DHE2_CLOSY
ID DHE2_CLOSY Reviewed; 450 AA.
AC P24295;
DT 01-MAR-1992, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 4.
DT 03-AUG-2022, entry version 137.
DE RecName: Full=NAD-specific glutamate dehydrogenase;
DE Short=NAD-GDH;
DE EC=1.4.1.2;
GN Name=gdh;
OS Clostridium symbiosum (Bacteroides symbiosus).
OC Bacteria; Firmicutes; Clostridia; Eubacteriales; Lachnospiraceae.
OX NCBI_TaxID=1512;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=1587267; DOI=10.1111/j.1432-1033.1992.tb16912.x;
RA Teller J.K., Smith R.M., McPherson M.J., Engel P.C., Guest J.R.;
RT "The glutamate dehydrogenase gene of Clostridium symbiosum. Cloning by
RT polymerase chain reaction, sequence analysis and over-expression in
RT Escherichia coli.";
RL Eur. J. Biochem. 206:151-159(1992).
RN [2]
RP PRELIMINARY PARTIAL PROTEIN SEQUENCE.
RX PubMed=1954226; DOI=10.1016/0167-4838(91)90001-g;
RA Lilley K.S., Baker P.J., Britton K.L., Stillman T.J., Brown P.E.,
RA Moir A.J.G., Engel P.C., Rice D.W., Bell J.E., Bell E.;
RT "The partial amino acid sequence of the NAD(+)-dependent glutamate
RT dehydrogenase of Clostridium symbiosum: implications for the evolution and
RT structural basis of coenzyme specificity.";
RL Biochim. Biophys. Acta 1080:191-197(1991).
RN [3]
RP PARTIAL PROTEIN SEQUENCE, AND MODIFICATION OF SOME LYSINES.
RX PubMed=1633808; DOI=10.1111/j.1432-1033.1992.tb17079.x;
RA Lilley K.S., Engel P.C.;
RT "The essential active-site lysines of clostridial glutamate dehydrogenase.
RT A study with pyridoxal-5'-phosphate.";
RL Eur. J. Biochem. 207:533-540(1992).
RN [4]
RP PROTEIN SEQUENCE OF 2-11, MUTAGENESIS OF ASP-166, AND BIOPHYSICOCHEMICAL
RP PROPERTIES.
RX PubMed=8037659; DOI=10.1042/bj3010013;
RA Dean J.L., Wang X.G., Teller J.K., Waugh M.L., Britton K.L., Baker P.J.,
RA Stillman T.J., Martin S.R., Rice D.W., Engel P.C.;
RT "The catalytic role of aspartate in the active site of glutamate
RT dehydrogenase.";
RL Biochem. J. 301:13-16(1994).
RN [5]
RP PROTEIN SEQUENCE OF 26-46; 154-158; 165-182 AND 325-339.
RX PubMed=8129708; DOI=10.1042/bj2980107;
RA Syed S.E., Hornby D.P., Brown P.E., Fitton J.E., Engel P.C.;
RT "Site and significance of chemically modifiable cysteine residues in
RT glutamate dehydrogenase of Clostridium symbiosum and the use of protection
RT studies to measure coenzyme binding.";
RL Biochem. J. 298:107-113(1994).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.96 ANGSTROMS), AND SUBUNIT.
RX PubMed=1553382; DOI=10.1002/prot.340120109;
RA Baker P.J., Britton K.L., Engel P.C., Farrants G.W., Lilley K.S.,
RA Rice D.W., Stillman T.J.;
RT "Subunit assembly and active site location in the structure of glutamate
RT dehydrogenase.";
RL Proteins 12:75-86(1992).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) OF 2-450 IN COMPLEX WITH SUBSTRATE,
RP AND ACTIVE SITE.
RX PubMed=8263917; DOI=10.1006/jmbi.1993.1665;
RA Stillman T.J., Baker P.J., Britton K.L., Rice D.W.;
RT "Conformational flexibility in glutamate dehydrogenase. Role of water in
RT substrate recognition and catalysis.";
RL J. Mol. Biol. 234:1131-1139(1993).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (1.96 ANGSTROMS) OF 2-449.
RX PubMed=8591026; DOI=10.1016/s0969-2126(01)00251-9;
RA Yip K.S.P., Stillman T.J., Britton K.L., Artymiuk P.J., Baker P.J.,
RA Sedelnikova S.E., Engel P.C., Pasquo A., Chiaraluce R., Consalvi V.,
RA Scandurra R., Rice D.W.;
RT "The structure of Pyrococcus furiosus glutamate dehydrogenase reveals a key
RT role for ion-pair networks in maintaining enzyme stability at extreme
RT temperatures.";
RL Structure 3:1147-1158(1995).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 2-450, MUTAGENESIS OF LYS-90 AND
RP SER-381, SUBSTRATE SPECIFICITY, AND SUBUNIT.
RX PubMed=9405044; DOI=10.1021/bi972024x;
RA Baker P.J., Waugh M.L., Wang X.G., Stillman T.J., Turnbull A.P.,
RA Engel P.C., Rice D.W.;
RT "Determinants of substrate specificity in the superfamily of amino acid
RT dehydrogenases.";
RL Biochemistry 36:16109-16115(1997).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) OF 2-449 OF MUTANT LEU-90, SUBSTRATE
RP SPECIFICITY, AND MUTAGENESIS OF LYS-90.
RX PubMed=9878450; DOI=10.1006/jmbi.1998.2335;
RA Stillman T.J., Migueis A.M., Wang X.G., Baker P.J., Britton K.L.,
RA Engel P.C., Rice D.W.;
RT "Insights into the mechanism of domain closure and substrate specificity of
RT glutamate dehydrogenase from Clostridium symbiosum.";
RL J. Mol. Biol. 285:875-885(1999).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS), AND SUBUNIT.
RA Oliveira T., Sharkey M.A., Hamza M., Engel P.C., Khan A.R.;
RT "Structural determinants of cofactor specificity and domain flexibility in
RT bacterial glutamate dehydrogenases.";
RL Submitted (APR-2011) to the PDB data bank.
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 -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=10.8 uM for NADH (at 25 degrees Celsius and at pH 7)
CC {ECO:0000269|PubMed:8037659};
CC KM=0.31 mM for 2-oxoglutarate (at 25 degrees Celsius and at pH 7)
CC {ECO:0000269|PubMed:8037659};
CC KM=61.1 mM for ammonium (at 25 degrees Celsius and at pH 7)
CC {ECO:0000269|PubMed:8037659};
CC Vmax=125 umol/min/mg enzyme for NADH (at 25 degrees Celsius and at pH
CC 7) {ECO:0000269|PubMed:8037659};
CC Vmax=191 umol/min/mg enzyme for 2-oxoglutarate (at 25 degrees Celsius
CC and at pH 7) {ECO:0000269|PubMed:8037659};
CC Vmax=296 umol/min/mg enzyme for ammonium (at 25 degrees Celsius and
CC at pH 7) {ECO:0000269|PubMed:8037659};
CC -!- PATHWAY: Amino-acid degradation; L-glutamate degradation via
CC hydroxyglutarate pathway; crotonoyl-CoA from L-glutamate: step 1/5.
CC -!- SUBUNIT: Homohexamer. {ECO:0000269|PubMed:1553382,
CC ECO:0000269|PubMed:8263917, ECO:0000269|PubMed:9405044,
CC ECO:0000269|Ref.11}.
CC -!- SIMILARITY: Belongs to the Glu/Leu/Phe/Val dehydrogenases family.
CC {ECO:0000305}.
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DR EMBL; Z11747; CAA77805.1; -; Genomic_DNA.
DR PIR; S22403; S22403.
DR RefSeq; WP_003506563.1; NZ_SPFP01000013.1.
DR PDB; 1AUP; X-ray; 2.50 A; A=2-450.
DR PDB; 1BGV; X-ray; 1.90 A; A=2-450.
DR PDB; 1HRD; X-ray; 1.96 A; A/B/C=2-450.
DR PDB; 1K89; X-ray; 2.05 A; A=2-450.
DR PDB; 2YFH; X-ray; 2.70 A; A/B/C/D/E/F=1-450.
DR PDBsum; 1AUP; -.
DR PDBsum; 1BGV; -.
DR PDBsum; 1HRD; -.
DR PDBsum; 1K89; -.
DR PDBsum; 2YFH; -.
DR AlphaFoldDB; P24295; -.
DR SMR; P24295; -.
DR STRING; 742741.HMPREF9475_00722; -.
DR PRIDE; P24295; -.
DR eggNOG; COG0334; Bacteria.
DR BRENDA; 1.4.1.2; 772.
DR SABIO-RK; P24295; -.
DR UniPathway; UPA00533; UER00591.
DR EvolutionaryTrace; P24295; -.
DR GO; GO:0004352; F:glutamate dehydrogenase (NAD+) activity; ISS:UniProtKB.
DR GO; GO:0006520; P:cellular amino acid metabolic process; ISS:UniProtKB.
DR GO; GO:0019552; P:glutamate catabolic process via 2-hydroxyglutarate; IEA:UniProtKB-UniPathway.
DR CDD; cd05313; NAD_bind_2_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; Direct protein sequencing; NAD; Oxidoreductase.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:8037659"
FT CHAIN 2..450
FT /note="NAD-specific glutamate dehydrogenase"
FT /id="PRO_0000182738"
FT ACT_SITE 126
FT /note="Proton donor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10011,
FT ECO:0000269|PubMed:8263917"
FT BINDING 90
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:8263917"
FT BINDING 111
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:8263917"
FT BINDING 114
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:8263917"
FT BINDING 165
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:8263917"
FT BINDING 210
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000305"
FT BINDING 241
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000305"
FT BINDING 381
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:8263917"
FT SITE 166
FT /note="Important for catalysis"
FT /evidence="ECO:0000250"
FT MUTAGEN 90
FT /note="K->L: Increased substrate activity for methionine
FT and norleucine but negligible activity with either
FT glutamate or leucine. Dramatic reduction in the
FT dehydrogenase activity with glutamate as the substrate;
FT when associated with V-381."
FT /evidence="ECO:0000269|PubMed:9405044,
FT ECO:0000269|PubMed:9878450"
FT MUTAGEN 166
FT /note="D->S: Dramatic reduction in the dehydrogenase
FT activity. Specific activity is decreased 1000-fold in the
FT reductive amination reaction and 100000-fold for oxidative
FT deamination."
FT /evidence="ECO:0000269|PubMed:8037659"
FT MUTAGEN 381
FT /note="S->V: Dramatic reduction in the dehydrogenase
FT activity with glutamate as the substrate; when associated
FT with L-90."
FT /evidence="ECO:0000269|PubMed:9405044"
FT CONFLICT 43
FT /note="Y -> S (in Ref. 5; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 165
FT /note="G -> V (in Ref. 5; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 326
FT /note="D -> A (in Ref. 5; AA sequence)"
FT /evidence="ECO:0000305"
FT HELIX 3..15
FT /evidence="ECO:0007829|PDB:1BGV"
FT TURN 16..18
FT /evidence="ECO:0007829|PDB:1BGV"
FT HELIX 20..31
FT /evidence="ECO:0007829|PDB:1BGV"
FT HELIX 34..38
FT /evidence="ECO:0007829|PDB:1BGV"
FT HELIX 41..45
FT /evidence="ECO:0007829|PDB:1BGV"
FT HELIX 48..52
FT /evidence="ECO:0007829|PDB:1BGV"
FT STRAND 56..66
FT /evidence="ECO:0007829|PDB:1BGV"
FT STRAND 72..83
FT /evidence="ECO:0007829|PDB:1BGV"
FT STRAND 85..95
FT /evidence="ECO:0007829|PDB:1BGV"
FT HELIX 101..117
FT /evidence="ECO:0007829|PDB:1BGV"
FT STRAND 119..121
FT /evidence="ECO:0007829|PDB:1BGV"
FT STRAND 124..130
FT /evidence="ECO:0007829|PDB:1BGV"
FT HELIX 138..152
FT /evidence="ECO:0007829|PDB:1BGV"
FT HELIX 153..155
FT /evidence="ECO:0007829|PDB:1BGV"
FT TURN 158..160
FT /evidence="ECO:0007829|PDB:1BGV"
FT STRAND 161..164
FT /evidence="ECO:0007829|PDB:1BGV"
FT HELIX 171..185
FT /evidence="ECO:0007829|PDB:1BGV"
FT HELIX 190..192
FT /evidence="ECO:0007829|PDB:1BGV"
FT STRAND 193..195
FT /evidence="ECO:0007829|PDB:1BGV"
FT HELIX 198..200
FT /evidence="ECO:0007829|PDB:1BGV"
FT TURN 204..208
FT /evidence="ECO:0007829|PDB:1BGV"
FT HELIX 209..224
FT /evidence="ECO:0007829|PDB:1BGV"
FT STRAND 233..236
FT /evidence="ECO:0007829|PDB:1BGV"
FT HELIX 241..253
FT /evidence="ECO:0007829|PDB:1BGV"
FT STRAND 259..262
FT /evidence="ECO:0007829|PDB:1BGV"
FT STRAND 265..268
FT /evidence="ECO:0007829|PDB:1BGV"
FT HELIX 276..288
FT /evidence="ECO:0007829|PDB:1BGV"
FT HELIX 294..300
FT /evidence="ECO:0007829|PDB:1BGV"
FT STRAND 303..306
FT /evidence="ECO:0007829|PDB:1BGV"
FT HELIX 310..312
FT /evidence="ECO:0007829|PDB:1BGV"
FT STRAND 316..319
FT /evidence="ECO:0007829|PDB:1BGV"
FT HELIX 329..337
FT /evidence="ECO:0007829|PDB:1BGV"
FT STRAND 342..344
FT /evidence="ECO:0007829|PDB:1BGV"
FT STRAND 347..349
FT /evidence="ECO:0007829|PDB:1BGV"
FT HELIX 353..361
FT /evidence="ECO:0007829|PDB:1BGV"
FT STRAND 366..368
FT /evidence="ECO:0007829|PDB:1BGV"
FT HELIX 370..373
FT /evidence="ECO:0007829|PDB:1BGV"
FT HELIX 376..390
FT /evidence="ECO:0007829|PDB:1BGV"
FT HELIX 396..420
FT /evidence="ECO:0007829|PDB:1BGV"
FT HELIX 427..446
FT /evidence="ECO:0007829|PDB:1BGV"
SQ SEQUENCE 450 AA; 49296 MW; 993BB613288974E6 CRC64;
MSKYVDRVIA EVEKKYADEP EFVQTVEEVL SSLGPVVDAH PEYEEVALLE RMVIPERVIE
FRVPWEDDNG KVHVNTGYRV QFNGAIGPYK GGLRFAPSVN LSIMKFLGFE QAFKDSLTTL
PMGGAKGGSD FDPNGKSDRE VMRFCQAFMT ELYRHIGPDI DVPAGDLGVG AREIGYMYGQ
YRKIVGGFYN GVLTGKARSF GGSLVRPEAT GYGSVYYVEA VMKHENDTLV GKTVALAGFG
NVAWGAAKKL AELGAKAVTL SGPDGYIYDP EGITTEEKIN YMLEMRASGR NKVQDYADKF
GVQFFPGEKP WGQKVDIIMP CATQNDVDLE QAKKIVANNV KYYIEVANMP TTNEALRFLM
QQPNMVVAPS KAVNAGGVLV SGFEMSQNSE RLSWTAEEVD SKLHQVMTDI HDGSAAAAER
YGLGYNLVAG ANIVGFQKIA DAMMAQGIAW
