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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)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei80 – 801SubstrateBy similarity
    Binding sitei104 – 1041SubstrateBy similarity
    Active sitei116 – 1161Proton donorPROSITE-ProRule annotation
    Sitei156 – 1561Important for catalysisBy similarity
    Binding sitei200 – 2001NADBy similarity
    Binding sitei231 – 2311NADBy similarity
    Binding sitei358 – 3581SubstrateBy similarity

    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)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi27 – 271E → F: Increase of thermostability 8 degrees Celsius higher than that of the wild-type. 1 Publication
    Mutagenesisi93 – 931E → K: Reduces the affinity for glutamate and ammonium. 1 Publication
    Mutagenesisi122 – 1221D → N: Unable to control gltAB expression via an inhibitory interactions with the transcriptional regulator GltC. Reduces the affinity for glutamate and ammonium. 1 Publication
    Mutagenesisi144 – 1441Q → R: Increase of thermostability 20 degrees Celsius higher than that of the wild-type. 1 Publication
    Mutagenesisi158 – 1581Y → H: Reduces the affinity for glutamate and ammonium. 1 Publication
    Mutagenesisi234 – 2341S → R: Reduces the affinity for glutamate and ammonium. 1 Publication
    Mutagenesisi324 – 3241A → R: No effect. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 424424Catabolic NAD-specific glutamate dehydrogenase RocGPRO_0000182735Add
    BLAST

    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 extend 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 interaction.
    STRINGi224308.Bsubs1_010100020411.

    Structurei

    Secondary structure

    1
    424
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi8 – 3124Combined sources
    Helixi36 – 427Combined sources
    Beta strandi46 – 5611Combined sources
    Beta strandi62 – 7110Combined sources
    Beta strandi75 – 806Combined sources
    Beta strandi83 – 864Combined sources
    Helixi91 – 10717Combined sources
    Beta strandi113 – 1208Combined sources
    Helixi123 – 1253Combined sources
    Helixi128 – 14215Combined sources
    Helixi143 – 1453Combined sources
    Turni148 – 1503Combined sources
    Helixi161 – 17515Combined sources
    Helixi180 – 1823Combined sources
    Helixi188 – 1903Combined sources
    Turni194 – 1985Combined sources
    Helixi199 – 21416Combined sources
    Helixi219 – 2213Combined sources
    Beta strandi223 – 2275Combined sources
    Helixi231 – 24313Combined sources
    Beta strandi246 – 2516Combined sources
    Beta strandi256 – 2583Combined sources
    Helixi265 – 2717Combined sources
    Beta strandi274 – 2763Combined sources
    Helixi279 – 2813Combined sources
    Helixi288 – 2936Combined sources
    Beta strandi297 – 3015Combined sources
    Turni310 – 3123Combined sources
    Helixi313 – 3153Combined sources
    Beta strandi319 – 3224Combined sources
    Beta strandi325 – 3273Combined sources
    Helixi331 – 3399Combined sources
    Beta strandi343 – 3453Combined sources
    Helixi347 – 3504Combined sources
    Helixi353 – 36715Combined sources
    Helixi373 – 39826Combined sources
    Helixi402 – 42019Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3K92X-ray2.30A/B/C/D/E/F1-424[»]
    ProteinModelPortaliP39633.
    SMRiP39633. Positions 7-424.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP39633.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105D82. Bacteria.
    COG0334. LUCA.
    HOGENOMiHOG000243801.
    InParanoidiP39633.
    KOiK00260.
    OMAiCPDVIAN.
    OrthoDBiEOG65XN4D.
    PhylomeDBiP39633.

    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]
    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)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti324 – 3241A → R in CAA51631 (PubMed:7934828).Curated
    Sequence conflicti419 – 4246RFRGWV → FPRMGLI in CAA51631 (PubMed:7934828).Curated

    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
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3K92X-ray2.30A/B/C/D/E/F1-424[»]
    ProteinModelPortaliP39633.
    SMRiP39633. Positions 7-424.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    IntActiP39633. 1 interaction.
    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.
    OMAiCPDVIAN.
    OrthoDBiEOG65XN4D.
    PhylomeDBiP39633.

    Enzyme and pathway databases

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

    Miscellaneous databases

    EvolutionaryTraceiP39633.

    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]
    SUPFAMiSSF51735. SSF51735. 1 hit.
    PROSITEiPS00074. GLFV_DEHYDROGENASE. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: 168.
    2. "Low thermostability of the NAD+ specific glutamate dehydrogenase from Bacillus subtilis ISW1214: cloning, purification and characterization."
      Khan M.H., Itoh K., Kim H., Ashida H., Ishikawa T., Shibata H., Sawa Y.
      Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ISW1214.
    3. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
      Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
      , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
      Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: 168.
    4. "From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later."
      Barbe V., Cruveiller S., Kunst F., Lenoble P., Meurice G., Sekowska A., Vallenet D., Wang T., Moszer I., Medigue C., Danchin A.
      Microbiology 155:1758-1775(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: SEQUENCE REVISION TO 324.
    5. "Molecular properties and enhancement of thermostability by random mutagenesis of glutamate dehydrogenase from Bacillus subtilis."
      Khan M.I., Ito K., Kim H., Ashida H., Ishikawa T., Shibata H., Sawa Y.
      Biosci. Biotechnol. Biochem. 69:1861-1870(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 1-15, MASS SPECTROMETRY, MUTAGENESIS OF GLU-27; GLN-144 AND ALA-324, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.
    6. "A binding site for activation by the Bacillus subtilis AhrC protein, a repressor/activator of arginine metabolism."
      Klingel U., Miller C.M., North A.K., Stockley P.G., Baumberg S.
      Mol. Gen. Genet. 248:329-340(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 418-424.
    7. "Role and regulation of Bacillus subtilis glutamate dehydrogenase genes."
      Belitsky B.R., Sonenshein A.L.
      J. Bacteriol. 180:6298-6305(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION AS A GLUTAMATE DEHYDROGENASE, DISRUPTION PHENOTYPE, SUBSTRATE SPECIFICITY, INDUCTION, NOMENCLATURE.
    8. "An enhancer element located downstream of the major glutamate dehydrogenase gene of Bacillus subtilis."
      Belitsky B.R., Sonenshein A.L.
      Proc. Natl. Acad. Sci. U.S.A. 96:10290-10295(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION.
    9. "Characterization of Bacillus subtilis mutants with carbon source-independent glutamate biosynthesis."
      Commichau F.M., Wacker I., Schleider J., Blencke H.M., Reif I., Tripal P., Stulke J.
      J. Mol. Microbiol. Biotechnol. 12:106-113(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN THE CONTROL OF GLTAB EXPRESSION.
    10. "Glutamate metabolism in Bacillus subtilis: gene expression and enzyme activities evolved to avoid futile cycles and to allow rapid responses to perturbations of the system."
      Commichau F.M., Gunka K., Landmann J.J., Stulke J.
      J. Bacteriol. 190:3557-3564(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN THE GLUTAMATE DEGRADATION.
    11. "CcpA-dependent regulation of Bacillus subtilis glutamate dehydrogenase gene expression."
      Belitsky B.R., Kim H.J., Sonenshein A.L.
      J. Bacteriol. 186:3392-3398(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION.
    12. "A regulatory protein-protein interaction governs glutamate biosynthesis in Bacillus subtilis: the glutamate dehydrogenase RocG moonlights in controlling the transcription factor GltC."
      Commichau F.M., Herzberg C., Tripal P., Valerius O., Stulke J.
      Mol. Microbiol. 65:642-654(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: INHIBITORY INTERACTION WITH GLTC.
    13. "Functional dissection of a trigger enzyme: mutations of the bacillus subtilis glutamate dehydrogenase RocG that affect differentially its catalytic activity and regulatory properties."
      Gunka K., Newman J.A., Commichau F.M., Herzberg C., Rodrigues C., Hewitt L., Lewis R.J., Stulke J.
      J. Mol. Biol. 400:815-827(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF MUTANT LYS-93, MUTAGENESIS OF GLU-93; ASP-122; TYR-158 AND SER-234, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.

    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: February 17, 2016
    This is version 116 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.