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Glycine dehydrogenase (decarboxylating) 1, mitochondrial (EC 1.4.4.2) (Glycine cleavage system P protein 1) (Glycine decarboxylase 1) (Glycine decarboxylase P-protein 1) (AtGLDP1) (Glycine dehydrogenase (aminomethyl-transferring) 1)

 GCSP1_ARATH             Reviewed;        1037 AA.
Q94B78; O82642; Q8GTY1; Q8VZF0;
26-APR-2004, integrated into UniProtKB/Swiss-Prot.
26-APR-2004, sequence version 2.
25-APR-2018, entry version 126.
RecName: Full=Glycine dehydrogenase (decarboxylating) 1, mitochondrial;
EC=1.4.4.2;
AltName: Full=Glycine cleavage system P protein 1;
AltName: Full=Glycine decarboxylase 1;
AltName: Full=Glycine decarboxylase P-protein 1;
Short=AtGLDP1;
AltName: Full=Glycine dehydrogenase (aminomethyl-transferring) 1;
Flags: Precursor;
Name=GLDP1; Synonyms=GDP1; OrderedLocusNames=At4g33010;
ORFNames=F26P21.130;
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
Arabidopsis.
NCBI_TaxID=3702;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=10617198; DOI=10.1038/47134;
Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G.,
Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N.,
Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M.,
Weichselgartner M., de Simone V., Obermaier B., Mache R., Mueller M.,
Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T.,
Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I.,
Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P.,
Langham S.-A., McCullagh B., Bilham L., Robben J.,
van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F.,
Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E.,
Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W.,
Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P.,
Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H.,
De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R.,
van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S.,
Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R.,
Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S.,
Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H.,
Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S.,
Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A.,
Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R.,
Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S.,
Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E.,
Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A.,
Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T.,
Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C.,
Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S.,
Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K.,
Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L.,
Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J.,
Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J.,
Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D.,
Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D.,
Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C.,
Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C.,
Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R.,
Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S.,
Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A.,
Chen E., Marra M.A., Martienssen R., McCombie W.R.;
"Sequence and analysis of chromosome 4 of the plant Arabidopsis
thaliana.";
Nature 402:769-777(1999).
[2]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
PubMed=27862469; DOI=10.1111/tpj.13415;
Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
Town C.D.;
"Araport11: a complete reannotation of the Arabidopsis thaliana
reference genome.";
Plant J. 89:789-804(2017).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=cv. Columbia;
PubMed=14593172; DOI=10.1126/science.1088305;
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.;
"Empirical analysis of transcriptional activity in the Arabidopsis
genome.";
Science 302:842-846(2003).
[4]
REVIEW.
PubMed=11286922; DOI=10.1016/S1360-1385(01)01892-1;
Douce R., Bourguignon J., Neuburger M., Rebeille F.;
"The glycine decarboxylase system: a fascinating complex.";
Trends Plant Sci. 6:167-176(2001).
[5]
REVIEW, AND NOMENCLATURE.
PubMed=12730263; DOI=10.1093/jxb/erg171;
Bauwe H., Kolukisaoglu U.;
"Genetic manipulation of glycine decarboxylation.";
J. Exp. Bot. 54:1523-1535(2003).
[6]
IDENTIFICATION BY MASS SPECTROMETRY, AND SUBCELLULAR LOCATION [LARGE
SCALE ANALYSIS].
STRAIN=cv. Landsberg erecta;
PubMed=14671022; DOI=10.1105/tpc.016055;
Heazlewood J.L., Tonti-Filippini J.S., Gout A.M., Day D.A., Whelan J.,
Millar A.H.;
"Experimental analysis of the Arabidopsis mitochondrial proteome
highlights signaling and regulatory components, provides assessment of
targeting prediction programs, and indicates plant-specific
mitochondrial proteins.";
Plant Cell 16:241-256(2004).
[7]
FUNCTION, DISRUPTION PHENOTYPE, AND TISSUE SPECIFICITY.
STRAIN=cv. Columbia, and cv. Wassilewskija;
PubMed=17496108; DOI=10.1104/pp.107.099317;
Engel N., van den Daele K., Kolukisaoglu U., Morgenthal K.,
Weckwerth W., Paernik T., Keerberg O., Bauwe H.;
"Deletion of glycine decarboxylase in Arabidopsis is lethal under
nonphotorespiratory conditions.";
Plant Physiol. 144:1328-1335(2007).
[8]
ENZYME REGULATION, S-NITROSYLATION, AND GLUTATHIONYLATION AT CYS-98;
CYS-402; CYS-463; CYS-777; CYS-943 AND CYS-1022.
PubMed=20089767; DOI=10.1104/pp.109.152579;
Palmieri M.C., Lindermayr C., Bauwe H., Steinhauser C., Durner J.;
"Regulation of plant glycine decarboxylase by s-nitrosylation and
glutathionylation.";
Plant Physiol. 152:1514-1528(2010).
-!- FUNCTION: The glycine decarboxylase (GDC) or glycine cleavage
system catalyzes the degradation of glycine. The P protein binds
the alpha-amino group of glycine through its pyridoxal phosphate
cofactor; CO(2) is released and the remaining methylamine moiety
is then transferred to the lipoamide cofactor of the H protein (By
similarity). {ECO:0000250, ECO:0000269|PubMed:17496108}.
-!- CATALYTIC ACTIVITY: Glycine + [glycine-cleavage complex H
protein]-N(6)-lipoyl-L-lysine = [glycine-cleavage complex H
protein]-S-aminomethyl-N(6)-dihydrolipoyl-L-lysine + CO(2).
-!- COFACTOR:
Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
Evidence={ECO:0000250};
-!- ENZYME REGULATION: Inhibited by harpin, S-nitrosoglutathione
(GSNO), nitric oxide, N-ethylmaleimide and 5,5'-dithiobis-(2-
nitrobenzoic acid). {ECO:0000269|PubMed:20089767}.
-!- SUBUNIT: Homodimer (By similarity). The glycine cleavage system is
composed of four proteins: P, T, L and H. {ECO:0000250}.
-!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14671022}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=1;
Comment=A number of isoforms are produced. According to EST
sequences.;
Name=1;
IsoId=Q94B78-1; Sequence=Displayed;
-!- TISSUE SPECIFICITY: Expressed in leaves. Detected in roots, stems,
flowers and siliques. {ECO:0000269|PubMed:17496108}.
-!- PTM: Glutathionylated at Cys-98, Cys-777, Cys-943 and Cys-1022
after S-nitrosoglutathione treatment.
{ECO:0000269|PubMed:20089767}.
-!- PTM: S-nitrosylated at unknown positions by nitric oxide.
{ECO:0000269|PubMed:20089767}.
-!- DISRUPTION PHENOTYPE: No visible phenotype; due to the redundancy
with GLDP2. Gldp1 and gldp2 double mutants have a seedling
development arrested at the cotyledon stage even under
nonphotorespiratory conditions. {ECO:0000269|PubMed:17496108}.
-!- SIMILARITY: Belongs to the GcvP family. {ECO:0000305}.
-!- CAUTION: This protein has also been shown to act as an inducible
nitric oxide synthase (iNOS) (PubMed:12757708), but the paper has
been retracted (PubMed:15599984). {ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=AAN17423.1; Type=Frameshift; Positions=942; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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EMBL; AL031804; CAA21210.1; -; Genomic_DNA.
EMBL; AL161582; CAB80018.1; -; Genomic_DNA.
EMBL; CP002687; AEE86159.1; -; Genomic_DNA.
EMBL; AY063903; AAL36259.1; -; mRNA.
EMBL; AY091186; AAM14125.1; -; mRNA.
EMBL; AY042800; AAK68740.1; -; mRNA.
EMBL; AY128922; AAM91322.1; -; mRNA.
EMBL; AY065004; AAL57651.1; -; mRNA.
EMBL; BT001132; AAN64523.1; -; mRNA.
EMBL; BT000446; AAN17423.1; ALT_FRAME; mRNA.
PIR; T05309; T05309.
RefSeq; NP_195027.1; NM_119455.3. [Q94B78-1]
UniGene; At.22214; -.
UniGene; At.24550; -.
ProteinModelPortal; Q94B78; -.
SMR; Q94B78; -.
BioGrid; 14723; 3.
IntAct; Q94B78; 1.
STRING; 3702.AT4G33010.1; -.
iPTMnet; Q94B78; -.
PaxDb; Q94B78; -.
PRIDE; Q94B78; -.
EnsemblPlants; AT4G33010.1; AT4G33010.1; AT4G33010. [Q94B78-1]
GeneID; 829438; -.
Gramene; AT4G33010.1; AT4G33010.1; AT4G33010. [Q94B78-1]
KEGG; ath:AT4G33010; -.
Araport; AT4G33010; -.
TAIR; locus:2123777; AT4G33010.
eggNOG; KOG2040; Eukaryota.
eggNOG; COG0403; LUCA.
eggNOG; COG1003; LUCA.
HOGENOM; HOG000239369; -.
InParanoid; Q94B78; -.
KO; K00281; -.
OMA; QTMVCDL; -.
OrthoDB; EOG093601A5; -.
PhylomeDB; Q94B78; -.
BioCyc; ARA:AT4G33010-MONOMER; -.
Reactome; R-ATH-6783984; Glycine degradation.
PRO; PR:Q94B78; -.
Proteomes; UP000006548; Chromosome 4.
ExpressionAtlas; Q94B78; baseline and differential.
Genevisible; Q94B78; AT.
GO; GO:0048046; C:apoplast; IDA:TAIR.
GO; GO:0009507; C:chloroplast; IDA:TAIR.
GO; GO:0009941; C:chloroplast envelope; IDA:TAIR.
GO; GO:0009570; C:chloroplast stroma; IDA:TAIR.
GO; GO:0009534; C:chloroplast thylakoid; IDA:TAIR.
GO; GO:0005739; C:mitochondrion; IDA:TAIR.
GO; GO:0004375; F:glycine dehydrogenase (decarboxylating) activity; IEA:UniProtKB-EC.
GO; GO:0006546; P:glycine catabolic process; IMP:TAIR.
GO; GO:0046686; P:response to cadmium ion; IEP:TAIR.
CDD; cd00613; GDC-P; 2.
Gene3D; 3.40.640.10; -; 2.
Gene3D; 3.90.1150.10; -; 1.
HAMAP; MF_00711; GcvP; 1.
InterPro; IPR003437; GcvP.
InterPro; IPR020581; GDC_P.
InterPro; IPR015424; PyrdxlP-dep_Trfase.
InterPro; IPR015422; PyrdxlP-dep_Trfase_dom1.
InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
PANTHER; PTHR11773; PTHR11773; 1.
Pfam; PF02347; GDC-P; 2.
SUPFAM; SSF53383; SSF53383; 3.
TIGRFAMs; TIGR00461; gcvP; 1.
1: Evidence at protein level;
Alternative splicing; Complete proteome; Glutathionylation;
Mitochondrion; Oxidoreductase; Pyridoxal phosphate;
Reference proteome; S-nitrosylation; Transit peptide.
TRANSIT 1 67 Mitochondrion. {ECO:0000305}.
CHAIN 68 1037 Glycine dehydrogenase (decarboxylating)
1, mitochondrial.
/FTId=PRO_0000010744.
MOD_RES 98 98 S-glutathionyl cysteine; transient.
{ECO:0000269|PubMed:20089767}.
MOD_RES 402 402 S-glutathionyl cysteine.
{ECO:0000269|PubMed:20089767}.
MOD_RES 463 463 S-glutathionyl cysteine.
{ECO:0000269|PubMed:20089767}.
MOD_RES 774 774 N6-(pyridoxal phosphate)lysine.
{ECO:0000250}.
MOD_RES 777 777 S-glutathionyl cysteine; transient.
{ECO:0000269|PubMed:20089767}.
MOD_RES 943 943 S-glutathionyl cysteine; transient.
{ECO:0000269|PubMed:20089767}.
MOD_RES 1022 1022 S-glutathionyl cysteine; transient.
{ECO:0000269|PubMed:20089767}.
CONFLICT 578 578 C -> R (in Ref. 3; AAN17423).
{ECO:0000305}.
CONFLICT 884 884 H -> R (in Ref. 3; AAL57651/AAN64523).
{ECO:0000305}.
CONFLICT 925 925 T -> A (in Ref. 3; AAN17423).
{ECO:0000305}.
CONFLICT 1032 1032 A -> T (in Ref. 3; AAK68740/AAM91322).
{ECO:0000305}.
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


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