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P24295

- DHE2_CLOSY

UniProt

P24295 - DHE2_CLOSY

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Protein
NAD-specific glutamate dehydrogenase
Gene
gdh
Organism
Clostridium symbiosum (Bacteroides symbiosus)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

Catalytic activityi

L-glutamate + H2O + NAD+ = 2-oxoglutarate + NH3 + NADH.

Kineticsi

  1. KM=10.8 µM for NADH (at 25 degrees Celsius and at pH 7)1 Publication
  2. KM=0.31 mM for 2-oxoglutarate (at 25 degrees Celsius and at pH 7)
  3. 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)

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei90 – 901Substrate
Binding sitei111 – 1111Substrate
Binding sitei114 – 1141Substrate
Active sitei126 – 1261Proton donor1 Publication
Binding sitei165 – 1651Substrate; via carbonyl oxygen
Sitei166 – 1661Important for catalysis By similarity
Sitei166 – 1661Important for catalytic activity
Binding sitei210 – 2101NAD Inferred
Binding sitei241 – 2411NAD Inferred
Binding sitei381 – 3811Substrate

GO - Molecular functioni

  1. glutamate dehydrogenase (NAD+) activity Source: UniProtKB

GO - Biological processi

  1. cellular amino acid metabolic process Source: UniProtKB
  2. glutamate catabolic process via 2-hydroxyglutarate Source: UniProtKB-UniPathway
  3. oxidation-reduction process Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

NAD

Enzyme and pathway databases

SABIO-RKP24295.
UniPathwayiUPA00533; UER00591.

Names & Taxonomyi

Protein namesi
Recommended name:
NAD-specific glutamate dehydrogenase (EC:1.4.1.2)
Short name:
NAD-GDH
Gene namesi
Name:gdh
OrganismiClostridium symbiosum (Bacteroides symbiosus)
Taxonomic identifieri1512 [NCBI]
Taxonomic lineageiBacteriaFirmicutesClostridiaClostridialesLachnospiraceae

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi90 – 901K → 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. 2 Publications
Mutagenesisi166 – 1661D → S: Dramatic reduction in the dehydrogenase activity. Specific activity is decreased 1000-fold in the reductive amination reaction and 100000-fold for oxidative deamination. 1 Publication
Mutagenesisi381 – 3811S → V: Dramatic reduction in the dehydrogenase activity with glutamate as the substrate; when associated with L-90. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 450449NAD-specific glutamate dehydrogenase
PRO_0000182738Add
BLAST

Interactioni

Subunit structurei

Homohexamer.3 Publications

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi3 – 1513
Turni16 – 183
Helixi20 – 3112
Helixi34 – 385
Helixi41 – 455
Helixi48 – 525
Beta strandi56 – 6611
Beta strandi72 – 8312
Beta strandi85 – 9511
Helixi101 – 11717
Beta strandi119 – 1213
Beta strandi124 – 1307
Helixi138 – 15215
Helixi153 – 1553
Turni158 – 1603
Beta strandi161 – 1644
Helixi171 – 18515
Helixi190 – 1923
Beta strandi193 – 1953
Helixi198 – 2003
Turni204 – 2085
Helixi209 – 22416
Beta strandi233 – 2364
Helixi241 – 25313
Beta strandi259 – 2624
Beta strandi265 – 2684
Helixi276 – 28813
Helixi294 – 3007
Beta strandi303 – 3064
Helixi310 – 3123
Beta strandi316 – 3194
Helixi329 – 3379
Beta strandi342 – 3443
Beta strandi347 – 3493
Helixi353 – 3619
Beta strandi366 – 3683
Helixi370 – 3734
Helixi376 – 39015
Helixi396 – 42025
Helixi427 – 44620

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1AUPX-ray2.50A2-450[»]
1BGVX-ray1.90A2-450[»]
1HRDX-ray1.96A/B/C2-450[»]
1K89X-ray2.05A2-450[»]
2YFHX-ray2.70A/B/C/D/E/F1-450[»]
ProteinModelPortaliP24295.
SMRiP24295. Positions 2-450.

Miscellaneous databases

EvolutionaryTraceiP24295.

Family & Domainsi

Sequence similaritiesi

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
InterProiIPR006095. 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]
PfamiPF00208. ELFV_dehydrog. 1 hit.
PF02812. ELFV_dehydrog_N. 1 hit.
[Graphical view]
PIRSFiPIRSF000185. Glu_DH. 1 hit.
PRINTSiPR00082. GLFDHDRGNASE.
SMARTiSM00839. ELFV_dehydrog. 1 hit.
[Graphical view]
PROSITEiPS00074. GLFV_DEHYDROGENASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P24295-1 [UniParc]FASTAAdd to Basket

« Hide

MSKYVDRVIA EVEKKYADEP EFVQTVEEVL SSLGPVVDAH PEYEEVALLE    50
RMVIPERVIE FRVPWEDDNG KVHVNTGYRV QFNGAIGPYK GGLRFAPSVN 100
LSIMKFLGFE QAFKDSLTTL PMGGAKGGSD FDPNGKSDRE VMRFCQAFMT 150
ELYRHIGPDI DVPAGDLGVG AREIGYMYGQ YRKIVGGFYN GVLTGKARSF 200
GGSLVRPEAT GYGSVYYVEA VMKHENDTLV GKTVALAGFG NVAWGAAKKL 250
AELGAKAVTL SGPDGYIYDP EGITTEEKIN YMLEMRASGR NKVQDYADKF 300
GVQFFPGEKP WGQKVDIIMP CATQNDVDLE QAKKIVANNV KYYIEVANMP 350
TTNEALRFLM QQPNMVVAPS KAVNAGGVLV SGFEMSQNSE RLSWTAEEVD 400
SKLHQVMTDI HDGSAAAAER YGLGYNLVAG ANIVGFQKIA DAMMAQGIAW 450
Length:450
Mass (Da):49,296
Last modified:January 23, 2007 - v4
Checksum:i993BB613288974E6
GO

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti43 – 431Y → S AA sequence 1 Publication
Sequence conflicti165 – 1651G → V AA sequence 1 Publication
Sequence conflicti326 – 3261D → A AA sequence 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
Z11747 Genomic DNA. Translation: CAA77805.1.
PIRiS22403.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
Z11747 Genomic DNA. Translation: CAA77805.1 .
PIRi S22403.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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 2-450 [» ]
1K89 X-ray 2.05 A 2-450 [» ]
2YFH X-ray 2.70 A/B/C/D/E/F 1-450 [» ]
ProteinModelPortali P24295.
SMRi P24295. Positions 2-450.
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Enzyme and pathway databases

UniPathwayi UPA00533 ; UER00591 .
SABIO-RK P24295.

Miscellaneous databases

EvolutionaryTracei P24295.

Family and domain databases

Gene3Di 3.40.50.720. 1 hit.
InterProi 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 ]
Pfami PF00208. ELFV_dehydrog. 1 hit.
PF02812. ELFV_dehydrog_N. 1 hit.
[Graphical view ]
PIRSFi PIRSF000185. Glu_DH. 1 hit.
PRINTSi PR00082. GLFDHDRGNASE.
SMARTi SM00839. ELFV_dehydrog. 1 hit.
[Graphical view ]
PROSITEi PS00074. GLFV_DEHYDROGENASE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  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.

Entry informationi

Entry nameiDHE2_CLOSY
AccessioniPrimary (citable) accession number: P24295
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 1, 1992
Last sequence update: January 23, 2007
Last modified: September 3, 2014
This is version 97 of the entry and version 4 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Direct protein sequencing

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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