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 24-JAN-2024, entry version 145. 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; Bacillota; 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}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; Z11747; CAA77805.1; -; Genomic_DNA. DR PIR; S22403; S22403. DR RefSeq; WP_003506563.1; NZ_WQPM01000101.1. 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 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: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 Gene3D; 1.10.285.10; Glutamate Dehydrogenase, chain A, domain 3; 2. DR Gene3D; 3.40.50.10860; Leucine Dehydrogenase, chain A, domain 1; 1. DR Gene3D; 3.40.50.720; NAD(P)-binding Rossmann-like Domain; 1. DR InterPro; IPR046346; Aminoacid_DH-like_N_sf. DR InterPro; IPR006095; Glu/Leu/Phe/Val/Trp_DH. DR InterPro; IPR006096; Glu/Leu/Phe/Val/Trp_DH_C. DR InterPro; IPR006097; Glu/Leu/Phe/Val/Trp_DH_dimer. DR InterPro; IPR033524; Glu/Leu/Phe/Val_DH_AS. DR InterPro; IPR014362; Glu_DH. DR InterPro; IPR036291; NAD(P)-bd_dom_sf. DR InterPro; IPR033922; NAD_bind_Glu_DH. DR PANTHER; PTHR43571; NADP-SPECIFIC GLUTAMATE DEHYDROGENASE 1-RELATED; 1. DR PANTHER; PTHR43571:SF1; NADP-SPECIFIC GLUTAMATE DEHYDROGENASE 1-RELATED; 1. 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; SSF53223; Aminoacid dehydrogenase-like, N-terminal domain; 1. DR SUPFAM; SSF51735; NAD(P)-binding Rossmann-fold domains; 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 //