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Q94B78

- GCSP1_ARATH

UniProt

Q94B78 - GCSP1_ARATH

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
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    • History
      Entry version 100 (01 Oct 2014)
      Sequence version 2 (26 Apr 2004)
      Previous versions | rss
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    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. protein binding Source: TAIR
    3. pyridoxal phosphate binding Source: InterPro

    GO - Biological processi

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

    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

    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

    ArrayExpressiQ94B78.
    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

    MERARRLAYR GIVKRLVNDT KRHRNAETPH LVPHAPARYV SSLSPFISTP     50
    RSVNHTAAFG RHQQTRSISV DAVKPSDTFP RRHNSATPDE QTHMAKFCGF 100
    DHIDSLIDAT VPKSIRLDSM KFSKFDAGLT ESQMIQHMVD LASKNKVFKS 150
    FIGMGYYNTH VPTVILRNIM ENPAWYTQYT PYQAEISQGR LESLLNFQTV 200
    ITDLTGLPMS NASLLDEGTA AAEAMAMCNN ILKGKKKTFV IASNCHPQTI 250
    DVCKTRADGF DLKVVTSDLK DIDYSSGDVC GVLVQYPGTE GEVLDYAEFV 300
    KNAHANGVKV VMATDLLALT VLKPPGEFGA DIVVGSAQRF GVPMGYGGPH 350
    AAFLATSQEY KRMMPGRIIG ISVDSSGKQA LRMAMQTREQ HIRRDKATSN 400
    ICTAQALLAN MAAMYAVYHG PAGLKSIAQR VHGLAGIFSL GLNKLGVAEV 450
    QELPFFDTVK IKCSDAHAIA DAASKSEINL RVVDSTTITA SFDETTTLDD 500
    VDKLFKVFAS GKPVPFTAES LAPEVQNSIP SSLTRESPYL THPIFNMYHT 550
    EHELLRYIHK LQSKDLSLCH SMIPLGSCTM KLNATTEMMP VTWPSFTDIH 600
    PFAPVEQAQG YQEMFENLGD LLCTITGFDS FSLQPNAGAA GEYAGLMVIR 650
    AYHMSRGDHH RNVCIIPVSA HGTNPASAAM CGMKIITVGT DAKGNINIEE 700
    VRKAAEANKD NLAALMVTYP STHGVYEEGI DEICNIIHEN GGQVYMDGAN 750
    MNAQVGLTSP GFIGADVCHL NLHKTFCIPH GGGGPGMGPI GVKNHLAPFL 800
    PSHPVIPTGG IPQPEKTAPL GAISAAPWGS ALILPISYTY IAMMGSGGLT 850
    DASKIAILNA NYMAKRLEKH YPVLFRGVNG TVAHEFIIDL RGFKNTAGIE 900
    PEDVAKRLMD YGFHGPTMSW PVPGTLMIEP TESESKAELD RFCDALISIR 950
    EEIAQIEKGN ADVQNNVLKG APHPPSLLMA DTWKKPYSRE YAAFPAPWLR 1000
    SSKFWPTTGR VDNVYGDRKL VCTLLPEEEQ VAAAVSA 1037
    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

    ArrayExpressi Q94B78.
    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

    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 1, 2014
    This is version 100 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