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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: L-glutamate degradation via hydroxyglutarate pathway

This protein is involved in step 1 of the subpathway that synthesizes crotonoyl-CoA from L-glutamate.
Proteins known to be involved in the 5 steps of the subpathway in this organism are:
  1. NAD-specific glutamate dehydrogenase (gdh)
  2. no protein annotated in this organism
  3. no protein annotated in this organism
  4. no protein annotated in this organism
  5. no protein annotated in this organism
This subpathway is part of the pathway L-glutamate degradation via hydroxyglutarate pathway, which is itself part of Amino-acid degradation.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes crotonoyl-CoA from L-glutamate, the pathway L-glutamate degradation via hydroxyglutarate pathway and in Amino-acid degradation.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei90Substrate1 Publication1
Binding sitei111Substrate1 Publication1
Binding sitei114Substrate1 Publication1
Active sitei126Proton donorPROSITE-ProRule annotation1 Publication1
Binding sitei165Substrate; via carbonyl oxygen1 Publication1
Sitei166Important for catalysisBy similarity1
Binding sitei210NADCurated1
Binding sitei241NADCurated1
Binding sitei381Substrate1 Publication1

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)DescriptionActionsGraphical viewLength
Mutagenesisi90K → 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 Publications1
Mutagenesisi166D → 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 Publication1
Mutagenesisi381S → V: Dramatic reduction in the dehydrogenase activity with glutamate as the substrate; when associated with L-90. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00001827382 – 450NAD-specific glutamate dehydrogenaseAdd BLAST449

Interactioni

Subunit structurei

Homohexamer.4 Publications

Protein-protein interaction databases

STRINGi742740.HMPREF9474_00114.

Structurei

Secondary structure

1450
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi3 – 15Combined sources13
Turni16 – 18Combined sources3
Helixi20 – 31Combined sources12
Helixi34 – 38Combined sources5
Helixi41 – 45Combined sources5
Helixi48 – 52Combined sources5
Beta strandi56 – 66Combined sources11
Beta strandi72 – 83Combined sources12
Beta strandi85 – 95Combined sources11
Helixi101 – 117Combined sources17
Beta strandi119 – 121Combined sources3
Beta strandi124 – 130Combined sources7
Helixi138 – 152Combined sources15
Helixi153 – 155Combined sources3
Turni158 – 160Combined sources3
Beta strandi161 – 164Combined sources4
Helixi171 – 185Combined sources15
Helixi190 – 192Combined sources3
Beta strandi193 – 195Combined sources3
Helixi198 – 200Combined sources3
Turni204 – 208Combined sources5
Helixi209 – 224Combined sources16
Beta strandi233 – 236Combined sources4
Helixi241 – 253Combined sources13
Beta strandi259 – 262Combined sources4
Beta strandi265 – 268Combined sources4
Helixi276 – 288Combined sources13
Helixi294 – 300Combined sources7
Beta strandi303 – 306Combined sources4
Helixi310 – 312Combined sources3
Beta strandi316 – 319Combined sources4
Helixi329 – 337Combined sources9
Beta strandi342 – 344Combined sources3
Beta strandi347 – 349Combined sources3
Helixi353 – 361Combined sources9
Turni362 – 364Combined sources3
Beta strandi366 – 368Combined sources3
Helixi370 – 373Combined sources4
Helixi376 – 390Combined sources15
Helixi396 – 420Combined sources25
Helixi427 – 446Combined sources20

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP24295.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105D82. Bacteria.
COG0334. LUCA.

Family and domain databases

CDDicd05313. NAD_bind_2_Glu_DH. 1 hit.
Gene3Di3.40.50.720. 1 hit.
InterProiIPR006095. Glu/Leu/Phe/Val_DH.
IPR033524. Glu/Leu/Phe/Val_DH_AS.
IPR006096. Glu/Leu/Phe/Val_DH_C.
IPR006097. Glu/Leu/Phe/Val_DH_dimer_dom.
IPR014362. Glu_DH.
IPR016040. NAD(P)-bd_dom.
IPR033922. NAD_bind_Glu_DH.
[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]
SUPFAMiSSF51735. SSF51735. 1 hit.
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)DescriptionActionsGraphical viewLength
Sequence conflicti43Y → S AA sequence (PubMed:8129708).Curated1
Sequence conflicti165G → V AA sequence (PubMed:8129708).Curated1
Sequence conflicti326D → A AA sequence (PubMed:8129708).Curated1

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
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi742740.HMPREF9474_00114.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Phylogenomic databases

eggNOGiENOG4105D82. Bacteria.
COG0334. LUCA.

Enzyme and pathway databases

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

Miscellaneous databases

EvolutionaryTraceiP24295.

Family and domain databases

CDDicd05313. NAD_bind_2_Glu_DH. 1 hit.
Gene3Di3.40.50.720. 1 hit.
InterProiIPR006095. Glu/Leu/Phe/Val_DH.
IPR033524. Glu/Leu/Phe/Val_DH_AS.
IPR006096. Glu/Leu/Phe/Val_DH_C.
IPR006097. Glu/Leu/Phe/Val_DH_dimer_dom.
IPR014362. Glu_DH.
IPR016040. NAD(P)-bd_dom.
IPR033922. NAD_bind_Glu_DH.
[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]
SUPFAMiSSF51735. SSF51735. 1 hit.
PROSITEiPS00074. GLFV_DEHYDROGENASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

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: November 30, 2016
This is version 117 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

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 one 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.