P24295 (DHE2_CLOSY) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
NAD-specific glutamate dehydrogenase
Short name=NAD-GDH
EC=1.4.1.2

Gene names

Name:

gdh

Organism

Clostridium symbiosum (Bacteroides symbiosus)

Taxonomic identifier

1512 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Clostridia › Clostridiales › Clostridiaceae › Clostridium

Protein attributes

Sequence length	450 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Catalytic activity	L-glutamate + H2O + NAD+ = 2-oxoglutarate + NH3 + NADH.
Pathway	Amino-acid degradation; L-glutamate degradation via hydroxyglutarate pathway; crotonoyl-CoA from L-glutamate: step 1/5.
Subunit structure	Homohexamer.
Sequence similarities	Belongs to the Glu/Leu/Phe/Val dehydrogenases family.

Ontologies

Keywords
Ligand	NAD
Molecular function	Oxidoreductase
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological process	cellular amino acid metabolic process Inferred from electronic annotation. Source: InterPro
Molecular function	glutamate dehydrogenase (NAD+) activity Inferred from electronic annotation. Source: EC nucleotide binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed

Chain

2 – 450

449

NAD-specific glutamate dehydrogenase

PRO_0000182738

Sites

Active site

126

1

Experimental info

Sequence conflict

43

1

Y → S AA sequence Ref.4

Sequence conflict

165

1

G → V AA sequence Ref.4

Sequence conflict

326

1

D → A AA sequence Ref.4

Secondary structure

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450

Helix Strand Turn

Details...

Helix

3 – 15

13

Turn

16 – 18

3

Helix

20 – 31

12

Helix

34 – 38

5

Helix

41 – 45

5

Helix

48 – 52

5

Beta strand

56 – 66

11

Beta strand

72 – 83

12

Beta strand

85 – 95

11

Helix

101 – 117

17

Beta strand

119 – 121

3

Beta strand

124 – 130

7

Helix

138 – 152

15

Helix

153 – 155

3

Turn

158 – 160

3

Beta strand

161 – 164

4

Helix

171 – 185

15

Helix

190 – 192

3

Beta strand

193 – 195

3

Helix

198 – 200

3

Turn

204 – 208

5

Helix

209 – 224

16

Beta strand

233 – 236

4

Helix

241 – 253

13

Beta strand

259 – 262

4

Beta strand

265 – 268

4

Helix

276 – 288

13

Helix

294 – 300

7

Beta strand

303 – 306

4

Helix

310 – 312

3

Beta strand

316 – 319

4

Helix

329 – 337

9

Beta strand

342 – 344

3

Beta strand

347 – 349

3

Helix

353 – 361

9

Beta strand

366 – 368

3

Helix

370 – 373

4

Helix

376 – 390

15

Helix

396 – 420

25

Helix

427 – 446

20

Sequences

	Sequence		Length	Mass (Da)
	P24295 [UniParc]. Last modified January 23, 2007. Version 4. Checksum: 993BB613288974E6	FASTA	450	49,296
	10 20 30 40 50 60 MSKYVDRVIA EVEKKYADEP EFVQTVEEVL SSLGPVVDAH PEYEEVALLE RMVIPERVIE 70 80 90 100 110 120 FRVPWEDDNG KVHVNTGYRV QFNGAIGPYK GGLRFAPSVN LSIMKFLGFE QAFKDSLTTL 130 140 150 160 170 180 PMGGAKGGSD FDPNGKSDRE VMRFCQAFMT ELYRHIGPDI DVPAGDLGVG AREIGYMYGQ 190 200 210 220 230 240 YRKIVGGFYN GVLTGKARSF GGSLVRPEAT GYGSVYYVEA VMKHENDTLV GKTVALAGFG 250 260 270 280 290 300 NVAWGAAKKL AELGAKAVTL SGPDGYIYDP EGITTEEKIN YMLEMRASGR NKVQDYADKF 310 320 330 340 350 360 GVQFFPGEKP WGQKVDIIMP CATQNDVDLE QAKKIVANNV KYYIEVANMP TTNEALRFLM 370 380 390 400 410 420 QQPNMVVAPS KAVNAGGVLV SGFEMSQNSE RLSWTAEEVD SKLHQVMTDI HDGSAAAAER 430 440 450 YGLGYNLVAG ANIVGFQKIA DAMMAQGIAW

References

[1]	"The glutamate dehydrogenase gene of Clostridium symbiosum. Cloning by polymerase chain reaction, sequence analysis and over-expression in Escherichia coli." Teller J.K., Smith R.M., McPherson M.J., Engel P.C., Guest J.R. Eur. J. Biochem. 206:151-159(1992) [PubMed: 1587267] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"The partial amino acid sequence of the NAD(+)-dependent glutamate dehydrogenase of Clostridium symbiosum: implications for the evolution and structural basis of coenzyme specificity." Lilley K.S., Baker P.J., Britton K.L., Stillman T.J., Brown P.E., Moir A.J.G., Engel P.C., Rice D.W., Bell J.E., Bell E. Biochim. Biophys. Acta 1080:191-197(1991) [PubMed: 1954226] [Abstract] Cited for: PRELIMINARY PARTIAL PROTEIN SEQUENCE.
[3]	"The essential active-site lysines of clostridial glutamate dehydrogenase. A study with pyridoxal-5'-phosphate." Lilley K.S., Engel P.C. Eur. J. Biochem. 207:533-540(1992) [PubMed: 1633808] [Abstract] Cited for: PARTIAL PROTEIN SEQUENCE, MODIFICATION OF SOME LYSINES.
[4]	"Site and significance of chemically modifiable cysteine residues in glutamate dehydrogenase of Clostridium symbiosum and the use of protection studies to measure coenzyme binding." Syed S.E., Hornby D.P., Brown P.E., Fitton J.E., Engel P.C. Biochem. J. 298:107-113(1994) [PubMed: 8129708] [Abstract] Cited for: PROTEIN SEQUENCE OF 26-46; 154-158; 165-182 AND 325-339.
[5]	"Subunit assembly and active site location in the structure of glutamate dehydrogenase." Baker P.J., Britton K.L., Engel P.C., Farrants G.W., Lilley K.S., Rice D.W., Stillman T.J. Proteins 12:75-86(1992) [PubMed: 1553382] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.96 ANGSTROMS).
[6]	"Conformational flexibility in glutamate dehydrogenase. Role of water in substrate recognition and catalysis." Stillman T.J., Baker P.J., Britton K.L., Rice D.W. J. Mol. Biol. 234:1131-1139(1993) [PubMed: 8263917] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
[7]	"Determinants of substrate specificity in the superfamily of amino acid dehydrogenases." Baker P.J., Waugh M.L., Wang X.G., Stillman T.J., Turnbull A.P., Engel P.C., Rice D.W. Biochemistry 36:16109-16115(1997) [PubMed: 9405044] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

Z11747 Genomic DNA. Translation: CAA77805.1.

PIR

S22403.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1AUP	X-ray	2.50	A	2-450	[»]
1BGV	X-ray	1.90	A	2-450	[»]
1HRD	X-ray	1.96	A/B/C	2-449	[»]
1K89	X-ray	2.05	A	2-449	[»]

ProteinModelPortal

P24295.

SMR

P24295. Positions 2-450.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Family and domain databases

InterPro

IPR006095. 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]

Gene3D

G3DSA:3.40.50.720. NAD(P)-bd. 1 hit.

Pfam

PF00208. ELFV_dehydrog. 1 hit.
PF02812. ELFV_dehydrog_N. 1 hit.
[Graphical view]

PIRSF

PIRSF000185. Glu_DH. 1 hit.

PRINTS

PR00082. GLFDHDRGNASE.

SMART

SM00839. ELFV_dehydrog. 1 hit.
[Graphical view]

PROSITE

PS00074. GLFV_DEHYDROGENASE. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

DHE2_CLOSY

Accession

Primary (citable) accession number: P24295

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 1, 1992
Last sequence update:	January 23, 2007
Last modified:	December 14, 2011
This is version 83 of the entry and version 4 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program