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Protein

Glycine dehydrogenase (decarboxylating) 2, mitochondrial

Gene

GLDP2

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

GO - Molecular functioni

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

GO - Biological processi

  1. glycine catabolic process Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

Pyridoxal phosphate

Enzyme and pathway databases

BioCyciARA:AT2G26080-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Glycine dehydrogenase (decarboxylating) 2, mitochondrial (EC:1.4.4.2)
Alternative name(s):
Glycine cleavage system P protein 2
Glycine decarboxylase 2
Glycine decarboxylase P-protein 2
Short name:
AtGLDP2
Glycine dehydrogenase (aminomethyl-transferring) 2
Gene namesi
Name:GLDP2
Synonyms:GDCSP, GDP2
Ordered Locus Names:At2g26080
ORF Names:T19L18.11
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548 Componenti: Chromosome 2

Organism-specific databases

TAIRiAT2G26080.

Subcellular locationi

Mitochondrion 1 Publication

GO - Cellular componenti

  1. apoplast Source: TAIR
  2. chloroplast Source: TAIR
  3. chloroplast envelope Source: TAIR
  4. mitochondrion Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion

Pathology & Biotechi

Disruption phenotypei

No visible phenotype; due to the redundancy with GLDP1. 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 – 7272MitochondrionSequence AnalysisAdd
BLAST
Chaini73 – 1044972Glycine dehydrogenase (decarboxylating) 2, mitochondrialPRO_0000010743Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei780 – 7801N6-(pyridoxal phosphate)lysineBy similarity

Proteomic databases

PaxDbiO80988.
PRIDEiO80988.

Expressioni

Tissue specificityi

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

Gene expression databases

GenevestigatoriO80988.

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

BioGridi2501. 2 interactions.
STRINGi3702.AT2G26080.1-P.

Structurei

3D structure databases

ProteinModelPortaliO80988.
SMRiO80988. Positions 76-1031.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the GcvP family.Curated

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiCOG1003.
HOGENOMiHOG000239369.
InParanoidiO80988.
KOiK00281.
OMAiIRVQVII.
PhylomeDBiO80988.

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.

O80988-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MERARRLAYR GIVKRLVNET KRHRNGESSL LPTTTVTPSR YVSSVSSFLH
60 70 80 90 100
RRRDVSGSAF TTSGRNQHQT RSISVDALKP SDTFPRRHNS ATPDEQAQMA
110 120 130 140 150
NYCGFDNLNT LIDSTVPKSI RLDSMKFSGI FDEGLTESQM IEHMSDLASK
160 170 180 190 200
NKVFKSFIGM GYYNTHVPPV ILRNIMENPA WYTQYTPYQA EISQGRLESL
210 220 230 240 250
LNYQTVITDL TGLPMSNASL LDEGTAAAEA MAMCNNILKG KKKTFVIASN
260 270 280 290 300
CHPQTIDVCK TRADGFDLKV VTVDIKDVDY SSGDVCGVLV QYPGTEGEVL
310 320 330 340 350
DYGEFVKNAH ANGVKVVMAT DLLALTMLKP PGEFGADIVV GSGQRFGVPM
360 370 380 390 400
GYGGPHAAFL ATSQEYKRMM PGRIIGVSVD SSGKQALRMA MQTREQHIRR
410 420 430 440 450
DKATSNICTA QALLANMTAM YAVYHGPEGL KSIAQRVHGL AGVFALGLKK
460 470 480 490 500
LGTAQVQDLP FFDTVKVTCS DATAIFDVAA KKEINLRLVD SNTITVAFDE
510 520 530 540 550
TTTLDDVDKL FEVFASGKPV QFTAESLAPE FNNAIPSSLT RESPYLTHPI
560 570 580 590 600
FNMYHTEHEL LRYIHKLQNK DLSLCHSMIP LGSCTMKLNA TTEMMPVTWP
610 620 630 640 650
SFTNMHPFAP VEQAQGYQEM FTNLGELLCT ITGFDSFSLQ PNAGAAGEYA
660 670 680 690 700
GLMVIRAYHM SRGDHHRNVC IIPVSAHGTN PASAAMCGMK IVAVGTDAKG
710 720 730 740 750
NINIEELRNA AEANKDNLAA LMVTYPSTHG VYEEGIDEIC NIIHENGGQV
760 770 780 790 800
YMDGANMNAQ VGLTSPGFIG ADVCHLNLHK TFCIPHGGGG PGMGPIGVKQ
810 820 830 840 850
HLAPFLPSHP VIPTGGIPEP EQTSPLGTIS AAPWGSALIL PISYTYIAMM
860 870 880 890 900
GSGGLTDASK IAILNANYMA KRLESHYPVL FRGVNGTVAH EFIIDLRGFK
910 920 930 940 950
NTAGIEPEDV AKRLMDYGFH GPTMSWPVPG TLMIEPTESE SKAELDRFCD
960 970 980 990 1000
ALISIREEIS QIEKGNADPN NNVLKGAPHP PSLLMADTWK KPYSREYAAF
1010 1020 1030 1040
PAPWLRSSKF WPTTGRVDNV YGDRNLVCTL QPANEEQAAA AVSA
Length:1,044
Mass (Da):113,776
Last modified:October 31, 1998 - v1
Checksum:i227C30B67D82A97D
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti534 – 5341A → T in BAE98954 (Ref. 3) Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC004747 Genomic DNA. Translation: AAC31228.1.
CP002685 Genomic DNA. Translation: AEC07793.1.
AK226865 mRNA. Translation: BAE98954.1.
PIRiT02615.
RefSeqiNP_180178.1. NM_128167.3.
UniGeneiAt.24550.
At.72082.

Genome annotation databases

EnsemblPlantsiAT2G26080.1; AT2G26080.1; AT2G26080.
GeneIDi817149.
KEGGiath:AT2G26080.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC004747 Genomic DNA. Translation: AAC31228.1.
CP002685 Genomic DNA. Translation: AEC07793.1.
AK226865 mRNA. Translation: BAE98954.1.
PIRiT02615.
RefSeqiNP_180178.1. NM_128167.3.
UniGeneiAt.24550.
At.72082.

3D structure databases

ProteinModelPortaliO80988.
SMRiO80988. Positions 76-1031.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi2501. 2 interactions.
STRINGi3702.AT2G26080.1-P.

Proteomic databases

PaxDbiO80988.
PRIDEiO80988.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT2G26080.1; AT2G26080.1; AT2G26080.
GeneIDi817149.
KEGGiath:AT2G26080.

Organism-specific databases

GeneFarmi1741. 130.
TAIRiAT2G26080.

Phylogenomic databases

eggNOGiCOG1003.
HOGENOMiHOG000239369.
InParanoidiO80988.
KOiK00281.
OMAiIRVQVII.
PhylomeDBiO80988.

Enzyme and pathway databases

BioCyciARA:AT2G26080-MONOMER.

Gene expression databases

GenevestigatoriO80988.

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.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  2. The Arabidopsis Information Resource (TAIR)
    Submitted (MAR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  3. "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs."
    Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A., Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y., Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.
    , Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y., Shinozaki K.
    Submitted (JUN-2006) to the EMBL/GenBank/DDBJ databases
    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(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW.
  5. "Genetic manipulation of glycine decarboxylation."
    Bauwe H., Kolukisaoglu U.
    J. Exp. Bot. 54:1523-1535(2002) [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(2003) [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(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DISRUPTION PHENOTYPE, TISSUE SPECIFICITY.
    Strain: cv. Columbia and cv. Wassilewskija.

Entry informationi

Entry nameiGCSP2_ARATH
AccessioniPrimary (citable) accession number: O80988
Secondary accession number(s): Q0WV94
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 30, 2000
Last sequence update: October 31, 1998
Last modified: January 6, 2015
This is version 120 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.