Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

NAD-specific glutamate dehydrogenase

Gene

gdh

Organism
Clostridium symbiosum (Bacteroides symbiosus)
Status
Reviewed-Annotation score: 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)1 Publication
  3. KM=61.1 mM for ammonium (at 25 degrees Celsius and at pH 7)1 Publication
  1. Vmax=125 µmol/min/mg enzyme for NADH (at 25 degrees Celsius and at pH 7)1 Publication
  2. Vmax=191 µmol/min/mg enzyme for 2-oxoglutarate (at 25 degrees Celsius and at pH 7)1 Publication
  3. Vmax=296 µmol/min/mg enzyme for ammonium (at 25 degrees Celsius and at pH 7)1 Publication

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei90 – 901Substrate1 Publication
Binding sitei111 – 1111Substrate1 Publication
Binding sitei114 – 1141Substrate1 Publication
Active sitei126 – 1261Proton donorPROSITE-ProRule annotation1 Publication
Binding sitei165 – 1651Substrate; via carbonyl oxygen1 Publication
Sitei166 – 1661Important for catalysisBy similarity
Binding sitei210 – 2101NADCurated
Binding sitei241 – 2411NADCurated
Binding sitei381 – 3811Substrate1 Publication

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

NAD

Enzyme and pathway databases

BRENDAi1.4.1.2. 772.
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 dehydrogenasePRO_0000182738Add
BLAST

Interactioni

Subunit structurei

Homohexamer.4 Publications

Structurei

Secondary structure

1
450
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi3 – 1513Combined sources
Turni16 – 183Combined sources
Helixi20 – 3112Combined sources
Helixi34 – 385Combined sources
Helixi41 – 455Combined sources
Helixi48 – 525Combined sources
Beta strandi56 – 6611Combined sources
Beta strandi72 – 8312Combined sources
Beta strandi85 – 9511Combined sources
Helixi101 – 11717Combined sources
Beta strandi119 – 1213Combined sources
Beta strandi124 – 1307Combined sources
Helixi138 – 15215Combined sources
Helixi153 – 1553Combined sources
Turni158 – 1603Combined sources
Beta strandi161 – 1644Combined sources
Helixi171 – 18515Combined sources
Helixi190 – 1923Combined sources
Beta strandi193 – 1953Combined sources
Helixi198 – 2003Combined sources
Turni204 – 2085Combined sources
Helixi209 – 22416Combined sources
Beta strandi233 – 2364Combined sources
Helixi241 – 25313Combined sources
Beta strandi259 – 2624Combined sources
Beta strandi265 – 2684Combined sources
Helixi276 – 28813Combined sources
Helixi294 – 3007Combined sources
Beta strandi303 – 3064Combined sources
Helixi310 – 3123Combined sources
Beta strandi316 – 3194Combined sources
Helixi329 – 3379Combined sources
Beta strandi342 – 3443Combined sources
Beta strandi347 – 3493Combined sources
Helixi353 – 3619Combined sources
Turni362 – 3643Combined sources
Beta strandi366 – 3683Combined sources
Helixi370 – 3734Combined sources
Helixi376 – 39015Combined sources
Helixi396 – 42025Combined sources
Helixi427 – 44620Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
ModBaseiSearch...
MobiDBiSearch...

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

        10         20         30         40         50
MSKYVDRVIA EVEKKYADEP EFVQTVEEVL SSLGPVVDAH PEYEEVALLE
60 70 80 90 100
RMVIPERVIE FRVPWEDDNG KVHVNTGYRV QFNGAIGPYK GGLRFAPSVN
110 120 130 140 150
LSIMKFLGFE QAFKDSLTTL PMGGAKGGSD FDPNGKSDRE VMRFCQAFMT
160 170 180 190 200
ELYRHIGPDI DVPAGDLGVG AREIGYMYGQ YRKIVGGFYN GVLTGKARSF
210 220 230 240 250
GGSLVRPEAT GYGSVYYVEA VMKHENDTLV GKTVALAGFG NVAWGAAKKL
260 270 280 290 300
AELGAKAVTL SGPDGYIYDP EGITTEEKIN YMLEMRASGR NKVQDYADKF
310 320 330 340 350
GVQFFPGEKP WGQKVDIIMP CATQNDVDLE QAKKIVANNV KYYIEVANMP
360 370 380 390 400
TTNEALRFLM QQPNMVVAPS KAVNAGGVLV SGFEMSQNSE RLSWTAEEVD
410 420 430 440 450
SKLHQVMTDI HDGSAAAAER YGLGYNLVAG ANIVGFQKIA DAMMAQGIAW
Length:450
Mass (Da):49,296
Last modified:January 23, 2007 - v4
Checksum:i993BB613288974E6
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti43 – 431Y → S AA sequence (PubMed:8129708).Curated
Sequence conflicti165 – 1651G → V AA sequence (PubMed:8129708).Curated
Sequence conflicti326 – 3261D → A AA sequence (PubMed:8129708).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z11747 Genomic DNA. Translation: CAA77805.1.
PIRiS22403.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z11747 Genomic DNA. Translation: CAA77805.1.
PIRiS22403.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

UniPathwayiUPA00533; UER00591.
BRENDAi1.4.1.2. 772.
SABIO-RKP24295.

Miscellaneous databases

EvolutionaryTraceiP24295.

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]
ProtoNetiSearch...

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: May 27, 2015
This is version 103 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.