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Q94B78

- GCSP1_ARATH

UniProt

Q94B78 - GCSP1_ARATH

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Protein

Glycine dehydrogenase (decarboxylating) 1, mitochondrial

Gene

GLDP1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

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; CO2 is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein By similarity.By similarity

Catalytic activityi

Glycine + [glycine-cleavage complex H protein]-N(6)-lipoyl-L-lysine = [glycine-cleavage complex H protein]-S-aminomethyl-N(6)-dihydrolipoyl-L-lysine + CO2.

Cofactori

Pyridoxal phosphate.By similarity

Enzyme regulationi

Inhibited by harpin, S-nitrosoglutathione (GSNO), nitric oxide, N-ethylmaleimide and 5,5'-dithiobis-(2-nitrobenzoic acid).1 Publication

GO - Molecular functioni

  1. glycine dehydrogenase (decarboxylating) activity Source: UniProtKB-EC
  2. pyridoxal phosphate binding Source: InterPro

GO - Biological processi

  1. glycine catabolic process Source: TAIR
  2. response to cadmium ion Source: TAIR
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

Pyridoxal phosphate

Enzyme and pathway databases

BioCyciARA:AT4G33010-MONOMER.
ARA:GQT-949-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Glycine dehydrogenase (decarboxylating) 1, mitochondrial (EC:1.4.4.2)
Alternative name(s):
Glycine cleavage system P protein 1
Glycine decarboxylase 1
Glycine decarboxylase P-protein 1
Short name:
AtGLDP1
Glycine dehydrogenase (aminomethyl-transferring) 1
Gene namesi
Name:GLDP1
Synonyms:GDP1
Ordered Locus Names:At4g33010
ORF Names:F26P21.130
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548: Chromosome 4

Organism-specific databases

TAIRiAT4G33010.

Subcellular locationi

Mitochondrion 1 Publication

GO - Cellular componenti

  1. apoplast Source: TAIR
  2. chloroplast Source: TAIR
  3. chloroplast envelope Source: TAIR
  4. chloroplast stroma Source: TAIR
  5. chloroplast thylakoid Source: TAIR
  6. mitochondrion Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion

Pathology & Biotechi

Disruption phenotypei

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.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 3939MitochondrionSequence AnalysisAdd
BLAST
Chaini40 – 1037998Glycine dehydrogenase (decarboxylating) 1, mitochondrialPRO_0000010744Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei98 – 981S-glutathionyl cysteine; transient1 Publication
Modified residuei402 – 4021S-glutathionyl cysteine1 Publication
Modified residuei463 – 4631S-glutathionyl cysteine1 Publication
Modified residuei774 – 7741N6-(pyridoxal phosphate)lysineBy similarity
Modified residuei777 – 7771S-glutathionyl cysteine; transient1 Publication
Modified residuei943 – 9431S-glutathionyl cysteine; transient1 Publication
Modified residuei1022 – 10221S-glutathionyl cysteine; transient1 Publication

Post-translational modificationi

Glutathionylated at Cys-98, Cys-777, Cys-943 and Cys-1022 after S-nitrosoglutathione treatment.1 Publication
S-nitrosylated at unknown positions by nitric oxide.1 Publication

Keywords - PTMi

Glutathionylation, S-nitrosylation

Proteomic databases

PRIDEiQ94B78.

Expressioni

Tissue specificityi

Expressed in leaves. Detected in roots, stems, flowers and siliques.1 Publication

Gene expression databases

ExpressionAtlasiQ94B78. baseline and differential.
GenevestigatoriQ94B78.

Interactioni

Subunit structurei

Homodimer By similarity. The glycine cleavage system is composed of four proteins: P, T, L and H.By similarity

Protein-protein interaction databases

BioGridi14723. 1 interaction.
IntActiQ94B78. 1 interaction.
MINTiMINT-8070384.

Structurei

3D structure databases

ProteinModelPortaliQ94B78.
SMRiQ94B78. Positions 67-1023.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the GcvP family.Curated

Keywords - Domaini

Transit peptide

Phylogenomic databases

HOGENOMiHOG000239369.
InParanoidiQ94B78.
KOiK00281.
OMAiTAYLTHP.
PhylomeDBiQ94B78.

Family and domain databases

Gene3Di3.40.640.10. 2 hits.
HAMAPiMF_00711. GcvP.
InterProiIPR020580. GDC-P_N.
IPR020581. GDC_P.
IPR003437. GDC_P_homo.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
[Graphical view]
PANTHERiPTHR11773. PTHR11773. 1 hit.
PfamiPF02347. GDC-P. 2 hits.
[Graphical view]
SUPFAMiSSF53383. SSF53383. 3 hits.
TIGRFAMsiTIGR00461. gcvP. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 1 isoform i produced by alternative splicing. Align

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

Isoform 1 (identifier: Q94B78-1) [UniParc]FASTAAdd to Basket

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.

« Hide

        10         20         30         40         50
MERARRLAYR GIVKRLVNDT KRHRNAETPH LVPHAPARYV SSLSPFISTP
60 70 80 90 100
RSVNHTAAFG RHQQTRSISV DAVKPSDTFP RRHNSATPDE QTHMAKFCGF
110 120 130 140 150
DHIDSLIDAT VPKSIRLDSM KFSKFDAGLT ESQMIQHMVD LASKNKVFKS
160 170 180 190 200
FIGMGYYNTH VPTVILRNIM ENPAWYTQYT PYQAEISQGR LESLLNFQTV
210 220 230 240 250
ITDLTGLPMS NASLLDEGTA AAEAMAMCNN ILKGKKKTFV IASNCHPQTI
260 270 280 290 300
DVCKTRADGF DLKVVTSDLK DIDYSSGDVC GVLVQYPGTE GEVLDYAEFV
310 320 330 340 350
KNAHANGVKV VMATDLLALT VLKPPGEFGA DIVVGSAQRF GVPMGYGGPH
360 370 380 390 400
AAFLATSQEY KRMMPGRIIG ISVDSSGKQA LRMAMQTREQ HIRRDKATSN
410 420 430 440 450
ICTAQALLAN MAAMYAVYHG PAGLKSIAQR VHGLAGIFSL GLNKLGVAEV
460 470 480 490 500
QELPFFDTVK IKCSDAHAIA DAASKSEINL RVVDSTTITA SFDETTTLDD
510 520 530 540 550
VDKLFKVFAS GKPVPFTAES LAPEVQNSIP SSLTRESPYL THPIFNMYHT
560 570 580 590 600
EHELLRYIHK LQSKDLSLCH SMIPLGSCTM KLNATTEMMP VTWPSFTDIH
610 620 630 640 650
PFAPVEQAQG YQEMFENLGD LLCTITGFDS FSLQPNAGAA GEYAGLMVIR
660 670 680 690 700
AYHMSRGDHH RNVCIIPVSA HGTNPASAAM CGMKIITVGT DAKGNINIEE
710 720 730 740 750
VRKAAEANKD NLAALMVTYP STHGVYEEGI DEICNIIHEN GGQVYMDGAN
760 770 780 790 800
MNAQVGLTSP GFIGADVCHL NLHKTFCIPH GGGGPGMGPI GVKNHLAPFL
810 820 830 840 850
PSHPVIPTGG IPQPEKTAPL GAISAAPWGS ALILPISYTY IAMMGSGGLT
860 870 880 890 900
DASKIAILNA NYMAKRLEKH YPVLFRGVNG TVAHEFIIDL RGFKNTAGIE
910 920 930 940 950
PEDVAKRLMD YGFHGPTMSW PVPGTLMIEP TESESKAELD RFCDALISIR
960 970 980 990 1000
EEIAQIEKGN ADVQNNVLKG APHPPSLLMA DTWKKPYSRE YAAFPAPWLR
1010 1020 1030
SSKFWPTTGR VDNVYGDRKL VCTLLPEEEQ VAAAVSA
Length:1,037
Mass (Da):112,925
Last modified:April 26, 2004 - v2
Checksum:i168C11DB642687A5
GO

Sequence cautioni

The sequence AAN17423.1 differs from that shown. Reason: Frameshift at position 942.

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti578 – 5781C → R in AAN17423. (PubMed:14593172)Curated
Sequence conflicti884 – 8841H → R in AAL57651. (PubMed:14593172)Curated
Sequence conflicti884 – 8841H → R in AAN64523. (PubMed:14593172)Curated
Sequence conflicti925 – 9251T → A in AAN17423. (PubMed:14593172)Curated
Sequence conflicti1032 – 10321A → T in AAK68740. (PubMed:14593172)Curated
Sequence conflicti1032 – 10321A → T in AAM91322. (PubMed:14593172)Curated

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AL031804 Genomic DNA. Translation: CAA21210.1.
AL161582 Genomic DNA. Translation: CAB80018.1.
CP002687 Genomic DNA. Translation: AEE86159.1.
AY063903 mRNA. Translation: AAL36259.1.
AY091186 mRNA. Translation: AAM14125.1.
AY042800 mRNA. Translation: AAK68740.1.
AY128922 mRNA. Translation: AAM91322.1.
AY065004 mRNA. Translation: AAL57651.1.
BT001132 mRNA. Translation: AAN64523.1.
BT000446 mRNA. Translation: AAN17423.1. Frameshift.
PIRiT05309.
RefSeqiNP_195027.1. NM_119455.2. [Q94B78-1]
UniGeneiAt.22214.
At.24550.

Genome annotation databases

EnsemblPlantsiAT4G33010.1; AT4G33010.1; AT4G33010. [Q94B78-1]
GeneIDi829438.
KEGGiath:AT4G33010.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AL031804 Genomic DNA. Translation: CAA21210.1 .
AL161582 Genomic DNA. Translation: CAB80018.1 .
CP002687 Genomic DNA. Translation: AEE86159.1 .
AY063903 mRNA. Translation: AAL36259.1 .
AY091186 mRNA. Translation: AAM14125.1 .
AY042800 mRNA. Translation: AAK68740.1 .
AY128922 mRNA. Translation: AAM91322.1 .
AY065004 mRNA. Translation: AAL57651.1 .
BT001132 mRNA. Translation: AAN64523.1 .
BT000446 mRNA. Translation: AAN17423.1 . Frameshift.
PIRi T05309.
RefSeqi NP_195027.1. NM_119455.2. [Q94B78-1 ]
UniGenei At.22214.
At.24550.

3D structure databases

ProteinModelPortali Q94B78.
SMRi Q94B78. Positions 67-1023.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 14723. 1 interaction.
IntActi Q94B78. 1 interaction.
MINTi MINT-8070384.

Proteomic databases

PRIDEi Q94B78.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblPlantsi AT4G33010.1 ; AT4G33010.1 ; AT4G33010 . [Q94B78-1 ]
GeneIDi 829438.
KEGGi ath:AT4G33010.

Organism-specific databases

GeneFarmi 1737. 130.
TAIRi AT4G33010.

Phylogenomic databases

HOGENOMi HOG000239369.
InParanoidi Q94B78.
KOi K00281.
OMAi TAYLTHP.
PhylomeDBi Q94B78.

Enzyme and pathway databases

BioCyci ARA:AT4G33010-MONOMER.
ARA:GQT-949-MONOMER.

Miscellaneous databases

PROi Q94B78.

Gene expression databases

ExpressionAtlasi Q94B78. baseline and differential.
Genevestigatori Q94B78.

Family and domain databases

Gene3Di 3.40.640.10. 2 hits.
HAMAPi MF_00711. GcvP.
InterProi IPR020580. GDC-P_N.
IPR020581. GDC_P.
IPR003437. GDC_P_homo.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
[Graphical view ]
PANTHERi PTHR11773. PTHR11773. 1 hit.
Pfami PF02347. GDC-P. 2 hits.
[Graphical view ]
SUPFAMi SSF53383. SSF53383. 3 hits.
TIGRFAMsi TIGR00461. gcvP. 1 hit.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana."
    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.
    Nature 402:769-777(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  2. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  3. "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.
  4. "The glycine decarboxylase system: a fascinating complex."
    Douce R., Bourguignon J., Neuburger M., Rebeille F.
    Trends Plant Sci. 6:167-176(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW.
  5. "Genetic manipulation of glycine decarboxylation."
    Bauwe H., Kolukisaoglu U.
    J. Exp. Bot. 54:1523-1535(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW, NOMENCLATURE.
  6. "Experimental analysis of the Arabidopsis mitochondrial proteome highlights signaling and regulatory components, provides assessment of targeting prediction programs, and indicates plant-specific mitochondrial proteins."
    Heazlewood J.L., Tonti-Filippini J.S., Gout A.M., Day D.A., Whelan J., Millar A.H.
    Plant Cell 16:241-256(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
    Strain: cv. Landsberg erecta.
  7. "Deletion of glycine decarboxylase in Arabidopsis is lethal under nonphotorespiratory conditions."
    Engel N., van den Daele K., Kolukisaoglu U., Morgenthal K., Weckwerth W., Paernik T., Keerberg O., Bauwe H.
    Plant Physiol. 144:1328-1335(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DISRUPTION PHENOTYPE, TISSUE SPECIFICITY.
    Strain: cv. Columbia and cv. Wassilewskija.
  8. "Regulation of plant glycine decarboxylase by s-nitrosylation and glutathionylation."
    Palmieri M.C., Lindermayr C., Bauwe H., Steinhauser C., Durner J.
    Plant Physiol. 152:1514-1528(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: ENZYME REGULATION, S-NITROSYLATION, GLUTATHIONYLATION AT CYS-98; CYS-402; CYS-463; CYS-777; CYS-943 AND CYS-1022.

Entry informationi

Entry nameiGCSP1_ARATH
AccessioniPrimary (citable) accession number: Q94B78
Secondary accession number(s): O82642, Q8GTY1, Q8VZF0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 26, 2004
Last sequence update: April 26, 2004
Last modified: October 29, 2014
This is version 101 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

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).Curated

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3