EzCatDB: T00011
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DB codeT00011
CATH domainDomain 11.10.287.140 : Helix Hairpins
Domain 23.40.192.10 : Leucine Dehydrogenase; Chain A, domain 1Catalytic domain
Domain 33.40.50.720 : Rossmann fold
E.C.1.4.1.3

CATH domainRelated DB codes (homologues)
3.40.192.10 : Leucine Dehydrogenase; Chain A, domain 1D00458,D00032,D00033,D00035,D00605,D00845,D00857,D00858,M00210,T00010,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,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,T00010,T00015,T00227,T00247,T00408,T00414,D00827,D00262,D00274,D00275,M00035,T00109

Enzyme Name
UniProtKBKEGG

P00366
Protein nameGlutamate dehydrogenase 1, mitochondrialglutamate dehydrogenase [NAD(P)+]
glutamic dehydrogenase
glutamate dehydrogenase [NAD(P)+]
SynonymsGDH
EC 1.4.1.3
RefSeqNP_872593.1 (Protein)
NM_182652.1 (DNA/RNA sequence)
PfamPF00208 (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 NumberP00366
Entry nameDHE3_BOVIN
ActivityL-glutamate + H(2)O + NAD(P)(+) = 2- oxoglutarate + NH(3) + NAD(P)H.
SubunitHomohexamer.
Subcellular locationMitochondrion matrix.
Cofactor

Compound table: links to PDB-related databases & PoSSuM

SubstratesProducts
KEGG-idC00025C00001C00003C00006C00026C00014C00080C00004C00005
CompoundL-GlutamateH2ONAD+NADP+2-OxoglutarateNH3H+NADHNADPH
Typeamino acids,carboxyl groupH2Oamide group,amine group,nucleotideamide group,amine group,nucleotidecarbohydrate,carboxyl groupamine group,organic ionothersamide group,amine group,nucleotideamide group,amine group,nucleotide
ChEBI16015
15377
15846
18009
30915
16134
15378
16908
16474
PubChem88747398
44272391
33032
962
22247451
5893
5886
51
222
1038
439153
5884
                 
1ch6A03Unbound UnboundUnboundUnboundUnbound UnboundUnbound
1ch6B03Unbound UnboundUnboundUnboundUnbound UnboundUnbound
1ch6C03Unbound UnboundUnboundUnboundUnbound UnboundUnbound
1ch6D03Unbound UnboundUnboundUnboundUnbound UnboundUnbound
1ch6E03Unbound UnboundUnboundUnboundUnbound UnboundUnbound
1ch6F03Unbound UnboundUnboundUnboundUnbound UnboundUnbound
1hwxA01Unbound UnboundUnboundUnboundUnbound UnboundUnbound
1hwxB01Unbound UnboundUnboundUnboundUnbound UnboundUnbound
1hwxC01Unbound UnboundUnboundUnboundUnbound UnboundUnbound
1hwxD01Unbound UnboundUnboundUnboundUnbound UnboundUnbound
1hwxE01Unbound UnboundUnboundUnboundUnbound UnboundUnbound
1hwxF01Unbound UnboundUnboundUnboundUnbound UnboundUnbound
1hwyA01Unbound UnboundUnboundUnboundUnbound UnboundUnbound
1hwyB01Unbound UnboundUnboundUnboundUnbound UnboundUnbound
1hwyC01Unbound UnboundUnboundUnboundUnbound UnboundUnbound
1hwyD01Unbound UnboundUnboundUnboundUnbound UnboundUnbound
1hwyE01Unbound UnboundUnboundUnboundUnbound UnboundUnbound
1hwyF01Unbound UnboundUnboundUnboundUnbound UnboundUnbound
1hwzA01Unbound UnboundUnboundUnboundUnbound UnboundUnbound
1hwzB01Unbound UnboundUnboundUnboundUnbound UnboundUnbound
1hwzC01Unbound UnboundUnboundUnboundUnbound UnboundUnbound
1hwzD01Unbound UnboundUnboundUnboundUnbound UnboundUnbound
1hwzE01Unbound UnboundUnboundUnboundUnbound UnboundUnbound
1hwzF01Unbound UnboundUnboundUnboundUnbound UnboundUnbound
1ch6A01Bound:GLU UnboundUnboundUnboundUnbound UnboundUnbound
1ch6B01Bound:GLU UnboundUnboundUnboundUnbound UnboundUnbound
1ch6C01Bound:GLU UnboundUnboundUnboundUnbound UnboundUnbound
1ch6D01Bound:GLU UnboundUnboundUnboundUnbound UnboundUnbound
1ch6E01Bound:GLU UnboundUnboundUnboundUnbound UnboundUnbound
1ch6F01Bound:GLU UnboundUnboundUnboundUnbound UnboundUnbound
1hwxA02Bound:GLU UnboundUnboundUnboundUnbound UnboundUnbound
1hwxB02Bound:GLU UnboundUnboundUnboundUnbound UnboundUnbound
1hwxC02Bound:GLU UnboundUnboundUnboundUnbound UnboundUnbound
1hwxD02Bound:GLU UnboundUnboundUnboundUnbound UnboundUnbound
1hwxE02Bound:GLU UnboundUnboundUnboundUnbound UnboundUnbound
1hwxF02Bound:GLU UnboundUnboundUnboundUnbound UnboundUnbound
1hwyA02Unbound UnboundUnboundBound:AKGUnbound UnboundUnbound
1hwyB02Unbound UnboundUnboundBound:AKGUnbound UnboundUnbound
1hwyC02Unbound UnboundUnboundBound:AKGUnbound UnboundUnbound
1hwyD02Unbound UnboundUnboundBound:AKGUnbound UnboundUnbound
1hwyE02Unbound UnboundUnboundBound:AKGUnbound UnboundUnbound
1hwyF02Unbound UnboundUnboundBound:AKGUnbound UnboundUnbound
1hwzA02Bound:GLU UnboundUnboundUnboundUnbound UnboundUnbound
1hwzB02Bound:GLU UnboundUnboundUnboundUnbound UnboundUnbound
1hwzC02Bound:GLU UnboundUnboundUnboundUnbound UnboundUnbound
1hwzD02Bound:GLU UnboundUnboundUnboundUnbound UnboundUnbound
1hwzE02Bound:GLU UnboundUnboundUnboundUnbound UnboundUnbound
1hwzF02Bound:GLU UnboundUnboundUnboundUnbound UnboundUnbound
1ch6A02Unbound Bound:NAD 551UnboundUnboundUnbound UnboundUnbound
1ch6B02Unbound Bound:NAD 561UnboundUnboundUnbound UnboundUnbound
1ch6C02Unbound Bound:NAD 571UnboundUnboundUnbound UnboundUnbound
1ch6D02Unbound Bound:NAD 581UnboundUnboundUnbound UnboundUnbound
1ch6E02Unbound Bound:NAD 591UnboundUnboundUnbound UnboundUnbound
1ch6F02Unbound Bound:NAD 601UnboundUnboundUnbound UnboundUnbound
1hwxA03Unbound UnboundUnboundUnboundUnbound Bound:NAI 17Unbound
1hwxB03Unbound UnboundUnboundUnboundUnbound Bound:NAI 14Unbound
1hwxC03Unbound UnboundUnboundUnboundUnbound Bound:NAI 20Unbound
1hwxD03Unbound UnboundUnboundUnboundUnbound Bound:NAI 19Unbound
1hwxE03Unbound UnboundUnboundUnboundUnbound Bound:NAI 15Unbound
1hwxF03Unbound UnboundUnboundUnboundUnbound Bound:NAI 21Unbound
1hwyA03Unbound Bound:NAD 38UnboundUnboundUnbound UnboundUnbound
1hwyB03Unbound Bound:NAD 40UnboundUnboundUnbound UnboundUnbound
1hwyC03Unbound Bound:NAD 37UnboundUnboundUnbound UnboundUnbound
1hwyD03Unbound Bound:NAD 41UnboundUnboundUnbound UnboundUnbound
1hwyE03Unbound Bound:NAD 42UnboundUnboundUnbound UnboundUnbound
1hwyF03Unbound Bound:NAD 33UnboundUnboundUnbound UnboundUnbound
1hwzA03Unbound UnboundUnboundUnboundUnbound UnboundBound:NDP
1hwzB03Unbound UnboundUnboundUnboundUnbound UnboundBound:NDP
1hwzC03Unbound UnboundUnboundUnboundUnbound UnboundBound:NDP
1hwzD03Unbound UnboundUnboundUnboundUnbound UnboundBound:NDP
1hwzE03Unbound UnboundUnboundUnboundUnbound UnboundBound:NDP
1hwzF03Unbound UnboundUnboundUnboundUnbound UnboundBound:NDP

Active-site residues
resource
Swiss-prot;P00366
pdbCatalytic residues
         
1ch6A03 
1ch6B03 
1ch6C03 
1ch6D03 
1ch6E03 
1ch6F03 
1hwxA01 
1hwxB01 
1hwxC01 
1hwxD01 
1hwxE01 
1hwxF01 
1hwyA01 
1hwyB01 
1hwyC01 
1hwyD01 
1hwyE01 
1hwyF01 
1hwzA01 
1hwzB01 
1hwzC01 
1hwzD01 
1hwzE01 
1hwzF01 
1ch6A01LYS 126
1ch6B01LYS 126
1ch6C01LYS 126
1ch6D01LYS 126
1ch6E01LYS 126
1ch6F01LYS 126
1hwxA02LYS 126
1hwxB02LYS 126
1hwxC02LYS 126
1hwxD02LYS 126
1hwxE02LYS 126
1hwxF02LYS 126
1hwyA02LYS 126
1hwyB02LYS 126
1hwyC02LYS 126
1hwyD02LYS 126
1hwyE02LYS 126
1hwyF02LYS 126
1hwzA02LYS 126
1hwzB02LYS 126
1hwzC02LYS 126
1hwzD02LYS 126
1hwzE02LYS 126
1hwzF02LYS 126
1ch6A02 
1ch6B02 
1ch6C02 
1ch6D02 
1ch6E02 
1ch6F02 
1hwxA03 
1hwxB03 
1hwxC03 
1hwxD03 
1hwxE03 
1hwxF03 
1hwyA03 
1hwyB03 
1hwyC03 
1hwyD03 
1hwyE03 
1hwyF03 
1hwzA03 
1hwzB03 
1hwzC03 
1hwzD03 
1hwzE03 
1hwzF03 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[2]Fig.4, p.8843
[4]p.2749-2751
[19]p.714

references
[1]
CommentsCHARACTERIZATION.
Medline ID74252258
PubMed ID4365183
JournalEur J Biochem
Year1974
Volume43
Pages319-25
AuthorsWitzemann V, Koberstein R, Sund H, Rasched I, Jornvall H, Noack K
TitleStudies of glutamate dehydrogenase: chemical modification and quantitative determination of tryptophan residues.
Related UniProtKBP00366
[2]
PubMed ID7024012
JournalInt J Biochem
Year1981
Volume13
Pages879-86
AuthorsGore MG
TitleL-Glutamic acid dehydrogenase.
[3]
PubMed ID6696727
JournalBiochem J
Year1984
Volume217
Pages327-30
AuthorsBell ET, Bell JE
TitleCatalytic activity of bovine glutamate dehydrogenase requires a hexamer structure.
[4]
PubMed ID6144102
JournalProc Natl Acad Sci U S A
Year1984
Volume81
Pages2747-51
AuthorsFisher HF, Viswanathan TS
TitleCarbonyl oxygen exchange evidence of imine formation in the glutamate dehydrogenase reaction and identification of the "occult role" of NADPH.
[5]
PubMed ID3442667
JournalBiochemistry
Year1987
Volume26
Pages8443-50
AuthorsBanerjee A, Levy HR, Levy GC, LiMuti C, Goldstein BM, Bell JE
TitleA transfer nuclear Overhauser effect study of coenzyme binding to distinct sites in binary and ternary complexes in glutamate dehydrogenase.
[6]
PubMed ID3569640
JournalInt J Biochem
Year1987
Volume19
Pages53-61
AuthorsPour-Rahimi F, Nemat-Gorgani M
TitleReversible association of ox liver glutamate dehydrogenase with the inner mitochondrial membrane.
[7]
PubMed ID3149742
JournalProtein Eng
Year1988
Volume2
Pages147-52
AuthorsMcPherson MJ, Baron AJ, Jones KM, Price GJ, Wootton JC
TitleMultiple interactions of lysine-128 of Escherichia coli glutamate dehydrogenase revealed by site-directed mutagenesis studies.
[8]
PubMed ID2575093
JournalJ Biochem (Tokyo)
Year1989
Volume106
Pages515-7
AuthorsNakajima N, Nakamura K, Esaki N, Tanaka H, Soda K
TitleEnzymatic in situ analysis by 1H-NMR of the hydrogen transfer stereospecificity of NAD(P)+-dependent dehydrogenases.
[9]
PubMed ID1743279
JournalFEBS Lett
Year1991
Volume294
Pages1-5
AuthorsFisher HF, Singh N
TitleTransduction of enzyme-ligand binding energy into catalytic driving force.
[10]
PubMed ID7961946
JournalJ Biol Chem
Year1994
Volume269
Pages29592-7
AuthorsSaha SK, Maniscalco SJ, Singh N, Fisher HF
TitleThe demonstration of a glutamate dehydrogenase-NADP-L-glutamate charge-transfer complex and its location on the reaction pathway.
[11]
PubMed ID9356294
JournalJ Struct Biol
Year1997
Volume120
Pages73-7
AuthorsPeterson PE, Pierce J, Smith TJ
TitleCrystallization and characterization of bovine liver glutamate dehydrogenase.
[12]
PubMed ID9772187
JournalBiochemistry
Year1998
Volume37
Pages14585-90
AuthorsManiscalco SJ, Saha SK, Fisher HF
TitleIdentification and characterization of kinetically competent carbinolamine and alpha-iminoglutarate complexes in the glutamate dehydrogenase-catalyzed oxidation of L-glutamate using a multiwavelength transient state approach.
[13]
PubMed ID10318805
JournalJ Biol Chem
Year1999
Volume274
Pages13948-53
AuthorsCho SW, Yoon HY
TitlePhotoaffinity labeling of brain glutamate dehydrogenase isoproteins with an azido-ADP.
[14]
CommentsX-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
Medline ID99354411
PubMed ID10425679
JournalStructure Fold Des
Year1999
Volume7
Pages769-82
AuthorsPeterson PE, Smith TJ
TitleThe structure of bovine glutamate dehydrogenase provides insights into the mechanism of allostery.
Related PDB1ch6,1hwx
Related UniProtKBP00366
[15]
PubMed ID11554732
JournalBiochem Biophys Res Commun
Year2001
Volume287
Pages343-7
AuthorsFisher HF, Maniscalco SJ, Tally J
TitleStabilization of noncovalent intermediates in enzymatically catalyzed reactions.
[16]
PubMed ID11327816
JournalBiochemistry
Year2001
Volume40
Pages1577-86
AuthorsMadhusoodanan KS, Colman RF
TitleAdenosine 5'-0-[S-(4-succinimidyl-benzophenone)thiophosphate]: a new photoaffinity label of the allosteric ADP site of bovine liver glutamate dehydrogenase.
[17]
PubMed ID11389722
JournalEur J Biochem
Year2001
Volume268
Pages3205-13
AuthorsCho SW, Yoon HY, Ahn JY, Lee EY, Lee J
TitleCassette mutagenesis of lysine 130 of human glutamate dehydrogenase. An essential residue in catalysis.
[18]
PubMed ID11686930
JournalJ Biochem (Tokyo)
Year2001
Volume130
Pages671-7
AuthorsGhobadi S, Safarian S, Moosavi-Movahedi AA, Ranjbar B
TitleOctyl glucoside induced formation of the molten globule-like state of glutamate dehydrogenase.
[19]
CommentsX-ray crystallography
PubMed ID11254391
JournalJ Mol Biol
Year2001
Volume307
Pages707-20
AuthorsSmith TJ, Peterson PE, Schmidt T, Fang J, Stanley CA
TitleStructures of bovine glutamate dehydrogenase complexes elucidate the mechanism of purine regulation.
Related PDB1hwy,1hwz
[20]
PubMed ID12324473
JournalJ Biol Chem
Year2002
Volume277
Pages46552-8
AuthorsZaganas I, Spanaki C, Karpusas M, Plaitakis A
TitleSubstitution of Ser for Arg-443 in the regulatory domain of human housekeeping (GLUD1) glutamate dehydrogenase virtually abolishes basal activity and markedly alters the activation of the enzyme by ADP and L-leucine.
[21]
PubMed ID11950837
JournalJ Biol Chem
Year2002
Volume277
Pages26422-8
AuthorsZaganas I, Plaitakis A
TitleSingle amino acid substitution (G456A) in the vicinity of the GTP binding domain of human housekeeping glutamate dehydrogenase markedly attenuates GTP inhibition and abolishes the cooperative behavior of the enzyme.
[22]
PubMed ID12054821
JournalJ Mol Biol
Year2002
Volume318
Pages765-77
AuthorsSmith TJ, Schmidt T, Fang J, Wu J, Siuzdak G, Stanley CA
TitleThe structure of apo human glutamate dehydrogenase details subunit communication and allostery.
Related PDB1l1f

comments
This enzyme has got a second coenzyme subsite for NAD(P), which seems to be involved in regulation.

createdupdated
2004-04-012009-02-26


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
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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