GCSP1_ARATH
ID GCSP1_ARATH Reviewed; 1037 AA.
AC Q94B78; O82642; Q8GTY1; Q8VZF0;
DT 26-APR-2004, integrated into UniProtKB/Swiss-Prot.
DT 26-APR-2004, sequence version 2.
DT 03-AUG-2022, entry version 144.
DE RecName: Full=Glycine dehydrogenase (decarboxylating) 1, mitochondrial;
DE EC=1.4.4.2;
DE AltName: Full=Glycine cleavage system P protein 1;
DE AltName: Full=Glycine decarboxylase 1;
DE AltName: Full=Glycine decarboxylase P-protein 1;
DE Short=AtGLDP1;
DE AltName: Full=Glycine dehydrogenase (aminomethyl-transferring) 1;
DE Flags: Precursor;
GN Name=GLDP1; Synonyms=GDP1; OrderedLocusNames=At4g33010;
GN ORFNames=F26P21.130;
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
RN [2]
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 [3]
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 [4]
RP REVIEW.
RX PubMed=11286922; DOI=10.1016/s1360-1385(01)01892-1;
RA Douce R., Bourguignon J., Neuburger M., Rebeille F.;
RT "The glycine decarboxylase system: a fascinating complex.";
RL Trends Plant Sci. 6:167-176(2001).
RN [5]
RP REVIEW, AND NOMENCLATURE.
RX PubMed=12730263; DOI=10.1093/jxb/erg171;
RA Bauwe H., Kolukisaoglu U.;
RT "Genetic manipulation of glycine decarboxylation.";
RL J. Exp. Bot. 54:1523-1535(2003).
RN [6]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND SUBCELLULAR LOCATION [LARGE SCALE
RP ANALYSIS].
RC STRAIN=cv. Landsberg erecta;
RX PubMed=14671022; DOI=10.1105/tpc.016055;
RA Heazlewood J.L., Tonti-Filippini J.S., Gout A.M., Day D.A., Whelan J.,
RA Millar A.H.;
RT "Experimental analysis of the Arabidopsis mitochondrial proteome highlights
RT signaling and regulatory components, provides assessment of targeting
RT prediction programs, and indicates plant-specific mitochondrial proteins.";
RL Plant Cell 16:241-256(2004).
RN [7]
RP FUNCTION, DISRUPTION PHENOTYPE, AND TISSUE SPECIFICITY.
RC STRAIN=cv. Columbia, and cv. Wassilewskija;
RX PubMed=17496108; DOI=10.1104/pp.107.099317;
RA Engel N., van den Daele K., Kolukisaoglu U., Morgenthal K., Weckwerth W.,
RA Paernik T., Keerberg O., Bauwe H.;
RT "Deletion of glycine decarboxylase in Arabidopsis is lethal under
RT nonphotorespiratory conditions.";
RL Plant Physiol. 144:1328-1335(2007).
RN [8]
RP ACTIVITY REGULATION, S-NITROSYLATION, AND GLUTATHIONYLATION AT CYS-98;
RP CYS-402; CYS-463; CYS-777; CYS-943 AND CYS-1022.
RX PubMed=20089767; DOI=10.1104/pp.109.152579;
RA Palmieri M.C., Lindermayr C., Bauwe H., Steinhauser C., Durner J.;
RT "Regulation of plant glycine decarboxylase by s-nitrosylation and
RT glutathionylation.";
RL Plant Physiol. 152:1514-1528(2010).
CC -!- FUNCTION: The glycine decarboxylase (GDC) or glycine cleavage system
CC catalyzes the degradation of glycine. The P protein binds the alpha-
CC amino group of glycine through its pyridoxal phosphate cofactor; CO(2)
CC is released and the remaining methylamine moiety is then transferred to
CC the lipoamide cofactor of the H protein (By similarity). {ECO:0000250,
CC ECO:0000269|PubMed:17496108}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(R)-N(6)-lipoyl-L-lysyl-[glycine-cleavage complex H protein] +
CC glycine + H(+) = (R)-N(6)-(S(8)-aminomethyldihydrolipoyl)-L-lysyl-
CC [glycine-cleavage complex H protein] + CO2; Xref=Rhea:RHEA:24304,
CC Rhea:RHEA-COMP:10494, Rhea:RHEA-COMP:10495, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16526, ChEBI:CHEBI:57305, ChEBI:CHEBI:83099,
CC ChEBI:CHEBI:83143; EC=1.4.4.2;
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000250};
CC -!- ACTIVITY REGULATION: Inhibited by harpin, S-nitrosoglutathione (GSNO),
CC nitric oxide, N-ethylmaleimide and 5,5'-dithiobis-(2-nitrobenzoic
CC acid). {ECO:0000269|PubMed:20089767}.
CC -!- SUBUNIT: Homodimer (By similarity). The glycine cleavage system is
CC composed of four proteins: P, T, L and H. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14671022}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=1;
CC Comment=A number of isoforms are produced. According to EST
CC sequences.;
CC Name=1;
CC IsoId=Q94B78-1; Sequence=Displayed;
CC -!- TISSUE SPECIFICITY: Expressed in leaves. Detected in roots, stems,
CC flowers and siliques. {ECO:0000269|PubMed:17496108}.
CC -!- PTM: Glutathionylated at Cys-98, Cys-777, Cys-943 and Cys-1022 after S-
CC nitrosoglutathione treatment. {ECO:0000269|PubMed:20089767}.
CC -!- PTM: S-nitrosylated at unknown positions by nitric oxide.
CC {ECO:0000269|PubMed:20089767}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype; due to the redundancy with
CC GLDP2. Gldp1 and gldp2 double mutants have a seedling development
CC arrested at the cotyledon stage even under nonphotorespiratory
CC conditions. {ECO:0000269|PubMed:17496108}.
CC -!- SIMILARITY: Belongs to the GcvP family. {ECO:0000305}.
CC -!- CAUTION: This protein has also been shown to act as an inducible nitric
CC oxide synthase (iNOS) (PubMed:12757708), but the paper has been
CC retracted (PubMed:15599984). {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAN17423.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; AL031804; CAA21210.1; -; Genomic_DNA.
DR EMBL; AL161582; CAB80018.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE86159.1; -; Genomic_DNA.
DR EMBL; AY063903; AAL36259.1; -; mRNA.
DR EMBL; AY091186; AAM14125.1; -; mRNA.
DR EMBL; AY042800; AAK68740.1; -; mRNA.
DR EMBL; AY128922; AAM91322.1; -; mRNA.
DR EMBL; AY065004; AAL57651.1; -; mRNA.
DR EMBL; BT001132; AAN64523.1; -; mRNA.
DR EMBL; BT000446; AAN17423.1; ALT_FRAME; mRNA.
DR PIR; T05309; T05309.
DR RefSeq; NP_195027.1; NM_119455.3. [Q94B78-1]
DR AlphaFoldDB; Q94B78; -.
DR SMR; Q94B78; -.
DR BioGRID; 14723; 8.
DR IntAct; Q94B78; 1.
DR STRING; 3702.AT4G33010.1; -.
DR iPTMnet; Q94B78; -.
DR PaxDb; Q94B78; -.
DR PRIDE; Q94B78; -.
DR ProteomicsDB; 222042; -. [Q94B78-1]
DR EnsemblPlants; AT4G33010.1; AT4G33010.1; AT4G33010. [Q94B78-1]
DR GeneID; 829438; -.
DR Gramene; AT4G33010.1; AT4G33010.1; AT4G33010. [Q94B78-1]
DR KEGG; ath:AT4G33010; -.
DR Araport; AT4G33010; -.
DR TAIR; locus:2123777; AT4G33010.
DR eggNOG; KOG2040; Eukaryota.
DR InParanoid; Q94B78; -.
DR OMA; CVPMSEY; -.
DR PhylomeDB; Q94B78; -.
DR BioCyc; ARA:AT4G33010-MON; -.
DR BRENDA; 1.4.1.27; 399.
DR PRO; PR:Q94B78; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q94B78; baseline and differential.
DR Genevisible; Q94B78; AT.
DR GO; GO:0048046; C:apoplast; HDA:TAIR.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0009941; C:chloroplast envelope; HDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0009534; C:chloroplast thylakoid; HDA:TAIR.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0005960; C:glycine cleavage complex; IBA:GO_Central.
DR GO; GO:0005739; C:mitochondrion; HDA:TAIR.
DR GO; GO:0005886; C:plasma membrane; HDA:TAIR.
DR GO; GO:0016594; F:glycine binding; IBA:GO_Central.
DR GO; GO:0004375; F:glycine dehydrogenase (decarboxylating) activity; IBA:GO_Central.
DR GO; GO:0003729; F:mRNA binding; IDA:TAIR.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IBA:GO_Central.
DR GO; GO:0006546; P:glycine catabolic process; IMP:TAIR.
DR GO; GO:0019464; P:glycine decarboxylation via glycine cleavage system; IBA:GO_Central.
DR GO; GO:0046686; P:response to cadmium ion; IEP:TAIR.
DR CDD; cd00613; GDC-P; 2.
DR Gene3D; 3.40.640.10; -; 2.
DR Gene3D; 3.90.1150.10; -; 2.
DR HAMAP; MF_00711; GcvP; 1.
DR InterPro; IPR003437; GcvP.
DR InterPro; IPR020581; GDC_P.
DR InterPro; IPR015424; PyrdxlP-dep_Trfase.
DR InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
DR InterPro; IPR015422; PyrdxlP-dep_Trfase_small.
DR PANTHER; PTHR11773; PTHR11773; 1.
DR Pfam; PF02347; GDC-P; 2.
DR SUPFAM; SSF53383; SSF53383; 2.
DR TIGRFAMs; TIGR00461; gcvP; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Glutathionylation; Mitochondrion; Oxidoreductase;
KW Pyridoxal phosphate; Reference proteome; S-nitrosylation; Transit peptide.
FT TRANSIT 1..67
FT /note="Mitochondrion"
FT /evidence="ECO:0000305"
FT CHAIN 68..1037
FT /note="Glycine dehydrogenase (decarboxylating) 1,
FT mitochondrial"
FT /id="PRO_0000010744"
FT MOD_RES 98
FT /note="S-glutathionyl cysteine; transient"
FT /evidence="ECO:0000269|PubMed:20089767"
FT MOD_RES 402
FT /note="S-glutathionyl cysteine"
FT /evidence="ECO:0000269|PubMed:20089767"
FT MOD_RES 463
FT /note="S-glutathionyl cysteine"
FT /evidence="ECO:0000269|PubMed:20089767"
FT MOD_RES 774
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000250"
FT MOD_RES 777
FT /note="S-glutathionyl cysteine; transient"
FT /evidence="ECO:0000269|PubMed:20089767"
FT MOD_RES 943
FT /note="S-glutathionyl cysteine; transient"
FT /evidence="ECO:0000269|PubMed:20089767"
FT MOD_RES 1022
FT /note="S-glutathionyl cysteine; transient"
FT /evidence="ECO:0000269|PubMed:20089767"
FT CONFLICT 578
FT /note="C -> R (in Ref. 3; AAN17423)"
FT /evidence="ECO:0000305"
FT CONFLICT 884
FT /note="H -> R (in Ref. 3; AAL57651/AAN64523)"
FT /evidence="ECO:0000305"
FT CONFLICT 925
FT /note="T -> A (in Ref. 3; AAN17423)"
FT /evidence="ECO:0000305"
FT CONFLICT 1032
FT /note="A -> T (in Ref. 3; AAK68740/AAM91322)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1037 AA; 112925 MW; 168C11DB642687A5 CRC64;
MERARRLAYR GIVKRLVNDT KRHRNAETPH LVPHAPARYV SSLSPFISTP RSVNHTAAFG
RHQQTRSISV DAVKPSDTFP RRHNSATPDE QTHMAKFCGF DHIDSLIDAT VPKSIRLDSM
KFSKFDAGLT ESQMIQHMVD LASKNKVFKS FIGMGYYNTH VPTVILRNIM ENPAWYTQYT
PYQAEISQGR LESLLNFQTV ITDLTGLPMS NASLLDEGTA AAEAMAMCNN ILKGKKKTFV
IASNCHPQTI DVCKTRADGF DLKVVTSDLK DIDYSSGDVC GVLVQYPGTE GEVLDYAEFV
KNAHANGVKV VMATDLLALT VLKPPGEFGA DIVVGSAQRF GVPMGYGGPH AAFLATSQEY
KRMMPGRIIG ISVDSSGKQA LRMAMQTREQ HIRRDKATSN ICTAQALLAN MAAMYAVYHG
PAGLKSIAQR VHGLAGIFSL GLNKLGVAEV QELPFFDTVK IKCSDAHAIA DAASKSEINL
RVVDSTTITA SFDETTTLDD VDKLFKVFAS GKPVPFTAES LAPEVQNSIP SSLTRESPYL
THPIFNMYHT EHELLRYIHK LQSKDLSLCH SMIPLGSCTM KLNATTEMMP VTWPSFTDIH
PFAPVEQAQG YQEMFENLGD LLCTITGFDS FSLQPNAGAA GEYAGLMVIR AYHMSRGDHH
RNVCIIPVSA HGTNPASAAM CGMKIITVGT DAKGNINIEE VRKAAEANKD NLAALMVTYP
STHGVYEEGI DEICNIIHEN GGQVYMDGAN MNAQVGLTSP GFIGADVCHL NLHKTFCIPH
GGGGPGMGPI GVKNHLAPFL PSHPVIPTGG IPQPEKTAPL GAISAAPWGS ALILPISYTY
IAMMGSGGLT DASKIAILNA NYMAKRLEKH YPVLFRGVNG TVAHEFIIDL RGFKNTAGIE
PEDVAKRLMD YGFHGPTMSW PVPGTLMIEP TESESKAELD RFCDALISIR EEIAQIEKGN
ADVQNNVLKG APHPPSLLMA DTWKKPYSRE YAAFPAPWLR SSKFWPTTGR VDNVYGDRKL
VCTLLPEEEQ VAAAVSA
