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P24295 (DHE2_CLOSY) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 94. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
NAD-specific glutamate dehydrogenase

Short name=NAD-GDH
EC=1.4.1.2
Gene names
Name:gdh
OrganismClostridium symbiosum (Bacteroides symbiosus)
Taxonomic identifier1512 [NCBI]
Taxonomic lineageBacteriaFirmicutesClostridiaClostridialesClostridiaceaeClostridium

Protein attributes

Sequence length450 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence 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:

KM=10.8 µM for NADH (at 25 degrees Celsius and at pH 7) Ref.4

KM=0.31 mM for 2-oxoglutarate (at 25 degrees Celsius and at pH 7)

KM=61.1 mM for ammonium (at 25 degrees Celsius and at pH 7)

Vmax=125 µmol/min/mg enzyme for NADH (at 25 degrees Celsius and at pH 7)

Vmax=191 µmol/min/mg enzyme for 2-oxoglutarate (at 25 degrees Celsius and at pH 7)

Vmax=296 µmol/min/mg enzyme for ammonium (at 25 degrees Celsius and at pH 7)

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.4
Chain2 – 450449NAD-specific glutamate dehydrogenase
PRO_0000182738

Sites

Active site1261Proton donor Ref.7
Binding site901Substrate
Binding site1111Substrate
Binding site1141Substrate
Binding site1651Substrate; via carbonyl oxygen
Binding site2101NAD Probable
Binding site2411NAD Probable
Binding site3811Substrate
Site1661Important for catalysis By similarity
Site1661Important for catalytic activity

Experimental info

Mutagenesis901K → 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
Mutagenesis1661D → 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
Mutagenesis3811S → V: Dramatic reduction in the dehydrogenase activity with glutamate as the substrate; when associated with L-90. Ref.9
Sequence conflict431Y → S AA sequence Ref.5
Sequence conflict1651G → V AA sequence Ref.5
Sequence conflict3261D → A AA sequence Ref.5

Secondary structure

............................................................................. 450
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P24295 [UniParc].

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

FASTA45049,296
        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.
PIRS22403.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1AUPX-ray2.50A2-450[»]
1BGVX-ray1.90A2-450[»]
1HRDX-ray1.96A/B/C2-449[»]
1K89X-ray2.05A2-449[»]
2YFHX-ray2.70A/B/C/D/E/F1-450[»]
ProteinModelPortalP24295.
SMRP24295. Positions 2-450.
ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Enzyme and pathway databases

SABIO-RKP24295.
UniPathwayUPA00533; UER00591.

Family and domain databases

Gene3D3.40.50.720. 1 hit.
InterProIPR006095. 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]
PfamPF00208. ELFV_dehydrog. 1 hit.
PF02812. ELFV_dehydrog_N. 1 hit.
[Graphical view]
PIRSFPIRSF000185. Glu_DH. 1 hit.
PRINTSPR00082. GLFDHDRGNASE.
SMARTSM00839. ELFV_dehydrog. 1 hit.
[Graphical view]
PROSITEPS00074. GLFV_DEHYDROGENASE. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP24295.

Entry information

Entry nameDHE2_CLOSY
AccessionPrimary (citable) accession number: P24295
Entry history
Integrated into UniProtKB/Swiss-Prot: March 1, 1992
Last sequence update: January 23, 2007
Last modified: April 16, 2014
This is version 94 of the entry and version 4 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways