Q42472 (DCE2_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Glutamate decarboxylase 2
Short name=GAD 2
EC=4.1.1.15

Gene names

Name:	GAD2
Synonyms:	GDH2
Ordered Locus Names:	At1g65960
ORF Names:	F12P19.12

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	494 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.1
Catalytic activity	L-glutamate = 4-aminobutanoate + CO2.
Cofactor	Pyridoxal phosphate.
Enzyme regulation	Up-regulatd by calmodulin binding at physiological pH. Ref.9
Subunit structure	Homohexamer By similarity. Interacts with calmodulin. Ref.1
Tissue specificity	Expressed in roots, inflorescence stems, flowers, siliques and leaves. Ref.1 Ref.6 Ref.8
Induction	Up-regulated by salt or nitrogen treatments. Down-regulated by hypoxia. Ref.6 Ref.8 Ref.9 Ref.10
Domain	The C-terminus (463-494) binds calmodulin in a calcium-dependent fashion.
Disruption phenotype	No visible phenotype. Ref.7
Sequence similarities	Belongs to the group II decarboxylase family.
Biophysicochemical properties	pH dependence: Optimum pH is 6.0. Ref.9
Sequence caution	The sequence AAL91148.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended. The sequence AAL91148.1 differs from that shown. Reason: Frameshift at position 70.

Ontologies

Keywords
Coding sequence diversity	Alternative splicing
Ligand	Calmodulin-binding Pyridoxal phosphate
Molecular function	Decarboxylase Lyase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	glutamate metabolic process Inferred from direct assay Ref.1Ref.6. Source: TAIR
Molecular_function	glutamate decarboxylase activity Inferred from direct assay Ref.1Ref.6. Source: TAIR pyridoxal phosphate binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Alternative products

This entry describes 1 isoform produced by alternative splicing. [Select]

Note: A number of isoforms are produced. According to EST sequences.

Isoform 1 (identifier: Q42472-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 494	494	Glutamate decarboxylase 2		PRO_0000146974
Regions
	Region	463 – 494	32	Calmodulin-binding
Sites
	Site	488	1	Anchoring site for calmodulin binding; modulates the equilibrium between pyridoxal phosphate tautomers By similarity
	Site	489	1	Anchoring site for calmodulin binding; modulates the equilibrium between pyridoxal phosphate tautomers By similarity
Amino acid modifications
	Modified residue	276	1	N6-(pyridoxal phosphate)lysine By similarity
Experimental info
	Sequence conflict	410	1	A → V in AAL16126. Ref.5
	Sequence conflict	461	1	E → K in AAL91148. Ref.5

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified November 1, 1997. Version 1. Checksum: 741E83A25DCBC48C	FASTA	494	56,141
	10 20 30 40 50 60 MVLTKTATND ESVCTMFGSR YVRTTLPKYE IGENSIPKDA AYQIIKDELM LDGNPRLNLA 70 80 90 100 110 120 SFVTTWMEPE CDKLIMDSIN KNYVDMDEYP VTTELQNRCV NIIARLFNAP LEESETAVGV 130 140 150 160 170 180 GTVGSSEAIM LAGLAFKRKW QNKRKAEGKP YDKPNIVTGA NVQVCWEKFA RYFEVELKEV 190 200 210 220 230 240 NLSEGYYVMD PDKAAEMVDE NTICVAAILG STLNGEFEDV KRLNDLLVKK NEETGWNTPI 250 260 270 280 290 300 HVDAASGGFI APFIYPELEW DFRLPLVKSI NVSGHKYGLV YAGIGWVVWR AAEDLPEELI 310 320 330 340 350 360 FHINYLGADQ PTFTLNFSKG SSQIIAQYYQ LIRLGFEGYK NVMENCIENM VVLKEGIEKT 370 380 390 400 410 420 ERFNIVSKDQ GVPVVAFSLK DHSFHNEFEI SEMLRRFGWI VPAYTMPADA QHITVLRVVI 430 440 450 460 470 480 REDFSRTLAE RLVADISKVL HELDTLPSKI SKKMGIEGIA ENVKEKKMEK EILMEVIVGW 490 RKFVKERKKM NGVC

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"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: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, INTERACTION WITH CLAMODULIN, TISSUE SPECIFICITY. Strain: cv. Columbia.
[2]	"Characterization and expression of NAD(H)-dependent glutamate dehydrogenase genes in Arabidopsis." Turano F.J., Thakkar S.S., Fang T., Weisemann J.M. Plant Physiol. 113:1329-1341(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA]. Strain: cv. Columbia.
[3]	"Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana." Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K. , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W. Nature 408:816-820(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[4]	The Arabidopsis Information Resource (TAIR) Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: cv. Columbia.
[5]	"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.
[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, INDUCTION BY NITROGEN.
[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: 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.
[9]	"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: BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION.
[10]	"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.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	U49937 mRNA. Translation: AAC31617.1. U46665 mRNA. Translation: AAC33485.1. AC009513 Genomic DNA. Translation: AAF06056.1. CP002684 Genomic DNA. Translation: AEE34445.1. AF428294 mRNA. Translation: AAL16126.1. AF428372 mRNA. Translation: AAL16302.1. AY124873 mRNA. Translation: AAM70582.1. AY081259 mRNA. Translation: AAL91148.1. Sequence problems.
IPI	IPI00534442.
PIR	H96683.
RefSeq	NP_001117556.1. NM_001124084.1.
UniGene	At.19149. At.20543. At.24993. At.66846.
3D structure databases
HSSP	HSSP built from PDB template 1PMM based on UniProtKB P28302.
ProteinModelPortal	Q42472.
SMR	Q42472. Positions 12-447.
ModBase	Search...
Protein-protein interaction databases
STRING	3702.AT1G65960.2-P.
Proteomic databases
PaxDb	Q42472.
PRIDE	Q42472.
Protocols and materials databases
DNASU	842908.
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	AT1G65960.2; AT1G65960.2; AT1G65960.
GeneID	842908.
KEGG	ath:AT1G65960.
Organism-specific databases
TAIR	At1g65960.
Phylogenomic databases
eggNOG	COG0076.
HOGENOM	HOG000070228.
InParanoid	Q42472.
KO	K01580.
OMA	MENCIEN.
PhylomeDB	Q42472.
ProtClustDB	CLSN2683665.
Gene expression databases
ArrayExpress	Q42472.
Genevestigator	Q42472.
GermOnline	AT1G65960. 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...

Entry information

Entry name

DCE2_ARATH

Accession

Primary (citable) accession number: Q42472
Secondary accession number(s): Q8RXH0, Q944L6

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	November 1, 1997
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

Plant Protein Annotation Program