T00010#3
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/1764463
journal: Biochim Biophys Acta
volume: 1115
pages: 123-30
published year: 1991
authors:
  item: Syed SE
  item: Engel PC
  item: 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.

The essential active-site lysines of clostridial glutamate dehydrogenase. A study with pyridoxal-5'-phosphate.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/1633808
journal: Eur J Biochem
volume: 207
pages: 533-40
published year: 1992
authors:
  item: Lilley KS
  item: Engel PC

Effect of additives on the crystallization of glutamate dehydrogenase from Clostridium symbiosum. Evidence for a ligand-induced conformational change.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/1349042
journal: J Mol Biol
volume: 224
pages: 1181-4
published year: 1992
authors:
  item: Stillman TJ
  item: Baker PJ
  item: Britton KL
  item: Rice DW
  item: Rodgers HF

Subunit assembly and active site location in the structure of glutamate dehydrogenase.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (1.96 ANGSTROMS).
medline id: 92204934
references: http://www.ncbi.nlm.nih.gov/pubmed/1553382
journal: Proteins
volume: 12
pages: 75-86
published year: 1992
authors:
  item: Baker PJ
  item: Britton KL
  item: Engel PC
  item: Farrants GW
  item: Lilley KS
  item: Rice DW
  item: Stillman TJ
references: P24295

Conformational flexibility in glutamate dehydrogenase. Role of water in substrate recognition and catalysis.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
medline id: 94087726
references: http://www.ncbi.nlm.nih.gov/pubmed/8263917
journal: J Mol Biol
volume: 234
pages: 1131-9
published year: 1993
authors:
  item: Stillman TJ
  item: Baker PJ
  item: Britton KL
  item: Rice DW
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P24295

Evolution of substrate diversity in the superfamily of amino acid dehydrogenases. Prospects for rational chiral synthesis.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/8263939
journal: J Mol Biol
volume: 234
pages: 938-45
published year: 1993
authors:
  item: Britton KL
  item: Baker PJ
  item: Engel PC
  item: Rice DW
  item: Stillman TJ

Site and significance of chemically modifiable cysteine residues in glutamate dehydrogenase of Clostridium symbiosum and the use of protection studies to measure coenzyme binding.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/8129708
journal: Biochem J
volume: 298
pages: 107-13
published year: 1994
authors:
  item: Syed SE
  item: Hornby DP
  item: Brown PE
  item: Fitton JE
  item: Engel PC

The catalytic role of aspartate in the active site of glutamate dehydrogenase.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/8037659
journal: Biochem J
volume: 301
pages: 13-6
published year: 1994
authors:
  item: Dean JL
  item: Wang XG
  item: Teller JK
  item: Waugh ML
  item: Britton KL
  item: Baker PJ
  item: Stillman TJ
  item: Martin SR
  item: Rice DW
  item: Engel PC

The structure of Pyrococcus furiosus glutamate dehydrogenase reveals a key role for ion-pair networks in maintaining enzyme stability at extreme temperatures.
type: BibliographicResource
comment: X-ray crystallography
references: http://www.ncbi.nlm.nih.gov/pubmed/8591026
journal: Structure
volume: 3
pages: 1147-58
published year: 1995
authors:
  item: Yip KS
  item: Stillman TJ
  item: Britton KL
  item: Artymiuk PJ
  item: Baker PJ
  item: Sedelnikova SE
  item: Engel PC
  item: Pasquo A
  item: Chiaraluce R
  item: Consalvi V
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

Determinants of substrate specificity in the superfamily of amino acid dehydrogenases.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
medline id: 98070235
references: http://www.ncbi.nlm.nih.gov/pubmed/9405044
journal: Biochemistry
volume: 36
pages: 16109-15
published year: 1997
authors:
  item: Baker PJ
  item: Waugh ML
  item: Wang XG
  item: Stillman TJ
  item: Turnbull AP
  item: Engel PC
  item: Rice DW
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P24295

Alteration of the quaternary structure of glutamate dehydrogenase from Clostridium symbiosum by a single mutation distant from the subunit interfaces.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/9188163
journal: Eur Biophys J
volume: 25
pages: 417-22
published year: 1997
authors:
  item: Dean JL
  item: Colfen H
  item: Harding SE
  item: Rice DW
  item: Engel PC

Chemical rescue of the catalytically disabled clostridial glutamate dehydrogenase mutant D165S by fluoride ion.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/10333502
journal: Biochem J
volume: 340
pages: 555-60
published year: 1999
authors:
  item: Hayden BM
  item: Dean JL
  item: Martin SR
  item: Engel PC

Amino acid residues involved in the catalytic mechanism of NAD-dependent glutamate dehydrogenase from Halobacterium salinarum.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/10076069
journal: Biochim Biophys Acta
volume: 1426
pages: 513-25
published year: 1999
authors:
  item: Perez-Pomares F
  item: Ferrer J
  item: Camacho M
  item: Pire C
  item: LLorca F
  item: Bonete MJ

Identification of lysine residue involved in inactivation of brain glutamate dehydrogenase isoproteins by o-phthalaldehyde.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/10607407
journal: Biochimie
volume: 81
pages: 1123-9
published year: 1999
authors:
  item: Ahn JY
  item: Choi S
  item: Cho SW

Insights into the mechanism of domain closure and substrate specificity of glutamate dehydrogenase from Clostridium symbiosum.
type: BibliographicResource
comment: X-ray crystallography
references: http://www.ncbi.nlm.nih.gov/pubmed/9878450
journal: J Mol Biol
volume: 285
pages: 875-85
published year: 1999
authors:
  item: Stillman TJ
  item: Migueis AM
  item: Wang XG
  item: Baker PJ
  item: Britton KL
  item: Engel PC
  item: Rice DW
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

Electrochemical study of the effect of ADP and AMP on the kinetics of glutamate dehydrogenase.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/10790778
journal: Bioelectrochemistry
volume: 51
pages: 35-9
published year: 2000
authors:
  item: Dai HC
  item: Zhuang QK
  item: Li NQ
  item: Luo HX
  item: Gao XX

A new class of glutamate dehydrogenases (GDH). Biochemical and genetic characterization of the first member, the AMP-requiring NAD-specific GDH of Streptomyces clavuligerus.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/10924516
journal: J Biol Chem
volume: 275
pages: 39529-42
published year: 2000
authors:
  item: Minambres B
  item: Olivera ER
  item: Jensen RA
  item: Luengo JM

Construction, separation and properties of hybrid hexamers of glutamate dehydrogenase in which five of the six subunits are contributed by the catalytically inert D165S.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11231268
journal: Eur J Biochem
volume: 268
pages: 1173-80
published year: 2001
authors:
  item: Hayden BM
  item: Engel PC

Detection of multiple active site domain motions in transient-state component time courses of the Clostridium symbiosum L-glutamate dehydrogenase-catalyzed oxidative deamination reaction.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/12220195
journal: Biochemistry
volume: 41
pages: 11284-93
published year: 2002
authors:
  item: Tally JF
  item: Maniscalco SJ
  item: Saha SK
  item: Fisher HF

ReferenceForCatalyticMechanism
reference index: 7
reference section: Fig.5, p.1136-1138
reference step: 3

ReferenceForCatalyticMechanism
reference index: 15
reference section: Fig.6, p.524

ReferenceForCatalyticMechanism
reference index: 21