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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.

Catalytic activityi

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

Cofactori

Mg2+Note: Binds 1 Mg(2+) 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-HAMAP
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 – 221 PublicationPRO_0000031415
Chaini3 – 475473Ribulose bisphosphate carboxylase large chainPRO_0000031416Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei3 – 31N-acetylproline
Modified residuei201 – 2011N6-carboxylysine1 Publication
Disulfide bondi247 – 247Interchain; in linked form

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.By similarity

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.1 Publication

Protein-protein interaction databases

DIPiDIP-27641N.
MINTiMINT-1522611.

Structurei

Secondary structure

1
475
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi21 – 244Combined sources
Beta strandi36 – 449Combined sources
Helixi50 – 5910Combined sources
Turni60 – 634Combined sources
Beta strandi66 – 683Combined sources
Helixi70 – 745Combined sources
Helixi77 – 804Combined sources
Beta strandi83 – 897Combined sources
Beta strandi93 – 953Combined sources
Beta strandi97 – 1037Combined sources
Helixi105 – 1073Combined sources
Helixi113 – 1219Combined sources
Helixi124 – 1263Combined sources
Beta strandi130 – 13910Combined sources
Helixi142 – 1454Combined sources
Helixi155 – 1628Combined sources
Beta strandi169 – 1713Combined sources
Beta strandi175 – 1784Combined sources
Helixi182 – 19413Combined sources
Beta strandi198 – 2014Combined sources
Beta strandi207 – 2093Combined sources
Helixi214 – 23219Combined sources
Beta strandi237 – 2415Combined sources
Helixi247 – 26014Combined sources
Beta strandi263 – 2686Combined sources
Helixi269 – 2724Combined sources
Helixi274 – 28714Combined sources
Beta strandi290 – 2945Combined sources
Helixi298 – 3025Combined sources
Beta strandi305 – 3095Combined sources
Helixi311 – 32111Combined sources
Beta strandi324 – 3274Combined sources
Beta strandi331 – 3355Combined sources
Helixi339 – 35012Combined sources
Beta strandi352 – 3543Combined sources
Helixi358 – 3603Combined sources
Beta strandi375 – 3817Combined sources
Helixi384 – 3863Combined sources
Helixi387 – 3948Combined sources
Beta strandi396 – 4016Combined sources
Helixi404 – 4074Combined sources
Helixi413 – 43220Combined sources
Helixi437 – 44812Combined sources
Turni449 – 4513Combined sources
Helixi453 – 46210Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
ModBaseiSearch...
MobiDBiSearch...

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

« Hide

        10         20         30         40         50
MSPQTETKAS VEFKAGVKDY KLTYYTPEYE TLDTDILAAF RVSPQPGVPP
60 70 80 90 100
EEAGAAVAAE SSTGTWTTVW TDGLTNLDRY KGRCYHIEPV AGEENQYICY
110 120 130 140 150
VAYPLDLFEE GSVTNMFTSI VGNVFGFKAL RALRLEDLRI PVAYVKTFQG
160 170 180 190 200
PPHGIQVERD KLNKYGRPLL GCTIKPKLGL SAKNYGRAVY ECLRGGLDFT
210 220 230 240 250
KDDENVNSQP FMRWRDRFLF CAEALYKAQA ETGEIKGHYL NATAGTCEDM
260 270 280 290 300
MKRAVFAREL GVPIVMHDYL TGGFTANTTL SHYCRDNGLL LHIHRAMHAV
310 320 330 340 350
IDRQKNHGMH FRVLAKALRL SGGDHIHSGT VVGKLEGERD ITLGFVDLLR
360 370 380 390 400
DDYTEKDRSR GIYFTQSWVS TPGVLPVASG GIHVWHMPAL TEIFGDDSVL
410 420 430 440 450
QFGGGTLGHP WGNAPGAVAN RVALEACVQA RNEGRDLARE GNTIIREATK
460 470
WSPELAAACE VWKEIKFEFP AMDTV
Length:475
Mass (Da):52,740
Last modified:July 21, 1986 - v1
Checksum:i484FFFFD36BB1238
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti12 – 121E → G in CAB88737. (PubMed:11292076)Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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:
PDBei
RCSB PDBi
PDBji
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: November 26, 2014
This is version 129 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