Reviewed, UniProtKB/Swiss-Prot P69910 (DCEB_ECOLI)

Names and origin

Protein names

Recommended name:
    Glutamate decarboxylase beta
      Short name=GAD-beta
    EC=4.1.1.15

Gene names

Name:	gadB
Ordered Locus Names:	b1493, JW1488

Organism

Escherichia coli (strain K12) [Complete proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	466 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Converts glutamate to gamma-aminobutyrate (GABA), consuming one intracellular proton in the reaction. The gad system helps to maintain a near-neutral intracellular pH when cells are exposed to extremely acidic conditions. The ability to survive transit through the acidic conditions of the stomach is essential for successful colonization of the mammalian host by commensal and pathogenic bacteria.
Catalytic activity	L-glutamate = 4-aminobutanoate + CO2.
Cofactor	Pyridoxal phosphate.
Subunit structure	Homohexamer composed of three dimers. Ref.16
Subcellular location	Cytoplasm. Membrane. Note: Localized exclusively in the cytoplasm at neutral pH, but is recruited to the membrane when the pH falls. Ref.16
Induction	By acidic conditions. Expression is regulated by a complex system involving rpoS, cAMP, CRP, evgAS, H-NS, gadE, gadW and gadX. The level of involvement for each regulator varies depending upon the growth phase and the medium.
Miscellaneous	Changing Lys-276 to Ala increases thermal stability and protease resistance. The unfolding temperature is increased by 11 degrees Celsius.
Sequence similarities	Belongs to the group II decarboxylase family.

Ontologies

Keywords
Cellular component	Cytoplasm Membrane
Ligand	Pyridoxal phosphate
Molecular function	Decarboxylase Lyase
PTM	Acetylation
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	glutamate metabolic process Inferred from electronic annotation. Source: InterPro
Cellular component	cytosol Inferred from direct assay. Source: UniProtKB membrane Inferred from direct assay. Source: UniProtKB
Molecular function	glutamate decarboxylase activity Inferred from electronic annotation. Source: EC protein binding Inferred from physical interaction. Source: IntAct pyridoxal phosphate binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
yadG	P36879	1	EBI-549514,EBI-550911

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 466

466

Glutamate decarboxylase beta

PRO_0000146982

Regions

Region

126 – 127

2

Pyridoxal phosphate binding

Sites

Binding site

62

1

Substrate

Binding site

83

1

Substrate

Binding site

212

1

Pyridoxal phosphate

Binding site

275

1

Pyridoxal phosphate

Amino acid modifications

Modified residue

276

1

N6-(pyridoxal phosphate)lysine

Modified residue

446

1

N6-acetyllysine Ref.15

Modified residue

453

1

N6-acetyllysine Ref.15

Modified residue

464

1

N6-acetyllysine Ref.15

Experimental info

Mutagenesis

276

1

K → A: Strongly reduces pyridoxal phosphate binding and increases stability of the polypeptide. Ref.8

Mutagenesis

276

1

K → H: Abolishes pyridoxal phosphate binding. Ref.8

Secondary structure

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466

Helix Strand Turn

Details...

Helix

4 – 14

11

Turn

17 – 19

3

Helix

21 – 23

3

Helix

39 – 49

11

Helix

50 – 52

3

Helix

56 – 58

3

Helix

70 – 78

9

Turn

79 – 81

3

Turn

87 – 89

3

Helix

91 – 107

17

Beta strand

119 – 125

7

Helix

126 – 148

23

Beta strand

156 – 161

6

Helix

164 – 172

9

Beta strand

176 – 179

4

Helix

191 – 197

7

Beta strand

202 – 206

5

Beta strand

208 – 210

3

Turn

212 – 214

3

Helix

220 – 234

15

Beta strand

240 – 243

4

Helix

247 – 249

3

Helix

251 – 254

4

Beta strand

267 – 273

7

Turn

274 – 278

5

Beta strand

285 – 291

7

Helix

292 – 294

3

Helix

297 – 299

3

Beta strand

301 – 305

5

Beta strand

308 – 312

5

Helix

322 – 358

37

Beta strand

363 – 368

6

Turn

371 – 373

3

Beta strand

374 – 382

9

Helix

392 – 400

9

Turn

401 – 403

3

Beta strand

408 – 410

3

Beta strand

419 – 424

6

Helix

431 – 450

20

Sequences

	Sequence		Length	Mass (Da)
	P69910-1 [UniParc]. Last modified January 4, 2005. Version 1. Checksum: 8E653330A3C5B4ED	FASTA	466	52,668
	10 20 30 40 50 60 MDKKQVTDLR SELLDSRFGA KSISTIAESK RFPLHEMRDD VAFQIINDEL YLDGNARQNL 70 80 90 100 110 120 ATFCQTWDDE NVHKLMDLSI NKNWIDKEEY PQSAAIDLRC VNMVADLWHA PAPKNGQAVG 130 140 150 160 170 180 TNTIGSSEAC MLGGMAMKWR WRKRMEAAGK PTDKPNLVCG PVQICWHKFA RYWDVELREI 190 200 210 220 230 240 PMRPGQLFMD PKRMIEACDE NTIGVVPTFG VTYTGNYEFP QPLHDALDKF QADTGIDIDM 250 260 270 280 290 300 HIDAASGGFL APFVAPDIVW DFRLPRVKSI SASGHKFGLA PLGCGWVIWR DEEALPQELV 310 320 330 340 350 360 FNVDYLGGQI GTFAINFSRP AGQVIAQYYE FLRLGREGYT KVQNASYQVA AYLADEIAKL 370 380 390 400 410 420 GPYEFICTGR PDEGIPAVCF KLKDGEDPGY TLYDLSERLR LRGWQVPAFT LGGEATDIVV 430 440 450 460 MRIMCRRGFE MDFAELLLED YKASLKYLSD HPKLQGIAQQ NSFKHT

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Escherichia coli has two homologous glutamate decarboxylase genes that map to distinct loci." Smith D.K., Kassam T., Singh B., Elliott J.F. J. Bacteriol. 174:5820-5826(1992) [PubMed: 1522060] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[2]	"A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 28.0-40.1 min region on the linkage map." Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T., Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T., Mizobuchi K., Mori H., Mori T., Motomura K. , Nakade S., Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G., Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Takeuchi Y., Wada C., Yamamoto Y., Horiuchi T. DNA Res. 3:363-377(1996) [PubMed: 9097039] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"Sequence and functional analysis of an Escherichia coli DNA fragment able to complement pqqE and pqqF mutants from Methylobacterium organophilum." Turlin E., Gasser F., Biville F. Biochimie 78:823-831(1996) [PubMed: 9116051] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-318. Strain: K12.
[6]	"Function of the Escherichia coli nucleoid protein, H-NS: molecular analysis of a subset of proteins whose expression is enhanced in a hns deletion mutant." Yoshida T., Ueguchi C., Yamada H., Mizuno T. Mol. Gen. Genet. 237:113-122(1993) [PubMed: 8455549] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-15. Strain: K12.
[7]	"The response to stationary-phase stress conditions in Escherichia coli: role and regulation of the glutamic acid decarboxylase system." De Biase D., Tramonti A., Bossa F., Visca P. Mol. Microbiol. 32:1198-1211(1999) [PubMed: 10383761] [Abstract] Cited for: TRANSCRIPTIONAL REGULATION. Strain: ATCC 11246.
[8]	"Contribution of Lys276 to the conformational flexibility of the active site of glutamate decarboxylase from Escherichia coli." Tramonti A., John R.A., Bossa F., De Biase D. Eur. J. Biochem. 269:4913-4920(2002) [PubMed: 12383249] [Abstract] Cited for: MUTAGENESIS OF LYS-276. Strain: K12 / JM109 / ATCC 53323.
[9]	"Functional characterization and regulation of gadX, a gene encoding an AraC/XylS-like transcriptional activator of the Escherichia coli glutamic acid decarboxylase system." Tramonti A., Visca P., De Canio M., Falconi M., De Biase D. J. Bacteriol. 184:2603-2613(2002) [PubMed: 11976288] [Abstract] Cited for: TRANSCRIPTIONAL REGULATION. Strain: ATCC 11246.
[10]	"Escherichia coli gene expression responsive to levels of the response regulator EvgA." Masuda N., Church G.M. J. Bacteriol. 184:6225-6234(2002) [PubMed: 12399493] [Abstract] Cited for: TRANSCRIPTIONAL REGULATION. Strain: K12 / MG1655 / ATCC 47076.
[11]	"Collaborative regulation of Escherichia coli glutamate-dependent acid resistance by two AraC-like regulators, GadX and GadW (YhiW)." Ma Z., Richard H., Tucker D.L., Conway T., Foster J.W. J. Bacteriol. 184:7001-7012(2002) [PubMed: 12446650] [Abstract] Cited for: TRANSCRIPTIONAL REGULATION. Strain: K12.
[12]	"Transcriptional expression of Escherichia coli glutamate-dependent acid resistance genes gadA and gadBC in an hns rpoS mutant." Waterman S.R., Small P.L.C. J. Bacteriol. 185:4644-4647(2003) [PubMed: 12867478] [Abstract] Cited for: TRANSCRIPTIONAL REGULATION.
[13]	"Regulatory network of acid resistance genes in Escherichia coli." Masuda N., Church G.M. Mol. Microbiol. 48:699-712(2003) [PubMed: 12694615] [Abstract] Cited for: TRANSCRIPTIONAL REGULATION. Strain: K12 / MG1655 / ATCC 47076.
[14]	"GadE (YhiE) activates glutamate decarboxylase-dependent acid resistance in Escherichia coli K-12." Ma Z., Gong S., Richard H., Tucker D.L., Conway T., Foster J.W. Mol. Microbiol. 49:1309-1320(2003) [PubMed: 12940989] [Abstract] Cited for: TRANSCRIPTIONAL REGULATION. Strain: K12.
[15]	"Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli." Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F., Grishin N.V., Zhao Y. Mol. Cell. Proteomics 8:215-225(2009) [PubMed: 18723842] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-446; LYS-453 AND LYS-464, MASS SPECTROMETRY.
[16]	"Crystal structure and functional analysis of Escherichia coli glutamate decarboxylase." Capitani G., De Biase D., Aurizi C., Gut H., Bossa F., Gruetter M.G. EMBO J. 22:4027-4037(2003) [PubMed: 12912902] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS), SUBUNIT, SUBCELLULAR LOCATION.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

M84025 Genomic DNA. Translation: AAA23834.1.
U00096 Genomic DNA. Translation: AAC74566.1.
AP009048 Genomic DNA. Translation: BAA15163.1.
X71917 Genomic DNA. Translation: CAA50736.1. Sequence problems.

PIR

B43332.

RefSeq

AP_002116.1.
NP_416010.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1PMM	X-ray	2.00	A/B/C/D/E/F	1-466	[»]
1PMO	X-ray	2.30	A/B/C/D/E/F	1-466	[»]
2DGK	X-ray	1.90	A/B/C/D/E/F	15-466	[»]
2DGL	X-ray	3.15	A/B/C/D/E/F	1-466	[»]
2DGM	X-ray	1.95	A/B/C/D/E/F	1-466	[»]
3FZ6	X-ray	2.82	A/B/C/D/E/F	1-466	[»]
3FZ7	X-ray	2.50	A/B/C/D/E/F	1-466	[»]
3FZ8	X-ray	3.00	A/B/C/D/E/F	1-466	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

P69910. 10 interactions.

STRING

P69910.

Genome annotation databases

GeneID

946058.

GenomeReviews

Gene locus JW1488 in contig AP009048_GR.
Gene locus b1493 in contig U00096_GR.

KEGG

ecj:JW1488.
eco:b1493.

Organism-specific databases

EchoBASE

EB1453.

EcoGene

EG11490. gadB.

CMR

Search...

Phylogenomic databases

HOGENOM

P69910.

OMA

AVDEDTI.

Enzyme and pathway databases

BioCyc

EcoCyc:GLUTDECARBOXB-MON.
MetaCyc:GLUTDECARBOXB-MON.

Gene expression databases

Genevestigator

P69910.

Family and domain databases

InterPro

IPR010107. Glutamate_decarboxylase.
IPR002129. PyrdxlP-dep_de-COase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
[Graphical view]

Gene3D

G3DSA:3.40.640.10. PyrdxlP-dep_Trfase_major_sub1. 1 hit.

PANTHER

PTHR11999:SF1. Glu_decarb_GAD. 1 hit.
PTHR11999. Pyridoxal_deC. 1 hit.

Pfam

PF00282. Pyridoxal_deC. 1 hit.
[Graphical view]

TIGRFAMs

TIGR01788. Glu-decarb-GAD. 1 hit.

PROSITE

PS00392. DDC_GAD_HDC_YDC. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

DCEB_ECOLI

Accession

Primary (citable) accession number: P69910
Secondary accession number(s): P28302, P76873

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 4, 2005
Last sequence update:	January 4, 2005
Last modified:	November 3, 2009
This is version 57 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)