GUDB_BACSU
ID GUDB_BACSU Reviewed; 427 AA.
AC P50735;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 07-JUL-2009, sequence version 2.
DT 03-AUG-2022, entry version 139.
DE RecName: Full=Cryptic catabolic NAD-specific glutamate dehydrogenase GudB;
DE Short=NAD-GDH;
DE EC=1.4.1.2;
GN Name=gudB {ECO:0000303|PubMed:9829940}; Synonyms=ypcA;
GN OrderedLocusNames=BSU22960;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB
RC 3610 / NRRL NRS-744 / VKM B-501;
RX PubMed=8760912; DOI=10.1099/13500872-142-8-2005;
RA Sorokin A.V., Azevedo V., Zumstein E., Galleron N., Ehrlich S.D.,
RA Serror P.;
RT "Sequence analysis of the Bacillus subtilis chromosome region between the
RT serA and kdg loci cloned in a yeast artificial chromosome.";
RL Microbiology 142:2005-2016(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [3]
RP SEQUENCE REVISION TO 71.
RX PubMed=19383706; DOI=10.1099/mic.0.027839-0;
RA Barbe V., Cruveiller S., Kunst F., Lenoble P., Meurice G., Sekowska A.,
RA Vallenet D., Wang T., Moszer I., Medigue C., Danchin A.;
RT "From a consortium sequence to a unified sequence: the Bacillus subtilis
RT 168 reference genome a decade later.";
RL Microbiology 155:1758-1775(2009).
RN [4]
RP FUNCTION AS A CRYPTIC GLUTAMATE DEHYDROGENASE, DISRUPTION PHENOTYPE,
RP INDUCTION, NOMENCLATURE, AND MUTAGENESIS OF 97-VAL--ALA-99.
RC STRAIN=168 / SMY;
RX PubMed=9829940; DOI=10.1128/jb.180.23.6298-6305.1998;
RA Belitsky B.R., Sonenshein A.L.;
RT "Role and regulation of Bacillus subtilis glutamate dehydrogenase genes.";
RL J. Bacteriol. 180:6298-6305(1998).
RN [5]
RP FUNCTION OF CRYPTIC GLUTAMATE DEHYDROGENASE.
RX PubMed=18326565; DOI=10.1128/jb.00099-08;
RA Commichau F.M., Gunka K., Landmann J.J., Stulke J.;
RT "Glutamate metabolism in Bacillus subtilis: gene expression and enzyme
RT activities evolved to avoid futile cycles and to allow rapid responses to
RT perturbations of the system.";
RL J. Bacteriol. 190:3557-3564(2008).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS), AND SUBUNIT.
RX PubMed=20630473; DOI=10.1016/j.jmb.2010.05.055;
RA Gunka K., Newman J.A., Commichau F.M., Herzberg C., Rodrigues C.,
RA Hewitt L., Lewis R.J., Stulke J.;
RT "Functional dissection of a trigger enzyme: mutations of the bacillus
RT subtilis glutamate dehydrogenase RocG that affect differentially its
RT catalytic activity and regulatory properties.";
RL J. Mol. Biol. 400:815-827(2010).
CC -!- FUNCTION: GudB seems to be intrinsically inactive, however spontaneous
CC mutations removing a 9-bp direct repeat within the wild-type gudB
CC sequence activated the GudB protein and allowed more-efficient
CC utilization of amino acids of the glutamate family (called gutB1). This
CC 3 amino acid insertion presumably causes severe destabilization of the
CC fold of the protein, leading to an inactive enzyme that is very quickly
CC degraded. The cryptic GudB serves as a buffer that may compensate for
CC mutations in the rocG gene and that can also be decryptified for the
CC utilization of glutamate as a single carbon source in the absence of
CC arginine. It is unable to synthesize glutamate.
CC {ECO:0000269|PubMed:18326565, ECO:0000269|PubMed:9829940}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + L-glutamate + NAD(+) = 2-oxoglutarate + H(+) + NADH +
CC NH4(+); Xref=Rhea:RHEA:15133, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16810, ChEBI:CHEBI:28938, ChEBI:CHEBI:29985,
CC ChEBI:CHEBI:57540, ChEBI:CHEBI:57945; EC=1.4.1.2;
CC -!- SUBUNIT: Homohexamer. {ECO:0000269|PubMed:20630473}.
CC -!- INDUCTION: Constitutively expressed. {ECO:0000269|PubMed:9829940}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype. Cells lacking this gene
CC show no growth defect; a double rocG-gudB disruption has the same
CC phenotype as a single rocG disruption. {ECO:0000269|PubMed:9829940}.
CC -!- SIMILARITY: Belongs to the Glu/Leu/Phe/Val dehydrogenases family.
CC {ECO:0000305}.
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DR EMBL; L47648; AAC83953.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB14212.2; -; Genomic_DNA.
DR PIR; G69933; G69933.
DR RefSeq; NP_390177.2; NC_000964.3.
DR RefSeq; WP_009967634.1; NZ_CM000487.1.
DR RefSeq; WP_010886557.1; NZ_JNCM01000036.1.
DR PDB; 3K8Z; X-ray; 2.40 A; A/B/C/D/E/F=1-427.
DR PDBsum; 3K8Z; -.
DR AlphaFoldDB; P50735; -.
DR SMR; P50735; -.
DR IntAct; P50735; 1.
DR MINT; P50735; -.
DR STRING; 224308.BSU22960; -.
DR jPOST; P50735; -.
DR PaxDb; P50735; -.
DR PRIDE; P50735; -.
DR EnsemblBacteria; CAB14212; CAB14212; BSU_22960.
DR GeneID; 938975; -.
DR KEGG; bsu:BSU22960; -.
DR PATRIC; fig|224308.179.peg.2503; -.
DR eggNOG; COG0334; Bacteria.
DR InParanoid; P50735; -.
DR OMA; WLQNRNG; -.
DR PhylomeDB; P50735; -.
DR BioCyc; BSUB:BSU22960-MON; -.
DR EvolutionaryTrace; P50735; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0004352; F:glutamate dehydrogenase (NAD+) activity; IMP:UniProtKB.
DR GO; GO:0006520; P:cellular amino acid metabolic process; IMP:UniProtKB.
DR GO; GO:0006538; P:glutamate catabolic process; IBA:GO_Central.
DR CDD; cd01076; NAD_bind_1_Glu_DH; 1.
DR InterPro; IPR046346; Aminiacid_DH-like_N_sf.
DR InterPro; IPR006095; Glu/Leu/Phe/Val_DH.
DR InterPro; IPR033524; Glu/Leu/Phe/Val_DH_AS.
DR InterPro; IPR006096; Glu/Leu/Phe/Val_DH_C.
DR InterPro; IPR006097; Glu/Leu/Phe/Val_DH_dimer_dom.
DR InterPro; IPR014362; Glu_DH.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR InterPro; IPR033922; NAD_bind_Glu_DH.
DR Pfam; PF00208; ELFV_dehydrog; 1.
DR Pfam; PF02812; ELFV_dehydrog_N; 1.
DR PIRSF; PIRSF000185; Glu_DH; 1.
DR PRINTS; PR00082; GLFDHDRGNASE.
DR SMART; SM00839; ELFV_dehydrog; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
DR SUPFAM; SSF53223; SSF53223; 1.
DR PROSITE; PS00074; GLFV_DEHYDROGENASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; NAD; Oxidoreductase; Reference proteome.
FT CHAIN 1..427
FT /note="Cryptic catabolic NAD-specific glutamate
FT dehydrogenase GudB"
FT /id="PRO_0000418372"
FT ACT_SITE 119
FT /note="Proton donor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10011"
FT BINDING 80
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 107
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 203
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 234
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 361
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT SITE 159
FT /note="Important for catalysis"
FT /evidence="ECO:0000250"
FT MUTAGEN 97..99
FT /note="Missing: In gudB1; gains glutamate dehydrogenase
FT activity, restores growth on proline, arginine, ornithine."
FT /evidence="ECO:0000269|PubMed:9829940"
FT CONFLICT 71
FT /note="Missing (in Ref. 1; AAC83953)"
FT /evidence="ECO:0000305"
FT HELIX 19..32
FT /evidence="ECO:0007829|PDB:3K8Z"
FT HELIX 36..42
FT /evidence="ECO:0007829|PDB:3K8Z"
FT STRAND 46..56
FT /evidence="ECO:0007829|PDB:3K8Z"
FT STRAND 62..70
FT /evidence="ECO:0007829|PDB:3K8Z"
FT STRAND 83..85
FT /evidence="ECO:0007829|PDB:3K8Z"
FT HELIX 91..96
FT /evidence="ECO:0007829|PDB:3K8Z"
FT HELIX 100..111
FT /evidence="ECO:0007829|PDB:3K8Z"
FT STRAND 116..122
FT /evidence="ECO:0007829|PDB:3K8Z"
FT HELIX 126..128
FT /evidence="ECO:0007829|PDB:3K8Z"
FT HELIX 131..145
FT /evidence="ECO:0007829|PDB:3K8Z"
FT HELIX 146..148
FT /evidence="ECO:0007829|PDB:3K8Z"
FT TURN 151..153
FT /evidence="ECO:0007829|PDB:3K8Z"
FT HELIX 164..178
FT /evidence="ECO:0007829|PDB:3K8Z"
FT HELIX 183..185
FT /evidence="ECO:0007829|PDB:3K8Z"
FT STRAND 186..188
FT /evidence="ECO:0007829|PDB:3K8Z"
FT HELIX 191..193
FT /evidence="ECO:0007829|PDB:3K8Z"
FT HELIX 202..217
FT /evidence="ECO:0007829|PDB:3K8Z"
FT HELIX 222..224
FT /evidence="ECO:0007829|PDB:3K8Z"
FT STRAND 226..230
FT /evidence="ECO:0007829|PDB:3K8Z"
FT HELIX 235..245
FT /evidence="ECO:0007829|PDB:3K8Z"
FT STRAND 249..254
FT /evidence="ECO:0007829|PDB:3K8Z"
FT STRAND 259..261
FT /evidence="ECO:0007829|PDB:3K8Z"
FT HELIX 282..284
FT /evidence="ECO:0007829|PDB:3K8Z"
FT HELIX 291..296
FT /evidence="ECO:0007829|PDB:3K8Z"
FT STRAND 301..304
FT /evidence="ECO:0007829|PDB:3K8Z"
FT TURN 313..315
FT /evidence="ECO:0007829|PDB:3K8Z"
FT HELIX 316..318
FT /evidence="ECO:0007829|PDB:3K8Z"
FT STRAND 322..325
FT /evidence="ECO:0007829|PDB:3K8Z"
FT STRAND 328..330
FT /evidence="ECO:0007829|PDB:3K8Z"
FT HELIX 334..342
FT /evidence="ECO:0007829|PDB:3K8Z"
FT STRAND 346..348
FT /evidence="ECO:0007829|PDB:3K8Z"
FT HELIX 350..353
FT /evidence="ECO:0007829|PDB:3K8Z"
FT HELIX 356..370
FT /evidence="ECO:0007829|PDB:3K8Z"
FT HELIX 376..400
FT /evidence="ECO:0007829|PDB:3K8Z"
FT HELIX 405..423
FT /evidence="ECO:0007829|PDB:3K8Z"
SQ SEQUENCE 427 AA; 47340 MW; 8FDF5BEB0ABEFB19 CRC64;
MAADRNTGHT EEDKLDVLKS TQTVIHKALE KLGYPEEVYE LLKEPMRLLT VKIPVRMDDG
SVKIFTGYRA QHNDSVGPTK GGIRFHPNVT EKEVKAVKAL SIWMSLKCGI IDLPYGGGKG
GIVCDPRDMS FRELERLSRG YVRAISQIVG PTKDVPAPDV FTNSQIMAWM MDEYSRIDEF
NSPGFITGKP LVLGGSHGRE SATAKGVTIC IKEAAKKRGI DIKGARVVVQ GFGNAGSYLA
KFMHDAGAKV VGISDAYGGL YDPEGLDIDY LLDRRDSFGT VTKLFNDTIT NQELLELDCD
ILVPAAIENQ ITEENAHNIR AKIVVEAANG PTTLEGTKIL SDRDILLVPD VLASAGGVTV
SYFEWVQNNQ GFYWSEEEVE EKLEKMMVKS FNNIYEMANN RRIDMRLAAY MVGVRKMAEA
SRFRGWI
