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   27-MAR-2024, entry version 150.
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=glycine + H(+) + N(6)-[(R)-lipoyl]-L-lysyl-[glycine-cleavage
CC         complex H protein] = CO2 + N(6)-[(R)-S(8)-aminomethyldihydrolipoyl]-
CC         L-lysyl-[glycine-cleavage complex H protein]; 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.Q94B78; -.
DR   iPTMnet; Q94B78; -.
DR   PaxDb; 3702-AT4G33010-1; -.
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; AT4G33010; GLDP1.
DR   eggNOG; KOG2040; Eukaryota.
DR   InParanoid; Q94B78; -.
DR   OMA; RNLICTC; -.
DR   OrthoDB; 177349at2759; -.
DR   PhylomeDB; Q94B78; -.
DR   BioCyc; ARA:AT4G33010-MONOMER; -.
DR   BioCyc; MetaCyc:AT4G33010-MONOMER; -.
DR   BRENDA; 1.4.1.27; 399.
DR   PRO; PR:Q94B78; -.
DR   Proteomes; UP000006548; Chromosome 4.
DR   ExpressionAtlas; Q94B78; baseline and differential.
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:0005739; C:mitochondrion; HDA:TAIR.
DR   GO; GO:0005886; C:plasma membrane; HDA:TAIR.
DR   GO; GO:0004375; F:glycine dehydrogenase (decarboxylating) activity; IEA:UniProtKB-EC.
DR   GO; GO:0003729; F:mRNA binding; IDA:TAIR.
DR   GO; GO:0006546; P:glycine catabolic process; IMP:TAIR.
DR   GO; GO:0046686; P:response to cadmium ion; IEP:TAIR.
DR   CDD; cd00613; GDC-P; 2.
DR   Gene3D; 3.90.1150.10; Aspartate Aminotransferase, domain 1; 2.
DR   Gene3D; 3.40.640.10; Type I PLP-dependent aspartate aminotransferase-like (Major domain); 2.
DR   HAMAP; MF_00711; GcvP; 1.
DR   InterPro; IPR003437; GcvP.
DR   InterPro; IPR049316; GDC-P_C.
DR   InterPro; IPR049315; GDC-P_N.
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   NCBIfam; TIGR00461; gcvP; 1.
DR   PANTHER; PTHR11773:SF1; GLYCINE DEHYDROGENASE (DECARBOXYLATING), MITOCHONDRIAL; 1.
DR   PANTHER; PTHR11773; GLYCINE DEHYDROGENASE, DECARBOXYLATING; 1.
DR   Pfam; PF21478; GcvP2_C; 1.
DR   Pfam; PF02347; GDC-P; 2.
DR   SUPFAM; SSF53383; PLP-dependent transferases; 2.
DR   Genevisible; Q94B78; AT.
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
//