NAD-specific glutamate dehydrogenase

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P24295 (DHE2_CLOSY) Reviewed, UniProtKB/Swiss-Prot

Last modified April 3, 2013. Version 90. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
NAD-specific glutamate dehydrogenase
Short name=NAD-GDH
EC=1.4.1.2

Gene names

Name:

gdh

Organism

Clostridium symbiosum (Bacteroides symbiosus)

Taxonomic identifier

1512 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Clostridia › Clostridiales › Clostridiaceae › Clostridium

Protein attributes

Sequence length	450 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Catalytic activity	L-glutamate + H₂O + NAD⁺ = 2-oxoglutarate + NH₃ + NADH.
Pathway	Amino-acid degradation; L-glutamate degradation via hydroxyglutarate pathway; crotonoyl-CoA from L-glutamate: step 1/5.
Subunit structure	Homohexamer. Ref.6 Ref.9 Ref.11
Sequence similarities	Belongs to the Glu/Leu/Phe/Val dehydrogenases family.
Biophysicochemical properties	Kinetic parameters: K_M=10.8 µM for NADH (at 25 degrees Celsius and at pH 7) Ref.4 K_M=0.31 mM for 2-oxoglutarate (at 25 degrees Celsius and at pH 7) K_M=61.1 mM for ammonium (at 25 degrees Celsius and at pH 7) V_max=125 µmol/min/mg enzyme for NADH (at 25 degrees Celsius and at pH 7) V_max=191 µmol/min/mg enzyme for 2-oxoglutarate (at 25 degrees Celsius and at pH 7) V_max=296 µmol/min/mg enzyme for ammonium (at 25 degrees Celsius and at pH 7)

Ontologies

Keywords
Ligand	NAD
Molecular function	Oxidoreductase
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological_process	cellular amino acid metabolic process Inferred from sequence or structural similarity. Source: UniProtKB glutamate catabolic process via 2-hydroxyglutarate Inferred from electronic annotation. Source: UniProtKB-UniPathway
Molecular_function	glutamate dehydrogenase (NAD+) activity Inferred from sequence or structural similarity. Source: UniProtKB nucleotide binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed Ref.4

Chain

2 – 450

449

NAD-specific glutamate dehydrogenase

PRO_0000182738

Sites

Active site

126

Proton donor Ref.7

Binding site

Substrate

Binding site

111

Substrate

Binding site

114

Substrate

Binding site

165

Substrate; via carbonyl oxygen

Binding site

210

NAD Probable

Binding site

241

NAD Probable

Binding site

381

Substrate

Site

166

Important for catalysis By similarity

Site

166

Important for catalytic activity

Experimental info

Mutagenesis

K → L: Increased substrate activity for methionine and norleucine but negligible activity with either glutamate or leucine. Dramatic reduction in the dehydrogenase activity with glutamate as the substrate; when associated with V-381. Ref.9 Ref.10

Mutagenesis

166

D → S: Dramatic reduction in the dehydrogenase activity. Specific activity is decreased 1000-fold in the reductive amination reaction and 100000-fold for oxidative deamination. Ref.4

Mutagenesis

381

S → V: Dramatic reduction in the dehydrogenase activity with glutamate as the substrate; when associated with L-90. Ref.9

Sequence conflict

Y → S AA sequence Ref.5

Sequence conflict

165

G → V AA sequence Ref.5

Sequence conflict

326

D → A AA sequence Ref.5

Secondary structure

450

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P24295 [UniParc].

Last modified January 23, 2007. Version 4.
Checksum: 993BB613288974E6
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FASTA

450

49,296

        10         20         30         40         50         60 
MSKYVDRVIA EVEKKYADEP EFVQTVEEVL SSLGPVVDAH PEYEEVALLE RMVIPERVIE 

        70         80         90        100        110        120 
FRVPWEDDNG KVHVNTGYRV QFNGAIGPYK GGLRFAPSVN LSIMKFLGFE QAFKDSLTTL 

       130        140        150        160        170        180 
PMGGAKGGSD FDPNGKSDRE VMRFCQAFMT ELYRHIGPDI DVPAGDLGVG AREIGYMYGQ 

       190        200        210        220        230        240 
YRKIVGGFYN GVLTGKARSF GGSLVRPEAT GYGSVYYVEA VMKHENDTLV GKTVALAGFG 

       250        260        270        280        290        300 
NVAWGAAKKL AELGAKAVTL SGPDGYIYDP EGITTEEKIN YMLEMRASGR NKVQDYADKF 

       310        320        330        340        350        360 
GVQFFPGEKP WGQKVDIIMP CATQNDVDLE QAKKIVANNV KYYIEVANMP TTNEALRFLM 

       370        380        390        400        410        420 
QQPNMVVAPS KAVNAGGVLV SGFEMSQNSE RLSWTAEEVD SKLHQVMTDI HDGSAAAAER 

       430        440        450 
YGLGYNLVAG ANIVGFQKIA DAMMAQGIAW

« Hide

References

[1]	"The glutamate dehydrogenase gene of Clostridium symbiosum. Cloning by polymerase chain reaction, sequence analysis and over-expression in Escherichia coli." Teller J.K., Smith R.M., McPherson M.J., Engel P.C., Guest J.R. Eur. J. Biochem. 206:151-159(1992) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"The partial amino acid sequence of the NAD(+)-dependent glutamate dehydrogenase of Clostridium symbiosum: implications for the evolution and structural basis of coenzyme specificity." Lilley K.S., Baker P.J., Britton K.L., Stillman T.J., Brown P.E., Moir A.J.G., Engel P.C., Rice D.W., Bell J.E., Bell E. Biochim. Biophys. Acta 1080:191-197(1991) [PubMed] [Europe PMC] [Abstract] Cited for: PRELIMINARY PARTIAL PROTEIN SEQUENCE.
[3]	"The essential active-site lysines of clostridial glutamate dehydrogenase. A study with pyridoxal-5'-phosphate." Lilley K.S., Engel P.C. Eur. J. Biochem. 207:533-540(1992) [PubMed] [Europe PMC] [Abstract] Cited for: PARTIAL PROTEIN SEQUENCE, MODIFICATION OF SOME LYSINES.
[4]	"The catalytic role of aspartate in the active site of glutamate dehydrogenase." Dean J.L., Wang X.G., Teller J.K., Waugh M.L., Britton K.L., Baker P.J., Stillman T.J., Martin S.R., Rice D.W., Engel P.C. Biochem. J. 301:13-16(1994) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-11, MUTAGENESIS OF ASP-166, BIOPHYSICOCHEMICAL PROPERTIES.
[5]	"Site and significance of chemically modifiable cysteine residues in glutamate dehydrogenase of Clostridium symbiosum and the use of protection studies to measure coenzyme binding." Syed S.E., Hornby D.P., Brown P.E., Fitton J.E., Engel P.C. Biochem. J. 298:107-113(1994) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 26-46; 154-158; 165-182 AND 325-339.
[6]	"Subunit assembly and active site location in the structure of glutamate dehydrogenase." Baker P.J., Britton K.L., Engel P.C., Farrants G.W., Lilley K.S., Rice D.W., Stillman T.J. Proteins 12:75-86(1992) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.96 ANGSTROMS), SUBUNIT.
[7]	"Conformational flexibility in glutamate dehydrogenase. Role of water in substrate recognition and catalysis." Stillman T.J., Baker P.J., Britton K.L., Rice D.W. J. Mol. Biol. 234:1131-1139(1993) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) OF 2-450 IN COMPLEX WITH SUBSTRATE, ACTIVE SITE.
[8]	"The structure of Pyrococcus furiosus glutamate dehydrogenase reveals a key role for ion-pair networks in maintaining enzyme stability at extreme temperatures." Yip K.S.P., Stillman T.J., Britton K.L., Artymiuk P.J., Baker P.J., Sedelnikova S.E., Engel P.C., Pasquo A., Chiaraluce R., Consalvi V., Scandurra R., Rice D.W. Structure 3:1147-1158(1995) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.96 ANGSTROMS) OF 2-449.
[9]	"Determinants of substrate specificity in the superfamily of amino acid dehydrogenases." Baker P.J., Waugh M.L., Wang X.G., Stillman T.J., Turnbull A.P., Engel P.C., Rice D.W. Biochemistry 36:16109-16115(1997) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 2-450, MUTAGENESIS OF LYS-90 AND SER-381, SUBSTRATE SPECIFICITY, SUBUNIT.
[10]	"Insights into the mechanism of domain closure and substrate specificity of glutamate dehydrogenase from Clostridium symbiosum." Stillman T.J., Migueis A.M., Wang X.G., Baker P.J., Britton K.L., Engel P.C., Rice D.W. J. Mol. Biol. 285:875-885(1999) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) OF 2-449 OF MUTANT LEU-90, SUBSTRATE SPECIFICITY, MUTAGENESIS OF LYS-90.
[11]	"Structural determinants of cofactor specificity and domain flexibility in bacterial glutamate dehydrogenases." Oliveira T., Sharkey M.A., Hamza M., Engel P.C., Khan A.R. Submitted (APR-2011) to the PDB data bank Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS), SUBUNIT.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

Z11747 Genomic DNA. Translation: CAA77805.1.

PIR

S22403.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1AUP	X-ray	2.50	A	2-450	[»]
1BGV	X-ray	1.90	A	2-450	[»]
1HRD	X-ray	1.96	A/B/C	2-449	[»]
1K89	X-ray	2.05	A	2-449	[»]
2YFH	X-ray	2.70	A/B/C/D/E/F	1-450	[»]

ProteinModelPortal

P24295.

SMR

P24295. Positions 2-450.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Enzyme and pathway databases

SABIO-RK

P24295.

UniPathway

UPA00533; UER00591.

Family and domain databases

Gene3D

3.40.50.720. 1 hit.

InterPro

IPR006095. Glu/Leu/Phe/Val_DH.
IPR006096. Glu/Leu/Phe/Val_DH_C.
IPR006097. Glu/Leu/Phe/Val_DH_dimer_dom.
IPR014362. Glu_DH.
IPR016040. NAD(P)-bd_dom.
[Graphical view]

Pfam

PF00208. ELFV_dehydrog. 1 hit.
PF02812. ELFV_dehydrog_N. 1 hit.
[Graphical view]

PIRSF

PIRSF000185. Glu_DH. 1 hit.

PRINTS

PR00082. GLFDHDRGNASE.

SMART

SM00839. ELFV_dehydrog. 1 hit.
[Graphical view]

PROSITE

PS00074. GLFV_DEHYDROGENASE. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P24295.

Entry information

Entry name

DHE2_CLOSY

Accession

Primary (citable) accession number: P24295

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 1, 1992
Last sequence update:	January 23, 2007
Last modified:	April 3, 2013
This is version 90 of the entry and version 4 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Sites

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protocols and materials databases

Enzyme and pathway databases

Family and domain databases

Other

Entry information

Relevant documents