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P24295

- DHE2_CLOSY

UniProt

P24295 - DHE2_CLOSY

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
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    • History
      Entry version 98 (01 Oct 2014)
      Sequence version 4 (23 Jan 2007)
      Previous versions | rss
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    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

    Vmax=125 µmol/min/mg enzyme for NADH (at 25 degrees Celsius and at pH 7)1 Publication

    Vmax=191 µmol/min/mg enzyme for 2-oxoglutarate (at 25 degrees Celsius and at pH 7)1 Publication

    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 donor1 PublicationPROSITE-ProRule annotation
    Binding sitei165 – 1651Substrate; via carbonyl oxygen1 Publication
    Sitei166 – 1661Important for catalysisBy similarity
    Sitei166 – 1661Important for catalytic activity
    Binding sitei210 – 2101NADCurated
    Binding sitei241 – 2411NADCurated
    Binding sitei381 – 3811Substrate1 Publication

    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

    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 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 – 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.
    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

    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

    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:
    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: October 1, 2014
    This is version 98 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