Q42521 (DCE1_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Glutamate decarboxylase 1
Short name=GAD 1
EC=4.1.1.15

Gene names

Name:	GAD1
Synonyms:	GAD, GDH1
Ordered Locus Names:	At5g17330
ORF Names:	MKP11.30, MKP11_18

Organism

Arabidopsis thaliana (Mouse-ear cress) [Reference proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Viridiplantae › Streptophyta › Streptophytina › Embryophyta › Tracheophyta › Euphyllophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	502 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the production of GABA. The calmodulin-binding is calcium-dependent and it is proposed that this may, directly or indirectly, form a calcium regulated control of GABA biosynthesis. Ref.5
Catalytic activity	L-glutamate = 4-aminobutanoate + CO2.
Cofactor	Pyridoxal phosphate.
Enzyme regulation	Up-regulatd by calmodulin binding at physiological pH. Ref.10
Subunit structure	Homohexamer. Interacts with clamodulin with a 1:3 stoichiometry. Ref.1 Ref.5 Ref.10
Tissue specificity	Expressed in roots. Detected at low levels in shoots of young seedlings. Not detected in the root tips or in the central vascular bundle in the elongating region of mature roots. Ref.5 Ref.6 Ref.7 Ref.8
Induction	Down-regulated by salt treatment. Not induced by hypoxia. Ref.8 Ref.9 Ref.10
Domain	The N-terminus (1-57) is involved in the formation of the multimer. The C-terminus (471-502) binds calmodulin in a calcium-dependent fashion and contains probably an autoinhibitory domain.
Disruption phenotype	No visible phenotype, but increased glutamate levels and decreased GABA levels in the roots, and loss of GABA accumulation upon heat stress. Ref.7 Ref.8
Sequence similarities	Belongs to the group II decarboxylase family.
Biophysicochemical properties	pH dependence: Optimum pH is 6.0. Ref.10

Ontologies

Keywords
Ligand	Calmodulin-binding Pyridoxal phosphate
Molecular function	Decarboxylase Lyase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	glutamate metabolic process Inferred from electronic annotation. Source: InterPro response to cadmium ion Inferred from expression pattern PubMed 16502469. Source: TAIR
Cellular_component	cytosol Inferred from direct assay PubMed 21166475. Source: TAIR
Molecular_function	calmodulin binding Inferred from direct assay Ref.5. Source: TAIR glutamate decarboxylase activity Inferred from direct assay Ref.5. Source: TAIR 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 – 502

502

Glutamate decarboxylase 1

PRO_0000146973

Regions

Region

469 – 502

34

Calmodulin-binding

Sites

Site

496

1

Anchoring site for calmodulin binding; modulates the equilibrium between pyridoxal phosphate tautomers

Site

497

1

Anchoring site for calmodulin binding; modulates the equilibrium between pyridoxal phosphate tautomers

Amino acid modifications

Modified residue

277

1

N6-(pyridoxal phosphate)lysine

Experimental info

Mutagenesis

474 – 475

2

KK → AA: No effect.

Mutagenesis

489 – 490

2

KK → AA: No effect.

Mutagenesis

496

1

K → A: Decreased activity. When associated with A-497; threefold decreased activity, but still pH-dependent. Ref.10

Mutagenesis

497

1

K → A: Decreased activity. When associated with A-496; threefold decreased activity, but still pH-dependent. Ref.10

Mutagenesis

502

1

C → A: No effect. Ref.10

Sequence conflict

208

1

A → D in AAA93132. Ref.1

Secondary structure

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502

Helix Strand Turn

Details...

Turn

17 – 19

3

Helix

22 – 24

3

Beta strand

29 – 31

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 – 147

22

Beta strand

156 – 160

5

Helix

165 – 173

9

Beta strand

177 – 181

5

Helix

192 – 198

7

Beta strand

203 – 211

9

Turn

213 – 215

3

Helix

221 – 235

15

Beta strand

241 – 244

4

Helix

248 – 250

3

Helix

252 – 255

4

Beta strand

268 – 274

7

Turn

275 – 279

5

Beta strand

286 – 292

7

Helix

293 – 295

3

Helix

298 – 300

3

Beta strand

302 – 304

3

Beta strand

306 – 309

4

Beta strand

311 – 313

3

Helix

323 – 359

37

Turn

360 – 362

3

Beta strand

364 – 366

3

Beta strand

370 – 382

13

Helix

388 – 396

9

Turn

397 – 399

3

Beta strand

404 – 406

3

Beta strand

415 – 420

6

Helix

427 – 445

19

Sequences

	Sequence		Length	Mass (Da)
	Q42521 [UniParc]. Last modified May 27, 2002. Version 2. Checksum: 4E8141FF523E0E22	FASTA	502	57,066
	10 20 30 40 50 60 MVLSHAVSES DVSVHSTFAS RYVRTSLPRF KMPENSIPKE AAYQIINDEL MLDGNPRLNL 70 80 90 100 110 120 ASFVTTWMEP ECDKLIMSSI NKNYVDMDEY PVTTELQNRC VNMIAHLFNA PLEEAETAVG 130 140 150 160 170 180 VGTVGSSEAI MLAGLAFKRK WQNKRKAEGK PVDKPNIVTG ANVQVCWEKF ARYFEVELKE 190 200 210 220 230 240 VKLSEGYYVM DPQQAVDMVD ENTICVAAIL GSTLNGEFED VKLLNDLLVE KNKETGWDTP 250 260 270 280 290 300 IHVDAASGGF IAPFLYPELE WDFRLPLVKS INVSGHKYGL VYAGIGWVIW RNKEDLPEEL 310 320 330 340 350 360 IFHINYLGAD QPTFTLNFSK GSSQVIAQYY QLIRLGHEGY RNVMENCREN MIVLREGLEK 370 380 390 400 410 420 TERFNIVSKD EGVPLVAFSL KDSSCHTEFE ISDMLRRYGW IVPAYTMPPN AQHITVLRVV 430 440 450 460 470 480 IREDFSRTLA ERLVIDIEKV MRELDELPSR VIHKISLGQE KSESNSDNLM VTVKKSDIDK 490 500 QRDIITGWKK FVADRKKTSG IC

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Molecular and biochemical analysis of calmodulin interactions with the calmodulin-binding domain of plant glutamate decarboxylase." Arazi T., Baum G., Snedden W.A., Shelp B.J., Fromm H. Plant Physiol. 108:551-561(1995) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], INTERACTION WITH CALMODULIN. Strain: cv. Columbia.
[2]	"Structural analysis of Arabidopsis thaliana chromosome 5. I. Sequence features of the 1.6 Mb regions covered by twenty physically assigned P1 clones." Sato S., Kotani H., Nakamura Y., Kaneko T., Asamizu E., Fukami M., Miyajima N., Tabata S. DNA Res. 4:215-230(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[3]	The Arabidopsis Information Resource (TAIR) Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: cv. Columbia.
[4]	"Empirical analysis of transcriptional activity in the Arabidopsis genome." Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G. , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R. Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: cv. Columbia.
[5]	"Two isoforms of glutamate decarboxylase in Arabidopsis are regulated by calcium/calmodulin and differ in organ distribution." Zik M., Arazi T., Snedden W.A., Fromm H. Plant Mol. Biol. 37:967-975(1998) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INTERACTION WITH CLAMODULIN, TISSUE SPECIFICITY. Strain: cv. Columbia.
[6]	"Characterization of two glutamate decarboxylase cDNA clones from Arabidopsis." Turano F.J., Fang T.K. Plant Physiol. 117:1411-1421(1998) [PubMed] [Europe PMC] [Abstract] Cited for: TISSUE SPECIFICITY.
[7]	"The root-specific glutamate decarboxylase (GAD1) is essential for sustaining GABA levels in Arabidopsis." Bouche N., Fait A., Zik M., Fromm H. Plant Mol. Biol. 55:315-325(2004) [PubMed] [Europe PMC] [Abstract] Cited for: TISSUE SPECIFICITY, DISRUPTION PHENOTYPE. Strain: cv. Columbia.
[8]	"Contribution of the GABA shunt to hypoxia-induced alanine accumulation in roots of Arabidopsis thaliana." Miyashita Y., Good A.G. Plant Cell Physiol. 49:92-102(2008) [PubMed] [Europe PMC] [Abstract] Cited for: TISSUE SPECIFICITY, INDUCTION BY HYPOXIA, DISRUPTION PHENOTYPE.
[9]	"The Arabidopsis pop2-1 mutant reveals the involvement of GABA transaminase in salt stress tolerance." Renault H., Roussel V., El Amrani A., Arzel M., Renault D., Bouchereau A., Deleu C. BMC Plant Biol. 10:20-20(2010) [PubMed] [Europe PMC] [Abstract] Cited for: INDUCTION BY SALT.
[10]	"A common structural basis for pH- and calmodulin-mediated regulation in plant glutamate decarboxylase." Gut H., Dominici P., Pilati S., Astegno A., Petoukhov M.V., Svergun D.I., Gruetter M.G., Capitani G. J. Mol. Biol. 392:334-351(2009) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.67 ANGSTROMS), SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION, MUTAGENESIS OF 474-LYS-LYS-475; 489-LYS-LYS-490; LYS-496; LYS-497 AND CYS-502.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U10034 mRNA. Translation: AAA93132.1.
AB005238 Genomic DNA. Translation: BAB10520.1.
CP002688 Genomic DNA. Translation: AED92414.1.
AY094464 mRNA. Translation: AAM19834.1.
BT001047 mRNA. Translation: AAN46801.1.

IPI

IPI00530557.

RefSeq

NP_197235.1. NM_121739.3.

UniGene

At.25228.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3HBX	X-ray	2.67	A/B/C/D/E/F	1-502	[»]

ProteinModelPortal

Q42521.

SMR

Q42521. Positions 12-448.

ModBase

Search...

Protein-protein interaction databases

STRING

3702.AT5G17330.1-P.

Proteomic databases

PaxDb

Q42521.

PRIDE

Q42521.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblPlants

AT5G17330.1; AT5G17330.1; AT5G17330.

GeneID

831599.

KEGG

ath:AT5G17330.

Organism-specific databases

TAIR

At5g17330.

Phylogenomic databases

eggNOG

COG0076.

HOGENOM

HOG000070228.

InParanoid

Q42521.

KO

K01580.

OMA

YYVMDPQ.

PhylomeDB

Q42521.

ProtClustDB

CLSN2683665.

Gene expression databases

Genevestigator

Q42521.

GermOnline

AT5G17330. Arabidopsis thaliana.

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.
[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. False negative.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q42521.

Entry information

Entry name

DCE1_ARATH

Accession

Primary (citable) accession number: Q42521
Secondary accession number(s): Q9FFH9

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	May 27, 2002
Last modified:	May 1, 2013
This is version 99 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program