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Protein

Ribulose bisphosphate carboxylase/oxygenase activase, chloroplastic

Gene

RCA

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

Functioni

Activation of RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase; EC 4.1.1.39) involves the ATP-dependent carboxylation of the epsilon-amino group of lysine leading to a carbamate structure.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi165 – 1728ATPSequence analysis

GO - Molecular functioni

  • ADP binding Source: TAIR
  • ATP binding Source: TAIR
  • enzyme regulator activity Source: TAIR
  • ribulose-1,5-bisphosphate carboxylase/oxygenase activator activity Source: TAIR

GO - Biological processi

  • defense response to bacterium Source: TAIR
  • leaf senescence Source: TAIR
  • positive regulation of catalytic activity Source: GOC
  • regulation of catalytic activity Source: GOC
  • response to cold Source: TAIR
  • response to jasmonic acid Source: TAIR
  • response to light stimulus Source: TAIR
Complete GO annotation...

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Ribulose bisphosphate carboxylase/oxygenase activase, chloroplastic
Short name:
RA
Short name:
RuBisCO activase
Gene namesi
Name:RCA
Ordered Locus Names:At2g39730
ORF Names:T5I7.3
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 2

Organism-specific databases

TAIRiAT2G39730.

Subcellular locationi

GO - Cellular componenti

  • apoplast Source: TAIR
  • cell wall Source: TAIR
  • chloroplast Source: TAIR
  • chloroplast envelope Source: TAIR
  • chloroplast stroma Source: TAIR
  • chloroplast thylakoid membrane Source: TAIR
  • membrane Source: TAIR
  • nucleus Source: TAIR
  • plastoglobule Source: TAIR
  • stromule Source: TAIR
  • thylakoid Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Chloroplast, Plastid

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 5858ChloroplastAdd
BLAST
Chaini59 – 474416Ribulose bisphosphate carboxylase/oxygenase activase, chloroplasticPRO_0000030228Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei283 – 2831PhosphothreonineCombined sources

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiP10896.
PRIDEiP10896.

2D gel databases

SWISS-2DPAGEP10896.
World-2DPAGE0003:P10896.

PTM databases

iPTMnetiP10896.

Expressioni

Gene expression databases

ExpressionAtlasiP10896. baseline and differential.
GenevisibleiP10896. AT.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
TRX3Q424031EBI-449165,EBI-449157

Protein-protein interaction databases

BioGridi3896. 3 interactions.
IntActiP10896. 2 interactions.
STRINGi3702.AT2G39730.1.

Structurei

Secondary structure

1
474
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi135 – 14713Combined sources
Beta strandi159 – 1646Combined sources
Helixi171 – 18111Combined sources
Beta strandi187 – 1904Combined sources
Helixi204 – 21815Combined sources
Beta strandi225 – 2273Combined sources
Helixi241 – 25313Combined sources
Beta strandi255 – 2573Combined sources
Beta strandi280 – 2867Combined sources
Helixi292 – 2976Combined sources
Beta strandi299 – 3046Combined sources
Helixi309 – 31911Combined sources
Beta strandi321 – 3244Combined sources
Helixi327 – 33610Combined sources
Helixi342 – 36423Combined sources
Helixi366 – 3683Combined sources
Helixi369 – 3735Combined sources
Beta strandi376 – 3783Combined sources
Helixi390 – 41425Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4W5WX-ray2.90A59-437[»]
ProteinModelPortaliP10896.
SMRiP10896. Positions 123-420.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the RuBisCO activase family.Curated

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiKOG0651. Eukaryota.
COG1222. LUCA.
HOGENOMiHOG000243931.
InParanoidiP10896.
OMAiDFDNTMD.
PhylomeDBiP10896.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
InterProiIPR003959. ATPase_AAA_core.
IPR027417. P-loop_NTPase.
[Graphical view]
PfamiPF00004. AAA. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.

Sequences (2)i

Sequence statusi: Complete.

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

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform Long (identifier: P10896-1) [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
MAAAVSTVGA INRAPLSLNG SGSGAVSAPA STFLGKKVVT VSRFAQSNKK
60 70 80 90 100
SNGSFKVLAV KEDKQTDGDR WRGLAYDTSD DQQDITRGKG MVDSVFQAPM
110 120 130 140 150
GTGTHHAVLS SYEYVSQGLR QYNLDNMMDG FYIAPAFMDK LVVHITKNFL
160 170 180 190 200
TLPNIKVPLI LGIWGGKGQG KSFQCELVMA KMGINPIMMS AGELESGNAG
210 220 230 240 250
EPAKLIRQRY REAADLIKKG KMCCLFINDL DAGAGRMGGT TQYTVNNQMV
260 270 280 290 300
NATLMNIADN PTNVQLPGMY NKEENARVPI ICTGNDFSTL YAPLIRDGRM
310 320 330 340 350
EKFYWAPTRE DRIGVCKGIF RTDKIKDEDI VTLVDQFPGQ SIDFFGALRA
360 370 380 390 400
RVYDDEVRKF VESLGVEKIG KRLVNSREGP PVFEQPEMTY EKLMEYGNML
410 420 430 440 450
VMEQENVKRV QLAETYLSQA ALGDANADAI GRGTFYGKGA QQVNLPVPEG
460 470
CTDPVAENFD PTARSDDGTC VYNF
Length:474
Mass (Da):51,981
Last modified:December 1, 2000 - v2
Checksum:i4AD07691E1892A4F
GO
Isoform Short (identifier: P10896-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     439-474: GAQQVNLPVPEGCTDPVAENFDPTARSDDGTCVYNF → TEEKEPSK

Show »
Length:446
Mass (Da):49,100
Checksum:i8C29E05DBC8593F4
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti163 – 1642IW → SR in CAA32429 (PubMed:2717419).Curated
Sequence conflicti202 – 2032PA → VR in CAA32429 (PubMed:2717419).Curated
Sequence conflicti292 – 2921A → G in CAA32429 (PubMed:2717419).Curated
Sequence conflicti296 – 2961R → L in CAA32429 (PubMed:2717419).Curated
Sequence conflicti304 – 3063YWA → LTG in CAA32429 (PubMed:2717419).Curated
Sequence conflicti316 – 3172CK → W in CAA32429 (PubMed:2717419).Curated
Sequence conflicti441 – 4422QQ → HE in CAA32429 (PubMed:2717419).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei439 – 47436GAQQV…CVYNF → TEEKEPSK in isoform Short. 1 PublicationVSP_005539Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X14212 mRNA. Translation: CAA32429.1.
M86720 Genomic DNA. Translation: AAA20202.1.
M86720 Genomic DNA. Translation: AAA20203.1.
AC003000 Genomic DNA. Translation: AAB87122.1.
CP002685 Genomic DNA. Translation: AEC09714.1.
CP002685 Genomic DNA. Translation: AEC09715.1.
AY052703 mRNA. Translation: AAK96607.1.
AF325049 mRNA. Translation: AAG40401.1.
AY056108 mRNA. Translation: AAL06995.1.
BT000710 mRNA. Translation: AAN31853.1.
AY088487 mRNA. Translation: AAM66023.1.
PIRiS04048.
T01002.
T01003.
RefSeqiNP_565913.1. NM_129531.2. [P10896-1]
NP_850320.1. NM_179989.2. [P10896-2]
UniGeneiAt.25263.
At.25299.
At.25319.
At.47493.

Genome annotation databases

EnsemblPlantsiAT2G39730.1; AT2G39730.1; AT2G39730. [P10896-1]
GeneIDi818558.
KEGGiath:AT2G39730.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X14212 mRNA. Translation: CAA32429.1.
M86720 Genomic DNA. Translation: AAA20202.1.
M86720 Genomic DNA. Translation: AAA20203.1.
AC003000 Genomic DNA. Translation: AAB87122.1.
CP002685 Genomic DNA. Translation: AEC09714.1.
CP002685 Genomic DNA. Translation: AEC09715.1.
AY052703 mRNA. Translation: AAK96607.1.
AF325049 mRNA. Translation: AAG40401.1.
AY056108 mRNA. Translation: AAL06995.1.
BT000710 mRNA. Translation: AAN31853.1.
AY088487 mRNA. Translation: AAM66023.1.
PIRiS04048.
T01002.
T01003.
RefSeqiNP_565913.1. NM_129531.2. [P10896-1]
NP_850320.1. NM_179989.2. [P10896-2]
UniGeneiAt.25263.
At.25299.
At.25319.
At.47493.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4W5WX-ray2.90A59-437[»]
ProteinModelPortaliP10896.
SMRiP10896. Positions 123-420.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi3896. 3 interactions.
IntActiP10896. 2 interactions.
STRINGi3702.AT2G39730.1.

PTM databases

iPTMnetiP10896.

2D gel databases

SWISS-2DPAGEP10896.
World-2DPAGE0003:P10896.

Proteomic databases

PaxDbiP10896.
PRIDEiP10896.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT2G39730.1; AT2G39730.1; AT2G39730. [P10896-1]
GeneIDi818558.
KEGGiath:AT2G39730.

Organism-specific databases

TAIRiAT2G39730.

Phylogenomic databases

eggNOGiKOG0651. Eukaryota.
COG1222. LUCA.
HOGENOMiHOG000243931.
InParanoidiP10896.
OMAiDFDNTMD.
PhylomeDBiP10896.

Miscellaneous databases

PROiP10896.

Gene expression databases

ExpressionAtlasiP10896. baseline and differential.
GenevisibleiP10896. AT.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
InterProiIPR003959. ATPase_AAA_core.
IPR027417. P-loop_NTPase.
[Graphical view]
PfamiPF00004. AAA. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Structure of an Arabidopsis thaliana cDNA encoding rubisco activase."
    Werneke J.M., Ogren W.L.
    Nucleic Acids Res. 17:2871-2871(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Tissue: Leaf.
  2. "Molecular basis of the ribulose-1,5-bisphosphate carboxylase/oxygenase activase mutation in Arabidopsis thaliana is a guanine-to-adenine transition at the 5'-splice junction of intron 3."
    Orozco B.M., McClung C.R., Werneke J.M., Ogren W.L.
    Plant Physiol. 102:227-232(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  4. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  5. "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] (ISOFORM SHORT).
    Strain: cv. Columbia.
  6. "Full-length cDNA from Arabidopsis thaliana."
    Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B., Feldmann K.A.
    Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
  7. "Alternative mRNA splicing generates the two ribulosebisphosphate carboxylase/oxygenase activase polypeptides in spinach and Arabidopsis."
    Werneke J.M., Chatfield J.M., Ogren W.L.
    Plant Cell 1:815-825(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: ALTERNATIVE SPLICING.
  8. "Proteomics of the chloroplast envelope membranes from Arabidopsis thaliana."
    Ferro M., Salvi D., Brugiere S., Miras S., Kowalski S., Louwagie M., Garin J., Joyard J., Rolland N.
    Mol. Cell. Proteomics 2:325-345(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
    Strain: cv. Wassilewskija.
  9. "Protein profiling of plastoglobules in chloroplasts and chromoplasts. A surprising site for differential accumulation of metabolic enzymes."
    Ytterberg A.J., Peltier J.-B., van Wijk K.J.
    Plant Physiol. 140:984-997(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
    Strain: cv. Columbia.
  10. "Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis thaliana."
    Jones A.M.E., MacLean D., Studholme D.J., Serna-Sanz A., Andreasson E., Rathjen J.P., Peck S.C.
    J. Proteomics 72:439-451(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: cv. Columbia.
  11. "Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks."
    Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A., Grossmann J., Gruissem W., Baginsky S.
    Plant Physiol. 150:889-903(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  12. "Identification of phosphoproteins in Arabidopsis thaliana leaves using polyethylene glycol fractionation, immobilized metal-ion affinity chromatography, two-dimensional gel electrophoresis and mass spectrometry."
    Aryal U.K., Krochko J.E., Ross A.R.
    J. Proteome Res. 11:425-437(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-283, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  13. "Comparative large-scale characterisation of plant vs. mammal proteins reveals similar and idiosyncratic N-alpha acetylation features."
    Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T., Giglione C.
    Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiRCA_ARATH
AccessioniPrimary (citable) accession number: P10896
Secondary accession number(s): Q39197, Q39198, Q940T8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1989
Last sequence update: December 1, 2000
Last modified: March 16, 2016
This is version 142 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

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 one 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.