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P00875

- RBL_SPIOL

UniProt

P00875 - RBL_SPIOL

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Protein
Ribulose bisphosphate carboxylase large chain
Gene
rbcL
Organism
Spinacia oleracea (Spinach)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate in the photorespiration process. Both reactions occur simultaneously and in competition at the same active site.UniRule annotation

Catalytic activityi

2 3-phospho-D-glycerate + 2 H+ = D-ribulose 1,5-bisphosphate + CO2 + H2O.UniRule annotation
3-phospho-D-glycerate + 2-phosphoglycolate = D-ribulose 1,5-bisphosphate + O2.UniRule annotation

Cofactori

Binds 1 magnesium ion per subunit.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei14 – 141Not N6-methylated
Binding sitei123 – 1231Substrate; in homodimeric partner
Binding sitei173 – 1731Substrate
Active sitei175 – 1751Proton acceptor1 Publication
Binding sitei177 – 1771Substrate
Metal bindingi201 – 2011Magnesium; via carbamate group
Metal bindingi203 – 2031Magnesium
Metal bindingi204 – 2041Magnesium
Active sitei294 – 2941Proton acceptor1 Publication
Binding sitei295 – 2951Substrate
Binding sitei327 – 3271Substrate
Sitei334 – 3341Transition state stabilizer
Binding sitei379 – 3791Substrate

GO - Molecular functioni

  1. magnesium ion binding Source: UniProtKB-HAMAP
  2. monooxygenase activity Source: UniProtKB-KW
  3. ribulose-bisphosphate carboxylase activity Source: UniProtKB-HAMAP

GO - Biological processi

  1. photorespiration Source: UniProtKB-KW
  2. reductive pentose-phosphate cycle Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Lyase, Monooxygenase, Oxidoreductase

Keywords - Biological processi

Calvin cycle, Carbon dioxide fixation, Photorespiration, Photosynthesis

Keywords - Ligandi

Magnesium, Metal-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Ribulose bisphosphate carboxylase large chain (EC:4.1.1.39)
Short name:
RuBisCO large subunit
Gene namesi
Name:rbcL
Encoded oniPlastid; Chloroplast
OrganismiSpinacia oleracea (Spinach)
Taxonomic identifieri3562 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaeCaryophyllalesAmaranthaceaeChenopodioideaeAnserineaeSpinacia

Subcellular locationi

GO - Cellular componenti

  1. chloroplast Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Chloroplast, Plastid

Pathology & Biotechi

Protein family/group databases

Allergomei3814. Spi o RuBisCO.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Propeptidei1 – 22UniRule annotation
PRO_0000031415
Chaini3 – 475473Ribulose bisphosphate carboxylase large chainUniRule annotation
PRO_0000031416Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei3 – 31N-acetylprolineUniRule annotation
Modified residuei201 – 2011N6-carboxylysineUniRule annotation
Disulfide bondi247 – 247Interchain; in linked formUniRule annotation

Post-translational modificationi

The disulfide bond which can form between Cys-247 in the large chain dimeric partners within the hexadecamer appears to be associated with oxidative stress and protein turnover By similarity. The disulfide bonds reported in 1RBO may be the result of oxidation during crystallization.UniRule annotation

Keywords - PTMi

Acetylation, Disulfide bond

Interactioni

Subunit structurei

Heterohexadecamer of 8 large chains and 8 small chains; disulfide-linked. The disulfide link is formed within the large subunit homodimers.

Protein-protein interaction databases

DIPiDIP-27641N.
MINTiMINT-1522611.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi21 – 244
Beta strandi36 – 449
Helixi50 – 5910
Turni60 – 634
Beta strandi66 – 683
Helixi70 – 745
Helixi77 – 804
Beta strandi83 – 897
Beta strandi93 – 953
Beta strandi97 – 1037
Helixi105 – 1073
Helixi113 – 1219
Helixi124 – 1263
Beta strandi130 – 13910
Helixi142 – 1454
Helixi155 – 1628
Beta strandi169 – 1713
Beta strandi175 – 1784
Helixi182 – 19413
Beta strandi198 – 2014
Beta strandi207 – 2093
Helixi214 – 23219
Beta strandi237 – 2415
Helixi247 – 26014
Beta strandi263 – 2686
Helixi269 – 2724
Helixi274 – 28714
Beta strandi290 – 2945
Helixi298 – 3025
Beta strandi305 – 3095
Helixi311 – 32111
Beta strandi324 – 3274
Beta strandi331 – 3355
Helixi339 – 35012
Beta strandi352 – 3543
Helixi358 – 3603
Beta strandi375 – 3817
Helixi384 – 3863
Helixi387 – 3948
Beta strandi396 – 4016
Helixi404 – 4074
Helixi413 – 43220
Helixi437 – 44812
Turni449 – 4513
Helixi453 – 46210

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1AA1X-ray2.20B/E/H/L1-475[»]
1AUSX-ray2.20L/M/N/O1-475[»]
1IR1X-ray1.80A/B/C/D1-475[»]
1RBOX-ray2.30B/E/H/L1-475[»]
1RCOX-ray2.30B/E/H/K/L/O/R/V1-475[»]
1RCXX-ray2.40B/E/H/K/L/O/R/V1-475[»]
1RXOX-ray2.20B/E/H/L1-475[»]
1UPMX-ray2.30B/E/H/K/L/O/R/V1-475[»]
1UPPX-ray2.30A/C/E/G1-475[»]
8RUCX-ray1.60A/C/E/G1-475[»]
ProteinModelPortaliP00875.
SMRiP00875. Positions 9-475.

Miscellaneous databases

EvolutionaryTraceiP00875.

Family & Domainsi

Sequence similaritiesi

Family and domain databases

Gene3Di3.20.20.110. 1 hit.
3.30.70.150. 1 hit.
HAMAPiMF_01338. RuBisCO_L_type1.
InterProiIPR020878. RuBisCo_large_chain_AS.
IPR020888. RuBisCO_lsu.
IPR000685. RuBisCO_lsu_C.
IPR017443. RuBisCO_lsu_fd_N.
IPR017444. RuBisCO_lsu_N.
[Graphical view]
PfamiPF00016. RuBisCO_large. 1 hit.
PF02788. RuBisCO_large_N. 1 hit.
[Graphical view]
SUPFAMiSSF51649. SSF51649. 1 hit.
SSF54966. SSF54966. 1 hit.
PROSITEiPS00157. RUBISCO_LARGE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

P00875-1 [UniParc]FASTAAdd to Basket

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MSPQTETKAS VEFKAGVKDY KLTYYTPEYE TLDTDILAAF RVSPQPGVPP    50
EEAGAAVAAE SSTGTWTTVW TDGLTNLDRY KGRCYHIEPV AGEENQYICY 100
VAYPLDLFEE GSVTNMFTSI VGNVFGFKAL RALRLEDLRI PVAYVKTFQG 150
PPHGIQVERD KLNKYGRPLL GCTIKPKLGL SAKNYGRAVY ECLRGGLDFT 200
KDDENVNSQP FMRWRDRFLF CAEALYKAQA ETGEIKGHYL NATAGTCEDM 250
MKRAVFAREL GVPIVMHDYL TGGFTANTTL SHYCRDNGLL LHIHRAMHAV 300
IDRQKNHGMH FRVLAKALRL SGGDHIHSGT VVGKLEGERD ITLGFVDLLR 350
DDYTEKDRSR GIYFTQSWVS TPGVLPVASG GIHVWHMPAL TEIFGDDSVL 400
QFGGGTLGHP WGNAPGAVAN RVALEACVQA RNEGRDLARE GNTIIREATK 450
WSPELAAACE VWKEIKFEFP AMDTV 475
Length:475
Mass (Da):52,740
Last modified:July 21, 1986 - v1
Checksum:i484FFFFD36BB1238
GO

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti12 – 121E → G in CAB88737. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
V00168 Genomic DNA. Translation: CAA23473.1.
AJ400848 Genomic DNA. Translation: CAB88737.1.
PIRiA01094. RKSPL.
A28965.
RefSeqiNP_054944.1. NC_002202.1.

Genome annotation databases

GeneIDi2715621.

Cross-referencesi

Web resourcesi

Protein Spotlight

The Plant Kingdom's sloth - Issue 38 of September 2003

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
V00168 Genomic DNA. Translation: CAA23473.1 .
AJ400848 Genomic DNA. Translation: CAB88737.1 .
PIRi A01094. RKSPL.
A28965.
RefSeqi NP_054944.1. NC_002202.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1AA1 X-ray 2.20 B/E/H/L 1-475 [» ]
1AUS X-ray 2.20 L/M/N/O 1-475 [» ]
1IR1 X-ray 1.80 A/B/C/D 1-475 [» ]
1RBO X-ray 2.30 B/E/H/L 1-475 [» ]
1RCO X-ray 2.30 B/E/H/K/L/O/R/V 1-475 [» ]
1RCX X-ray 2.40 B/E/H/K/L/O/R/V 1-475 [» ]
1RXO X-ray 2.20 B/E/H/L 1-475 [» ]
1UPM X-ray 2.30 B/E/H/K/L/O/R/V 1-475 [» ]
1UPP X-ray 2.30 A/C/E/G 1-475 [» ]
8RUC X-ray 1.60 A/C/E/G 1-475 [» ]
ProteinModelPortali P00875.
SMRi P00875. Positions 9-475.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-27641N.
MINTi MINT-1522611.

Protein family/group databases

Allergomei 3814. Spi o RuBisCO.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

GeneIDi 2715621.

Miscellaneous databases

EvolutionaryTracei P00875.

Family and domain databases

Gene3Di 3.20.20.110. 1 hit.
3.30.70.150. 1 hit.
HAMAPi MF_01338. RuBisCO_L_type1.
InterProi IPR020878. RuBisCo_large_chain_AS.
IPR020888. RuBisCO_lsu.
IPR000685. RuBisCO_lsu_C.
IPR017443. RuBisCO_lsu_fd_N.
IPR017444. RuBisCO_lsu_N.
[Graphical view ]
Pfami PF00016. RuBisCO_large. 1 hit.
PF02788. RuBisCO_large_N. 1 hit.
[Graphical view ]
SUPFAMi SSF51649. SSF51649. 1 hit.
SSF54966. SSF54966. 1 hit.
PROSITEi PS00157. RUBISCO_LARGE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "The structure of the gene for the large subunit of ribulose 1,5-bisphosphate carboxylase from spinach chloroplast DNA."
    Zurawski G., Perrot B., Bottomley W., Whitfeld P.R.
    Nucleic Acids Res. 9:3251-3270(1981) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "The plastid chromosome of spinach (Spinacia oleracea): complete nucleotide sequence and gene organization."
    Schmitz-Linneweber C., Maier R.M., Alcaraz J.-P., Cottet A., Herrmann R.G., Mache R.
    Plant Mol. Biol. 45:307-315(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Geant d'hiver and cv. Monatol.
  3. "Post-translational modifications in the large subunit of ribulose bisphosphate carboxylase/oxygenase."
    Houtz R.L., Stults J.T., Mulligan R.M., Tolbert N.E.
    Proc. Natl. Acad. Sci. U.S.A. 86:1855-1859(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 3-18, LACK OF METHYLATION.
  4. "Reaction-intermediate analogue binding by ribulose bisphosphate carboxylase/oxygenase causes specific changes in proteolytic sensitivity: the amino-terminal residue of the large subunit is acetylated proline."
    Mulligan R.M., Houtz R.L., Tolbert N.E.
    Proc. Natl. Acad. Sci. U.S.A. 85:1513-1517(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 8-14 AND 466-475.
  5. "Sequences of two active-site peptides from spinach ribulosebisphosphate carboxylase/oxygenase."
    Stringer C.D., Hartman F.C.
    Biochem. Biophys. Res. Commun. 80:1043-1048(1978) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACTIVE SITE.
  6. Lorimer G.H.
    Submitted (OCT-1982) to the PIR data bank
    Cited for: ACTIVATION.
  7. "Reexamination of the three-dimensional structure of the small subunit of RuBisCo from higher plants."
    Knight S., Andersson I., Braenden C.-I.
    Science 244:702-705(1989)
    Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
  8. "Crystallographic analysis of ribulose 1,5-bisphosphate carboxylase from spinach at 2.4-A resolution. Subunit interactions and active site."
    Knight S., Andersson I., Braenden C.-I.
    J. Mol. Biol. 215:113-160(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).
  9. "Large structures at high resolution: the 1.6-A crystal structure of spinach ribulose-1,5-bisphosphate carboxylase/oxygenase complexed with 2-carboxyarabinitol bisphosphate."
    Andersson I.
    J. Mol. Biol. 259:160-174(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
  10. "A common structural basis for the inhibition of ribulose 1,5-bisphosphate carboxylase by 4-carboxyarabinitol 1,5-bisphosphate and xylulose 1,5-bisphosphate."
    Taylor T.C., Fothergill M.D., Andersson I.
    J. Biol. Chem. 271:32894-32899(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH INHIBITORS 4-CABP AND XUBP.
  11. "Structure of a product complex of spinach ribulose-1,5-bisphosphate carboxylase/oxygenase."
    Taylor T.C., Andersson I.
    Biochemistry 36:4041-4046(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS), CARBAMYLATION AT LYS-201.
  12. "The structure of the complex between rubisco and its natural substrate ribulose 1,5-bisphosphate."
    Taylor T.C., Andersson I.
    J. Mol. Biol. 265:432-444(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
  13. "Calcium supports loop closure but not catalysis in Rubisco."
    Karkehabadi S., Taylor T.C., Andersson I.
    J. Mol. Biol. 334:65-73(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).

Entry informationi

Entry nameiRBL_SPIOL
AccessioniPrimary (citable) accession number: P00875
Secondary accession number(s): Q9M3L8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: July 21, 1986
Last modified: September 3, 2014
This is version 126 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Miscellaneous

The basic functional RuBisCO is composed of a large chain homodimer in a "head-to-tail" conformation. In form I RuBisCO this homodimer is arranged in a barrel-like tetramer with the small subunits forming a tetrameric "cap" on each end of the "barrel".

Keywords - Technical termi

3D-structure, Direct protein sequencing

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Protein Spotlight
    Protein Spotlight articles and cited UniProtKB/Swiss-Prot entries
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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