DCE1_ARATH
ID DCE1_ARATH Reviewed; 502 AA.
AC Q42521; Q9FFH9;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 27-MAY-2002, sequence version 2.
DT 03-AUG-2022, entry version 157.
DE RecName: Full=Glutamate decarboxylase 1;
DE Short=GAD 1 {ECO:0000303|PubMed:9700069};
DE EC=4.1.1.15 {ECO:0000305|PubMed:9700069};
GN Name=GAD1; Synonyms=GAD, GDH1; OrderedLocusNames=At5g17330;
GN ORFNames=MKP11.30, MKP11_18;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], AND INTERACTION WITH CALMODULIN.
RC STRAIN=cv. Columbia;
RX PubMed=7610159; DOI=10.1104/pp.108.2.551;
RA Arazi T., Baum G., Snedden W.A., Shelp B.J., Fromm H.;
RT "Molecular and biochemical analysis of calmodulin interactions with the
RT calmodulin-binding domain of plant glutamate decarboxylase.";
RL Plant Physiol. 108:551-561(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=9330910; DOI=10.1093/dnares/4.3.215;
RA Sato S., Kotani H., Nakamura Y., Kaneko T., Asamizu E., Fukami M.,
RA Miyajima N., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. I. Sequence
RT features of the 1.6 Mb regions covered by twenty physically assigned P1
RT clones.";
RL DNA Res. 4:215-230(1997).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, INTERACTION WITH CALMODULIN, AND TISSUE
RP SPECIFICITY.
RC STRAIN=cv. Columbia;
RX PubMed=9700069; DOI=10.1023/a:1006047623263;
RA Zik M., Arazi T., Snedden W.A., Fromm H.;
RT "Two isoforms of glutamate decarboxylase in Arabidopsis are regulated by
RT calcium/calmodulin and differ in organ distribution.";
RL Plant Mol. Biol. 37:967-975(1998).
RN [6]
RP TISSUE SPECIFICITY.
RX PubMed=9701597; DOI=10.1104/pp.117.4.1411;
RA Turano F.J., Fang T.K.;
RT "Characterization of two glutamate decarboxylase cDNA clones from
RT Arabidopsis.";
RL Plant Physiol. 117:1411-1421(1998).
RN [7]
RP TISSUE SPECIFICITY, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=15604684; DOI=10.1007/s11103-004-0650-z;
RA Bouche N., Fait A., Zik M., Fromm H.;
RT "The root-specific glutamate decarboxylase (GAD1) is essential for
RT sustaining GABA levels in Arabidopsis.";
RL Plant Mol. Biol. 55:315-325(2004).
RN [8]
RP TISSUE SPECIFICITY, INDUCTION BY HYPOXIA, AND DISRUPTION PHENOTYPE.
RX PubMed=18077464; DOI=10.1093/pcp/pcm171;
RA Miyashita Y., Good A.G.;
RT "Contribution of the GABA shunt to hypoxia-induced alanine accumulation in
RT roots of Arabidopsis thaliana.";
RL Plant Cell Physiol. 49:92-102(2008).
RN [9]
RP INDUCTION BY SALT.
RX PubMed=20122158; DOI=10.1186/1471-2229-10-20;
RA Renault H., Roussel V., El Amrani A., Arzel M., Renault D., Bouchereau A.,
RA Deleu C.;
RT "The Arabidopsis pop2-1 mutant reveals the involvement of GABA transaminase
RT in salt stress tolerance.";
RL BMC Plant Biol. 10:20-20(2010).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (2.67 ANGSTROMS), SUBUNIT, BIOPHYSICOCHEMICAL
RP PROPERTIES, ACTIVITY REGULATION, AND MUTAGENESIS OF 474-LYS-LYS-475;
RP 489-LYS-LYS-490; LYS-496; LYS-497 AND CYS-502.
RX PubMed=19580813; DOI=10.1016/j.jmb.2009.06.080;
RA Gut H., Dominici P., Pilati S., Astegno A., Petoukhov M.V., Svergun D.I.,
RA Gruetter M.G., Capitani G.;
RT "A common structural basis for pH- and calmodulin-mediated regulation in
RT plant glutamate decarboxylase.";
RL J. Mol. Biol. 392:334-351(2009).
CC -!- FUNCTION: Catalyzes the conversion of glutamate to 4-aminobutanoate
CC (GABA). The calmodulin-binding is calcium-dependent and it is proposed
CC to directly or indirectly form a calcium regulated control of GABA
CC biosynthesis. {ECO:0000269|PubMed:9700069}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H(+) + L-glutamate = 4-aminobutanoate + CO2;
CC Xref=Rhea:RHEA:17785, ChEBI:CHEBI:15378, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:29985, ChEBI:CHEBI:59888; EC=4.1.1.15;
CC Evidence={ECO:0000305|PubMed:9700069};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:17786;
CC Evidence={ECO:0000305|PubMed:9700069};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC -!- ACTIVITY REGULATION: Up-regulated by calmodulin binding at
CC physiological pH. {ECO:0000269|PubMed:19580813}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 6.0. {ECO:0000269|PubMed:19580813};
CC -!- SUBUNIT: Homohexamer. Interacts with calmodulin with a 1:3
CC stoichiometry. {ECO:0000269|PubMed:19580813,
CC ECO:0000269|PubMed:7610159, ECO:0000269|PubMed:9700069}.
CC -!- TISSUE SPECIFICITY: Expressed in roots. Detected at low levels in
CC shoots of young seedlings. Not detected in the root tips or in the
CC central vascular bundle in the elongating region of mature roots.
CC {ECO:0000269|PubMed:15604684, ECO:0000269|PubMed:18077464,
CC ECO:0000269|PubMed:9700069, ECO:0000269|PubMed:9701597}.
CC -!- INDUCTION: Down-regulated by salt treatment. Not induced by hypoxia.
CC {ECO:0000269|PubMed:18077464, ECO:0000269|PubMed:20122158}.
CC -!- DOMAIN: The N-terminus (1-57) is involved in the formation of the
CC multimer. The C-terminus (471-502) binds calmodulin in a calcium-
CC dependent fashion and contains probably an autoinhibitory domain.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype, but increased glutamate
CC levels and decreased GABA levels in the roots, and loss of GABA
CC accumulation upon heat stress. {ECO:0000269|PubMed:15604684,
CC ECO:0000269|PubMed:18077464}.
CC -!- SIMILARITY: Belongs to the group II decarboxylase family.
CC {ECO:0000305}.
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DR EMBL; U10034; AAA93132.1; -; mRNA.
DR EMBL; AB005238; BAB10520.1; -; Genomic_DNA.
DR EMBL; CP002688; AED92414.1; -; Genomic_DNA.
DR EMBL; AY094464; AAM19834.1; -; mRNA.
DR EMBL; BT001047; AAN46801.1; -; mRNA.
DR RefSeq; NP_197235.1; NM_121739.4.
DR PDB; 3HBX; X-ray; 2.67 A; A/B/C/D/E/F=1-502.
DR PDBsum; 3HBX; -.
DR AlphaFoldDB; Q42521; -.
DR SMR; Q42521; -.
DR BioGRID; 16875; 4.
DR STRING; 3702.AT5G17330.1; -.
DR iPTMnet; Q42521; -.
DR MetOSite; Q42521; -.
DR PaxDb; Q42521; -.
DR PRIDE; Q42521; -.
DR ProteomicsDB; 222197; -.
DR EnsemblPlants; AT5G17330.1; AT5G17330.1; AT5G17330.
DR GeneID; 831599; -.
DR Gramene; AT5G17330.1; AT5G17330.1; AT5G17330.
DR KEGG; ath:AT5G17330; -.
DR Araport; AT5G17330; -.
DR TAIR; locus:2167240; AT5G17330.
DR eggNOG; KOG1383; Eukaryota.
DR HOGENOM; CLU_019582_2_2_1; -.
DR InParanoid; Q42521; -.
DR OMA; KKTSGIC; -.
DR OrthoDB; 521159at2759; -.
DR PhylomeDB; Q42521; -.
DR BioCyc; ARA:AT5G17330-MON; -.
DR BRENDA; 4.1.1.15; 399.
DR EvolutionaryTrace; Q42521; -.
DR PRO; PR:Q42521; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q42521; baseline and differential.
DR Genevisible; Q42521; AT.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005516; F:calmodulin binding; IDA:TAIR.
DR GO; GO:0004351; F:glutamate decarboxylase activity; IDA:TAIR.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IEA:InterPro.
DR GO; GO:0006538; P:glutamate catabolic process; IBA:GO_Central.
DR DisProt; DP02726; -.
DR Gene3D; 3.40.640.10; -; 1.
DR InterPro; IPR010107; Glutamate_decarboxylase.
DR InterPro; IPR002129; PyrdxlP-dep_de-COase.
DR InterPro; IPR015424; PyrdxlP-dep_Trfase.
DR InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
DR PANTHER; PTHR43321; PTHR43321; 1.
DR Pfam; PF00282; Pyridoxal_deC; 1.
DR SUPFAM; SSF53383; SSF53383; 1.
DR TIGRFAMs; TIGR01788; Glu-decarb-GAD; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Calmodulin-binding; Decarboxylase; Lyase; Phosphoprotein;
KW Pyridoxal phosphate; Reference proteome.
FT CHAIN 1..502
FT /note="Glutamate decarboxylase 1"
FT /id="PRO_0000146973"
FT REGION 469..502
FT /note="Calmodulin-binding"
FT SITE 496
FT /note="Anchoring site for calmodulin binding; modulates the
FT equilibrium between pyridoxal phosphate tautomers"
FT SITE 497
FT /note="Anchoring site for calmodulin binding; modulates the
FT equilibrium between pyridoxal phosphate tautomers"
FT MOD_RES 8
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9ZPS3"
FT MOD_RES 277
FT /note="N6-(pyridoxal phosphate)lysine"
FT MUTAGEN 474..475
FT /note="KK->AA: No effect."
FT /evidence="ECO:0000269|PubMed:19580813"
FT MUTAGEN 489..490
FT /note="KK->AA: No effect."
FT /evidence="ECO:0000269|PubMed:19580813"
FT MUTAGEN 496
FT /note="K->A: Decreased activity. When associated with A-
FT 497; threefold decreased activity, but still pH-dependent."
FT /evidence="ECO:0000269|PubMed:19580813"
FT MUTAGEN 497
FT /note="K->A: Decreased activity. When associated with A-
FT 496; threefold decreased activity, but still pH-dependent."
FT /evidence="ECO:0000269|PubMed:19580813"
FT MUTAGEN 502
FT /note="C->A: No effect."
FT /evidence="ECO:0000269|PubMed:19580813"
FT CONFLICT 208
FT /note="A -> D (in Ref. 1; AAA93132)"
FT /evidence="ECO:0000305"
FT TURN 17..19
FT /evidence="ECO:0007829|PDB:3HBX"
FT HELIX 22..24
FT /evidence="ECO:0007829|PDB:3HBX"
FT STRAND 29..31
FT /evidence="ECO:0007829|PDB:3HBX"
FT HELIX 39..49
FT /evidence="ECO:0007829|PDB:3HBX"
FT HELIX 50..52
FT /evidence="ECO:0007829|PDB:3HBX"
FT HELIX 56..58
FT /evidence="ECO:0007829|PDB:3HBX"
FT HELIX 70..78
FT /evidence="ECO:0007829|PDB:3HBX"
FT TURN 79..81
FT /evidence="ECO:0007829|PDB:3HBX"
FT TURN 87..89
FT /evidence="ECO:0007829|PDB:3HBX"
FT HELIX 91..107
FT /evidence="ECO:0007829|PDB:3HBX"
FT STRAND 119..125
FT /evidence="ECO:0007829|PDB:3HBX"
FT HELIX 126..147
FT /evidence="ECO:0007829|PDB:3HBX"
FT STRAND 156..160
FT /evidence="ECO:0007829|PDB:3HBX"
FT HELIX 165..173
FT /evidence="ECO:0007829|PDB:3HBX"
FT STRAND 177..181
FT /evidence="ECO:0007829|PDB:3HBX"
FT HELIX 192..198
FT /evidence="ECO:0007829|PDB:3HBX"
FT STRAND 203..211
FT /evidence="ECO:0007829|PDB:3HBX"
FT TURN 213..215
FT /evidence="ECO:0007829|PDB:3HBX"
FT HELIX 221..235
FT /evidence="ECO:0007829|PDB:3HBX"
FT STRAND 241..244
FT /evidence="ECO:0007829|PDB:3HBX"
FT HELIX 248..250
FT /evidence="ECO:0007829|PDB:3HBX"
FT HELIX 252..255
FT /evidence="ECO:0007829|PDB:3HBX"
FT STRAND 268..274
FT /evidence="ECO:0007829|PDB:3HBX"
FT STRAND 286..292
FT /evidence="ECO:0007829|PDB:3HBX"
FT HELIX 293..295
FT /evidence="ECO:0007829|PDB:3HBX"
FT HELIX 298..300
FT /evidence="ECO:0007829|PDB:3HBX"
FT STRAND 302..304
FT /evidence="ECO:0007829|PDB:3HBX"
FT STRAND 306..309
FT /evidence="ECO:0007829|PDB:3HBX"
FT STRAND 311..313
FT /evidence="ECO:0007829|PDB:3HBX"
FT HELIX 323..359
FT /evidence="ECO:0007829|PDB:3HBX"
FT TURN 360..362
FT /evidence="ECO:0007829|PDB:3HBX"
FT STRAND 364..366
FT /evidence="ECO:0007829|PDB:3HBX"
FT STRAND 370..382
FT /evidence="ECO:0007829|PDB:3HBX"
FT HELIX 388..396
FT /evidence="ECO:0007829|PDB:3HBX"
FT TURN 397..399
FT /evidence="ECO:0007829|PDB:3HBX"
FT STRAND 404..406
FT /evidence="ECO:0007829|PDB:3HBX"
FT STRAND 415..420
FT /evidence="ECO:0007829|PDB:3HBX"
FT HELIX 427..445
FT /evidence="ECO:0007829|PDB:3HBX"
SQ SEQUENCE 502 AA; 57066 MW; 4E8141FF523E0E22 CRC64;
MVLSHAVSES DVSVHSTFAS RYVRTSLPRF KMPENSIPKE AAYQIINDEL MLDGNPRLNL
ASFVTTWMEP ECDKLIMSSI NKNYVDMDEY PVTTELQNRC VNMIAHLFNA PLEEAETAVG
VGTVGSSEAI MLAGLAFKRK WQNKRKAEGK PVDKPNIVTG ANVQVCWEKF ARYFEVELKE
VKLSEGYYVM DPQQAVDMVD ENTICVAAIL GSTLNGEFED VKLLNDLLVE KNKETGWDTP
IHVDAASGGF IAPFLYPELE WDFRLPLVKS INVSGHKYGL VYAGIGWVIW RNKEDLPEEL
IFHINYLGAD QPTFTLNFSK GSSQVIAQYY QLIRLGHEGY RNVMENCREN MIVLREGLEK
TERFNIVSKD EGVPLVAFSL KDSSCHTEFE ISDMLRRYGW IVPAYTMPPN AQHITVLRVV
IREDFSRTLA ERLVIDIEKV MRELDELPSR VIHKISLGQE KSESNSDNLM VTVKKSDIDK
QRDIITGWKK FVADRKKTSG IC
