Glutamate decarboxylase beta - Escherichia coli (strain K12)

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P69910 (DCEB_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 87. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

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) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	466 AA.
Sequence status	Complete.
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. Ref.7 Ref.9 Ref.10 Ref.11 Ref.12 Ref.13 Ref.14
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 Reference proteome
Gene Ontology (GO)
Biological_process	glutamate metabolic process Inferred from electronic annotation. Source: InterPro intracellular pH elevation Inferred from mutant phenotype PubMed 10348866. Source: EcoCyc
Cellular_component	cytosol Inferred from direct assay PubMed 16858726. Source: UniProtKB membrane Inferred from direct assay PubMed 16858726. Source: UniProtKB
Molecular_function	glutamate decarboxylase activity Inferred from direct assay PubMed 8954890. Source: EcoCyc pyridoxal phosphate 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

Chain

1 – 466

466

Glutamate decarboxylase beta

PRO_0000146982

Regions

Region

126 – 127

Pyridoxal phosphate binding

Sites

Binding site

Substrate

Binding site

Substrate

Binding site

212

Pyridoxal phosphate

Binding site

275

Pyridoxal phosphate

Amino acid modifications

Modified residue

276

N6-(pyridoxal phosphate)lysine

Modified residue

446

N6-acetyllysine Ref.15

Modified residue

453

N6-acetyllysine Ref.15

Modified residue

464

N6-acetyllysine Ref.15

Experimental info

Mutagenesis

276

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

Mutagenesis

276

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

Secondary structure

466

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P69910 [UniParc].

Last modified January 4, 2005. Version 1.
Checksum: 8E653330A3C5B4ED
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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

« Hide

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] [Europe PMC] [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. Horiuchi T. DNA Res. 3:363-377(1996) [PubMed] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-446; LYS-453 AND LYS-464, MASS SPECTROMETRY. Strain: K12 / JW1106 and K12 / MG1655 / ATCC 47076.
[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] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS), SUBUNIT, SUBCELLULAR LOCATION.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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

NP_416010.1. NC_000913.2.
YP_489758.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

P69910.

SMR

P69910. Positions 3-456.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-36202N.

IntAct

P69910. 10 interactions.

MINT

MINT-1256225.

STRING

511145.b1493.

Proteomic databases

PaxDb

P69910.

PRIDE

P69910.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC74566; AAC74566; b1493.
BAA15163; BAA15163; BAA15163.

GeneID

12931794.
946058.

KEGG

ecj:Y75_p1469.
eco:b1493.

PATRIC

32118280. VBIEscCol129921_1560.

Organism-specific databases

EchoBASE

EB1453.

EcoGene

EG11490. gadB.

Phylogenomic databases

eggNOG

COG0076.

HOGENOM

HOG000070228.

K01580.

OMA

PMDKEHM.

ProtClustDB

CLSK880040.

Enzyme and pathway databases

BioCyc

EcoCyc:GLUTDECARBOXB-MONOMER.
ECOL316407:JW1488-MONOMER.
MetaCyc:GLUTDECARBOXB-MONOMER.

Gene expression databases

Genevestigator

P69910.

Family and domain databases

Gene3D

3.40.640.10. 1 hit.

InterPro

IPR010107. Glutamate_decarboxylase.
IPR002129. PyrdxlP-dep_de-COase.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR021115. Pyridoxal-P_BS.
[Graphical view]

PANTHER

PTHR11999:SF1. PTHR11999:SF1. 1 hit.

Pfam

PF00282. Pyridoxal_deC. 1 hit.
[Graphical view]

SUPFAM

SSF53383. PyrdxlP-dep_Trfase_major. 1 hit.

TIGRFAMs

TIGR01788. Glu-decarb-GAD. 1 hit.

PROSITE

PS00392. DDC_GAD_HDC_YDC. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P69910.

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:	May 1, 2013
This is version 87 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Amino acid modifications

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents