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Protein

Catabolic NAD-specific glutamate dehydrogenase RocG

Gene

rocG

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Devoted to catabolic function of glutamate (and other amino acids of the glutamate family) utilization as sole nitrogen source. It is not involved in anabolic function of glutamate biosynthesis since B.subtilis possesses only one route of glutamate biosynthesis from ammonia, catalyzed by glutamate synthase. RocG is unable to utilize glutamate or glutamine as sole carbon source and to synthesize glutamate, but it is involved in the utilization of arginine, and proline as carbon or nitrogen source. The catabolic RocG is essential for controlling gltAB expression via an inhibitory interactions with the transcriptional regulator GltC in response to the availability of sugars.3 Publications

Catalytic activityi

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

Kineticsi

  1. KM=0.08 mM for NAD (at 37 degrees Celsius and at pH 7.3)2 Publications
  2. KM=0.34 mM for L-glutamate (at 37 degrees Celsius and at pH 7.3)2 Publications
  3. KM=2.9 mM for L-glutamate (at 37 degrees Celsius and at pH 7.3)2 Publications
  4. KM=0.65 mM for 2-oxoglutarate (at 37 degrees Celsius and at pH 7.3)2 Publications
  5. KM=2.9 mM for L-glutamate (at pH 7.3)2 Publications
  6. KM=18.5 mM for ammonium (at pH 7.7)2 Publications
  7. KM=55.6 mM for ammonium (at 37 degrees Celsius and at pH 7.3)2 Publications

    pH dependencei

    Optimum pH is 7.7 and 7.3 for L-glutamate deamination and 2-oxoglutarate amination, respectively. Half-maximal activity for deamination is observed at pH 6.9 and 7.8 and that for amination is at pH 6.9 and 7.8.2 Publications

    Temperature dependencei

    Low thermostability at 41 degrees Celsius due to the dissociation of the hexamer.2 Publications

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei80SubstrateBy similarity1
    Binding sitei104SubstrateBy similarity1
    Active sitei116Proton donorPROSITE-ProRule annotation1
    Sitei156Important for catalysisBy similarity1
    Binding sitei200NADBy similarity1
    Binding sitei231NADBy similarity1
    Binding sitei358SubstrateBy similarity1

    GO - Molecular functioni

    • glutamate dehydrogenase (NAD+) activity Source: UniProtKB

    GO - Biological processi

    • cellular amino acid metabolic process Source: UniProtKB
    • oxidation-reduction process Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Ligandi

    NAD

    Enzyme and pathway databases

    BioCyciBSUB:BSU37790-MONOMER.
    BRENDAi1.4.1.2. 658.
    SABIO-RKP39633.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Catabolic NAD-specific glutamate dehydrogenase RocG (EC:1.4.1.2)
    Short name:
    NAD-GDH
    Alternative name(s):
    Glutamate dehydrogenase
    Short name:
    GlutDH
    Trigger enzyme RocG
    Gene namesi
    Name:rocG
    Synonyms:gudA, yweB
    Ordered Locus Names:BSU37790
    ORF Names:ipa-75d
    OrganismiBacillus subtilis (strain 168)
    Taxonomic identifieri224308 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
    Proteomesi
    • UP000001570 Componenti: Chromosome

    Pathology & Biotechi

    Disruption phenotypei

    Cells lacking this gene lose the ability to utilize proline, ornithine, or arginine as sole carbon source and grow more slowly when proline or ornithine is utilized as sole nitrogen source.1 Publication

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi27E → F: Increase of thermostability 8 degrees Celsius higher than that of the wild-type. 1 Publication1
    Mutagenesisi93E → K: Reduces the affinity for glutamate and ammonium. 1 Publication1
    Mutagenesisi122D → N: Unable to control gltAB expression via an inhibitory interactions with the transcriptional regulator GltC. Reduces the affinity for glutamate and ammonium. 1 Publication1
    Mutagenesisi144Q → R: Increase of thermostability 20 degrees Celsius higher than that of the wild-type. 1 Publication1
    Mutagenesisi158Y → H: Reduces the affinity for glutamate and ammonium. 1 Publication1
    Mutagenesisi234S → R: Reduces the affinity for glutamate and ammonium. 1 Publication1
    Mutagenesisi324A → R: No effect. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001827351 – 424Catabolic NAD-specific glutamate dehydrogenase RocGAdd BLAST424

    Proteomic databases

    PaxDbiP39633.

    Expressioni

    Inductioni

    Expression depends on the alternative sigma-L factor and the transcription factor RocR. Induced by arginine, ornithine, or to a lesser extent proline. Repressed by glucose.3 Publications

    Interactioni

    Subunit structurei

    Homohexamer.2 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    gltCP206682EBI-1642022,EBI-1642006

    Protein-protein interaction databases

    IntActiP39633. 1 interactor.
    STRINGi224308.Bsubs1_010100020411.

    Structurei

    Secondary structure

    1424
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi8 – 31Combined sources24
    Helixi36 – 42Combined sources7
    Beta strandi46 – 56Combined sources11
    Beta strandi62 – 71Combined sources10
    Beta strandi75 – 80Combined sources6
    Beta strandi83 – 86Combined sources4
    Helixi91 – 107Combined sources17
    Beta strandi113 – 120Combined sources8
    Helixi123 – 125Combined sources3
    Helixi128 – 142Combined sources15
    Helixi143 – 145Combined sources3
    Turni148 – 150Combined sources3
    Helixi161 – 175Combined sources15
    Helixi180 – 182Combined sources3
    Helixi188 – 190Combined sources3
    Turni194 – 198Combined sources5
    Helixi199 – 214Combined sources16
    Helixi219 – 221Combined sources3
    Beta strandi223 – 227Combined sources5
    Helixi231 – 243Combined sources13
    Beta strandi246 – 251Combined sources6
    Beta strandi256 – 258Combined sources3
    Helixi265 – 271Combined sources7
    Beta strandi274 – 276Combined sources3
    Helixi279 – 281Combined sources3
    Helixi288 – 293Combined sources6
    Beta strandi297 – 301Combined sources5
    Turni310 – 312Combined sources3
    Helixi313 – 315Combined sources3
    Beta strandi319 – 322Combined sources4
    Beta strandi325 – 327Combined sources3
    Helixi331 – 339Combined sources9
    Beta strandi343 – 345Combined sources3
    Helixi347 – 350Combined sources4
    Helixi353 – 367Combined sources15
    Helixi373 – 398Combined sources26
    Helixi402 – 420Combined sources19

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3K92X-ray2.30A/B/C/D/E/F1-424[»]
    ProteinModelPortaliP39633.
    SMRiP39633.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP39633.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105D82. Bacteria.
    COG0334. LUCA.
    HOGENOMiHOG000243801.
    InParanoidiP39633.
    KOiK00260.
    OMAiVAQDNKV.
    PhylomeDBiP39633.

    Family and domain databases

    CDDicd01076. NAD_bind_1_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.

    P39633-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSAKQVSKDE EKEALNLFLS TQTIIKEALR KLGYPGDMYE LMKEPQRMLT
    60 70 80 90 100
    VRIPVKMDNG SVKVFTGYRS QHNDAVGPTK GGVRFHPEVN EEEVKALSIW
    110 120 130 140 150
    MTLKCGIANL PYGGGKGGII CDPRTMSFGE LERLSRGYVR AISQIVGPTK
    160 170 180 190 200
    DIPAPDVYTN SQIMAWMMDE YSRLREFDSP GFITGKPLVL GGSQGRETAT
    210 220 230 240 250
    AQGVTICIEE AVKKKGIKLQ NARIIIQGFG NAGSFLAKFM HDAGAKVIGI
    260 270 280 290 300
    SDANGGLYNP DGLDIPYLLD KRDSFGMVTN LFTDVITNEE LLEKDCDILV
    310 320 330 340 350
    PAAISNQITA KNAHNIQASI VVEAANGPTT IDATKILNER GVLLVPDILA
    360 370 380 390 400
    SAGGVTVSYF EWVQNNQGYY WSEEEVAEKL RSVMVSSFET IYQTAATHKV
    410 420
    DMRLAAYMTG IRKSAEASRF RGWV
    Length:424
    Mass (Da):46,553
    Last modified:July 28, 2009 - v3
    Checksum:i019AE0A833BE48DD
    GO

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti324A → R in CAA51631 (PubMed:7934828).Curated1
    Sequence conflicti419 – 424RFRGWV → FPRMGLI in CAA51631 (PubMed:7934828).Curated6

    Mass spectrometryi

    Molecular mass is 46587 Da from positions 1 - 424. Determined by MALDI. 1 Publication

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X73124 Genomic DNA. Translation: CAA51631.1.
    AB194695 Genomic DNA. Translation: BAD69594.1.
    AL009126 Genomic DNA. Translation: CAB15806.2.
    S79622 Genomic DNA. No translation available.
    PIRiA70055.
    RefSeqiNP_391659.2. NC_000964.3.
    WP_003227482.1. NZ_JNCM01000034.1.

    Genome annotation databases

    EnsemblBacteriaiCAB15806; CAB15806; BSU37790.
    GeneIDi937066.
    KEGGibsu:BSU37790.
    PATRICi18979598. VBIBacSub10457_3961.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X73124 Genomic DNA. Translation: CAA51631.1.
    AB194695 Genomic DNA. Translation: BAD69594.1.
    AL009126 Genomic DNA. Translation: CAB15806.2.
    S79622 Genomic DNA. No translation available.
    PIRiA70055.
    RefSeqiNP_391659.2. NC_000964.3.
    WP_003227482.1. NZ_JNCM01000034.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3K92X-ray2.30A/B/C/D/E/F1-424[»]
    ProteinModelPortaliP39633.
    SMRiP39633.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    IntActiP39633. 1 interactor.
    STRINGi224308.Bsubs1_010100020411.

    Proteomic databases

    PaxDbiP39633.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiCAB15806; CAB15806; BSU37790.
    GeneIDi937066.
    KEGGibsu:BSU37790.
    PATRICi18979598. VBIBacSub10457_3961.

    Phylogenomic databases

    eggNOGiENOG4105D82. Bacteria.
    COG0334. LUCA.
    HOGENOMiHOG000243801.
    InParanoidiP39633.
    KOiK00260.
    OMAiVAQDNKV.
    PhylomeDBiP39633.

    Enzyme and pathway databases

    BioCyciBSUB:BSU37790-MONOMER.
    BRENDAi1.4.1.2. 658.
    SABIO-RKP39633.

    Miscellaneous databases

    EvolutionaryTraceiP39633.

    Family and domain databases

    CDDicd01076. NAD_bind_1_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_BACSU
    AccessioniPrimary (citable) accession number: P39633
    Secondary accession number(s): Q53548, Q5W7E9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: July 28, 2009
    Last modified: November 30, 2016
    This is version 121 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Bacillus subtilis
      Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
    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.