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Catabolic NAD-specific glutamate dehydrogenase RocG (NAD-GDH) (EC 1.4.1.2) (Glutamate dehydrogenase) (GlutDH) (Trigger enzyme RocG)

 DHE2_BACSU              Reviewed;         424 AA.
P39633; Q53548; Q5W7E9;
01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
28-JUL-2009, sequence version 3.
07-JUN-2017, entry version 123.
RecName: Full=Catabolic NAD-specific glutamate dehydrogenase RocG;
Short=NAD-GDH;
EC=1.4.1.2;
AltName: Full=Glutamate dehydrogenase;
Short=GlutDH;
AltName: Full=Trigger enzyme RocG;
Name=rocG; Synonyms=gudA, yweB; OrderedLocusNames=BSU37790;
ORFNames=ipa-75d;
Bacillus subtilis (strain 168).
Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
NCBI_TaxID=224308;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=168;
PubMed=7934828; DOI=10.1111/j.1365-2958.1993.tb01963.x;
Glaser P., Kunst F., Arnaud M., Coudart M.P., Gonzales W.,
Hullo M.-F., Ionescu M., Lubochinsky B., Marcelino L., Moszer I.,
Presecan E., Santana M., Schneider E., Schweizer J., Vertes A.,
Rapoport G., Danchin A.;
"Bacillus subtilis genome project: cloning and sequencing of the 97 kb
region from 325 degrees to 333 degrees.";
Mol. Microbiol. 10:371-384(1993).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ISW1214;
Khan M.H., Itoh K., Kim H., Ashida H., Ishikawa T., Shibata H.,
Sawa Y.;
"Low thermostability of the NAD+ specific glutamate dehydrogenase from
Bacillus subtilis ISW1214: cloning, purification and
characterization.";
Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases.
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=168;
PubMed=9384377; DOI=10.1038/36786;
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.;
"The complete genome sequence of the Gram-positive bacterium Bacillus
subtilis.";
Nature 390:249-256(1997).
[4]
SEQUENCE REVISION TO 324.
PubMed=19383706; DOI=10.1099/mic.0.027839-0;
Barbe V., Cruveiller S., Kunst F., Lenoble P., Meurice G.,
Sekowska A., Vallenet D., Wang T., Moszer I., Medigue C., Danchin A.;
"From a consortium sequence to a unified sequence: the Bacillus
subtilis 168 reference genome a decade later.";
Microbiology 155:1758-1775(2009).
[5]
PROTEIN SEQUENCE OF 1-15, MASS SPECTROMETRY, MUTAGENESIS OF GLU-27;
GLN-144 AND ALA-324, BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
PubMed=16244435; DOI=10.1271/bbb.69.1861;
Khan M.I., Ito K., Kim H., Ashida H., Ishikawa T., Shibata H.,
Sawa Y.;
"Molecular properties and enhancement of thermostability by random
mutagenesis of glutamate dehydrogenase from Bacillus subtilis.";
Biosci. Biotechnol. Biochem. 69:1861-1870(2005).
[6]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 418-424.
PubMed=7565595; DOI=10.1007/BF02191600;
Klingel U., Miller C.M., North A.K., Stockley P.G., Baumberg S.;
"A binding site for activation by the Bacillus subtilis AhrC protein,
a repressor/activator of arginine metabolism.";
Mol. Gen. Genet. 248:329-340(1995).
[7]
FUNCTION AS A GLUTAMATE DEHYDROGENASE, DISRUPTION PHENOTYPE, SUBSTRATE
SPECIFICITY, INDUCTION, AND NOMENCLATURE.
PubMed=9829940;
Belitsky B.R., Sonenshein A.L.;
"Role and regulation of Bacillus subtilis glutamate dehydrogenase
genes.";
J. Bacteriol. 180:6298-6305(1998).
[8]
INDUCTION.
PubMed=10468601; DOI=10.1073/pnas.96.18.10290;
Belitsky B.R., Sonenshein A.L.;
"An enhancer element located downstream of the major glutamate
dehydrogenase gene of Bacillus subtilis.";
Proc. Natl. Acad. Sci. U.S.A. 96:10290-10295(1999).
[9]
FUNCTION IN THE CONTROL OF GLTAB EXPRESSION.
PubMed=17183217; DOI=10.1159/000096465;
Commichau F.M., Wacker I., Schleider J., Blencke H.M., Reif I.,
Tripal P., Stulke J.;
"Characterization of Bacillus subtilis mutants with carbon source-
independent glutamate biosynthesis.";
J. Mol. Microbiol. Biotechnol. 12:106-113(2007).
[10]
FUNCTION IN THE GLUTAMATE DEGRADATION.
PubMed=18326565; DOI=10.1128/JB.00099-08;
Commichau F.M., Gunka K., Landmann J.J., Stulke J.;
"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.";
J. Bacteriol. 190:3557-3564(2008).
[11]
INDUCTION.
PubMed=15150224; DOI=10.1128/JB.186.11.3392-3398.2004;
Belitsky B.R., Kim H.J., Sonenshein A.L.;
"CcpA-dependent regulation of Bacillus subtilis glutamate
dehydrogenase gene expression.";
J. Bacteriol. 186:3392-3398(2004).
[12]
INHIBITORY INTERACTION WITH GLTC.
PubMed=17608797; DOI=10.1111/j.1365-2958.2007.05816.x;
Commichau F.M., Herzberg C., Tripal P., Valerius O., Stulke J.;
"A regulatory protein-protein interaction governs glutamate
biosynthesis in Bacillus subtilis: the glutamate dehydrogenase RocG
moonlights in controlling the transcription factor GltC.";
Mol. Microbiol. 65:642-654(2007).
[13]
X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF MUTANT LYS-93, MUTAGENESIS OF
GLU-93; ASP-122; TYR-158 AND SER-234, BIOPHYSICOCHEMICAL PROPERTIES,
AND SUBUNIT.
PubMed=20630473; DOI=10.1016/j.jmb.2010.05.055;
Gunka K., Newman J.A., Commichau F.M., Herzberg C., Rodrigues C.,
Hewitt L., Lewis R.J., Stulke J.;
"Functional dissection of a trigger enzyme: mutations of the bacillus
subtilis glutamate dehydrogenase RocG that affect differentially its
catalytic activity and regulatory properties.";
J. Mol. Biol. 400:815-827(2010).
-!- FUNCTION: 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.
{ECO:0000269|PubMed:17183217, ECO:0000269|PubMed:18326565,
ECO:0000269|PubMed:9829940}.
-!- CATALYTIC ACTIVITY: L-glutamate + H(2)O + NAD(+) = 2-oxoglutarate
+ NH(3) + NADH.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=0.08 mM for NAD (at 37 degrees Celsius and at pH 7.3)
{ECO:0000269|PubMed:16244435, ECO:0000269|PubMed:20630473};
KM=0.34 mM for L-glutamate (at 37 degrees Celsius and at pH 7.3)
{ECO:0000269|PubMed:16244435, ECO:0000269|PubMed:20630473};
KM=2.9 mM for L-glutamate (at 37 degrees Celsius and at pH 7.3)
{ECO:0000269|PubMed:16244435, ECO:0000269|PubMed:20630473};
KM=0.65 mM for 2-oxoglutarate (at 37 degrees Celsius and at pH
7.3) {ECO:0000269|PubMed:16244435, ECO:0000269|PubMed:20630473};
KM=2.9 mM for L-glutamate (at pH 7.3)
{ECO:0000269|PubMed:16244435, ECO:0000269|PubMed:20630473};
KM=18.5 mM for ammonium (at pH 7.7)
{ECO:0000269|PubMed:16244435, ECO:0000269|PubMed:20630473};
KM=55.6 mM for ammonium (at 37 degrees Celsius and at pH 7.3)
{ECO:0000269|PubMed:16244435, ECO:0000269|PubMed:20630473};
pH dependence:
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. {ECO:0000269|PubMed:16244435,
ECO:0000269|PubMed:20630473};
Temperature dependence:
Low thermostability at 41 degrees Celsius due to the
dissociation of the hexamer. {ECO:0000269|PubMed:16244435,
ECO:0000269|PubMed:20630473};
-!- SUBUNIT: Homohexamer. {ECO:0000269|PubMed:16244435,
ECO:0000269|PubMed:20630473}.
-!- INTERACTION:
P20668:gltC; NbExp=2; IntAct=EBI-1642022, EBI-1642006;
-!- INDUCTION: 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.
{ECO:0000269|PubMed:10468601, ECO:0000269|PubMed:15150224,
ECO:0000269|PubMed:9829940}.
-!- MASS SPECTROMETRY: Mass=46587; Method=MALDI; Range=1-424;
Evidence={ECO:0000269|PubMed:16244435};
-!- DISRUPTION PHENOTYPE: 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. {ECO:0000269|PubMed:9829940}.
-!- SIMILARITY: Belongs to the Glu/Leu/Phe/Val dehydrogenases family.
{ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; X73124; CAA51631.1; -; Genomic_DNA.
EMBL; AB194695; BAD69594.1; -; Genomic_DNA.
EMBL; AL009126; CAB15806.2; -; Genomic_DNA.
EMBL; S79622; -; NOT_ANNOTATED_CDS; Genomic_DNA.
PIR; A70055; A70055.
RefSeq; NP_391659.2; NC_000964.3.
RefSeq; WP_003227482.1; NZ_JNCM01000034.1.
PDB; 3K92; X-ray; 2.30 A; A/B/C/D/E/F=1-424.
PDBsum; 3K92; -.
ProteinModelPortal; P39633; -.
SMR; P39633; -.
IntAct; P39633; 1.
STRING; 224308.Bsubs1_010100020411; -.
PaxDb; P39633; -.
EnsemblBacteria; CAB15806; CAB15806; BSU37790.
GeneID; 937066; -.
KEGG; bsu:BSU37790; -.
PATRIC; fig|224308.179.peg.4091; -.
eggNOG; ENOG4105D82; Bacteria.
eggNOG; COG0334; LUCA.
HOGENOM; HOG000243801; -.
InParanoid; P39633; -.
KO; K00260; -.
OMA; WEEDRVN; -.
PhylomeDB; P39633; -.
BioCyc; BSUB:BSU37790-MONOMER; -.
BRENDA; 1.4.1.2; 658.
SABIO-RK; P39633; -.
EvolutionaryTrace; P39633; -.
Proteomes; UP000001570; Chromosome.
GO; GO:0004352; F:glutamate dehydrogenase (NAD+) activity; IDA:UniProtKB.
GO; GO:0006520; P:cellular amino acid metabolic process; IMP:UniProtKB.
GO; GO:0055114; P:oxidation-reduction process; IMP:UniProtKB.
CDD; cd01076; NAD_bind_1_Glu_DH; 1.
InterPro; IPR006095; Glu/Leu/Phe/Val_DH.
InterPro; IPR033524; Glu/Leu/Phe/Val_DH_AS.
InterPro; IPR006096; Glu/Leu/Phe/Val_DH_C.
InterPro; IPR006097; Glu/Leu/Phe/Val_DH_dimer_dom.
InterPro; IPR014362; Glu_DH.
InterPro; IPR016040; NAD(P)-bd_dom.
InterPro; IPR033922; NAD_bind_Glu_DH.
Pfam; PF00208; ELFV_dehydrog; 1.
Pfam; PF02812; ELFV_dehydrog_N; 1.
PIRSF; PIRSF000185; Glu_DH; 1.
PRINTS; PR00082; GLFDHDRGNASE.
SMART; SM00839; ELFV_dehydrog; 1.
SUPFAM; SSF51735; SSF51735; 1.
PROSITE; PS00074; GLFV_DEHYDROGENASE; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Direct protein sequencing; NAD;
Oxidoreductase; Reference proteome.
CHAIN 1 424 Catabolic NAD-specific glutamate
dehydrogenase RocG.
/FTId=PRO_0000182735.
ACT_SITE 116 116 Proton donor. {ECO:0000255|PROSITE-
ProRule:PRU10011}.
BINDING 80 80 Substrate. {ECO:0000250}.
BINDING 104 104 Substrate. {ECO:0000250}.
BINDING 200 200 NAD. {ECO:0000250}.
BINDING 231 231 NAD. {ECO:0000250}.
BINDING 358 358 Substrate. {ECO:0000250}.
SITE 156 156 Important for catalysis. {ECO:0000250}.
MUTAGEN 27 27 E->F: Increase of thermostability 8
degrees Celsius higher than that of the
wild-type. {ECO:0000269|PubMed:16244435}.
MUTAGEN 93 93 E->K: Reduces the affinity for glutamate
and ammonium.
{ECO:0000269|PubMed:20630473}.
MUTAGEN 122 122 D->N: Unable to control gltAB expression
via an inhibitory interactions with the
transcriptional regulator GltC. Reduces
the affinity for glutamate and ammonium.
{ECO:0000269|PubMed:20630473}.
MUTAGEN 144 144 Q->R: Increase of thermostability 20
degrees Celsius higher than that of the
wild-type. {ECO:0000269|PubMed:16244435}.
MUTAGEN 158 158 Y->H: Reduces the affinity for glutamate
and ammonium.
{ECO:0000269|PubMed:20630473}.
MUTAGEN 234 234 S->R: Reduces the affinity for glutamate
and ammonium.
{ECO:0000269|PubMed:20630473}.
MUTAGEN 324 324 A->R: No effect.
{ECO:0000269|PubMed:16244435}.
CONFLICT 324 324 A -> R (in Ref. 1; CAA51631).
{ECO:0000305}.
CONFLICT 419 424 RFRGWV -> FPRMGLI (in Ref. 1; CAA51631).
{ECO:0000305}.
HELIX 8 31 {ECO:0000244|PDB:3K92}.
HELIX 36 42 {ECO:0000244|PDB:3K92}.
STRAND 46 56 {ECO:0000244|PDB:3K92}.
STRAND 62 71 {ECO:0000244|PDB:3K92}.
STRAND 75 80 {ECO:0000244|PDB:3K92}.
STRAND 83 86 {ECO:0000244|PDB:3K92}.
HELIX 91 107 {ECO:0000244|PDB:3K92}.
STRAND 113 120 {ECO:0000244|PDB:3K92}.
HELIX 123 125 {ECO:0000244|PDB:3K92}.
HELIX 128 142 {ECO:0000244|PDB:3K92}.
HELIX 143 145 {ECO:0000244|PDB:3K92}.
TURN 148 150 {ECO:0000244|PDB:3K92}.
HELIX 161 175 {ECO:0000244|PDB:3K92}.
HELIX 180 182 {ECO:0000244|PDB:3K92}.
HELIX 188 190 {ECO:0000244|PDB:3K92}.
TURN 194 198 {ECO:0000244|PDB:3K92}.
HELIX 199 214 {ECO:0000244|PDB:3K92}.
HELIX 219 221 {ECO:0000244|PDB:3K92}.
STRAND 223 227 {ECO:0000244|PDB:3K92}.
HELIX 231 243 {ECO:0000244|PDB:3K92}.
STRAND 246 251 {ECO:0000244|PDB:3K92}.
STRAND 256 258 {ECO:0000244|PDB:3K92}.
HELIX 265 271 {ECO:0000244|PDB:3K92}.
STRAND 274 276 {ECO:0000244|PDB:3K92}.
HELIX 279 281 {ECO:0000244|PDB:3K92}.
HELIX 288 293 {ECO:0000244|PDB:3K92}.
STRAND 297 301 {ECO:0000244|PDB:3K92}.
TURN 310 312 {ECO:0000244|PDB:3K92}.
HELIX 313 315 {ECO:0000244|PDB:3K92}.
STRAND 319 322 {ECO:0000244|PDB:3K92}.
STRAND 325 327 {ECO:0000244|PDB:3K92}.
HELIX 331 339 {ECO:0000244|PDB:3K92}.
STRAND 343 345 {ECO:0000244|PDB:3K92}.
HELIX 347 350 {ECO:0000244|PDB:3K92}.
HELIX 353 367 {ECO:0000244|PDB:3K92}.
HELIX 373 398 {ECO:0000244|PDB:3K92}.
HELIX 402 420 {ECO:0000244|PDB:3K92}.
SEQUENCE 424 AA; 46553 MW; 019AE0A833BE48DD CRC64;
MSAKQVSKDE EKEALNLFLS TQTIIKEALR KLGYPGDMYE LMKEPQRMLT VRIPVKMDNG
SVKVFTGYRS QHNDAVGPTK GGVRFHPEVN EEEVKALSIW MTLKCGIANL PYGGGKGGII
CDPRTMSFGE LERLSRGYVR AISQIVGPTK DIPAPDVYTN SQIMAWMMDE YSRLREFDSP
GFITGKPLVL GGSQGRETAT AQGVTICIEE AVKKKGIKLQ NARIIIQGFG NAGSFLAKFM
HDAGAKVIGI SDANGGLYNP DGLDIPYLLD KRDSFGMVTN LFTDVITNEE LLEKDCDILV
PAAISNQITA KNAHNIQASI VVEAANGPTT IDATKILNER GVLLVPDILA SAGGVTVSYF
EWVQNNQGYY WSEEEVAEKL RSVMVSSFET IYQTAATHKV DMRLAAYMTG IRKSAEASRF
RGWV


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