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Protein

Ribulose bisphosphate carboxylase large chain

Gene

rbcL

Organism
Oryza sativa subsp. japonica (Rice)
Status
Reviewed-Annotation score: -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.

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".
NADPH and 6-phosphogluconate function as positive effectors to promote enzyme activation.1 Publication

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+1 PublicationNote: Binds 1 Mg2+ ion per subunit.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei60NADPCombined sources1 Publication1
Binding sitei65SubstrateCombined sources1 Publication1
Binding sitei68NADPCombined sources1 Publication1
Binding sitei123Substrate; in homodimeric partnerCombined sources1 Publication1
Binding sitei127NADP; via amide nitrogenCombined sources1 Publication1
Active sitei175Proton acceptorUniRule annotation1
Binding sitei175NADPCombined sources1 Publication1
Metal bindingi201Magnesium; via carbamate groupCombined sources1 Publication1
Metal bindingi203MagnesiumCombined sources1 Publication1
Metal bindingi204MagnesiumCombined sources1 Publication1
Active sitei294Proton acceptorUniRule annotation1
Binding sitei327SubstrateCombined sources1 Publication1
Binding sitei334SubstrateCombined sources1
Sitei334Transition state stabilizer1
Binding sitei381NADP; via amide nitrogenCombined sources1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi295 – 298NADPCombined sources1 Publication4
Nucleotide bindingi404 – 405NADP1 Publication2

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionLyase, Monooxygenase, Oxidoreductase
Biological processCalvin cycle, Carbon dioxide fixation, Photorespiration, Photosynthesis
LigandMagnesium, Metal-binding, NADP, Nucleotide-binding

Enzyme and pathway databases

BRENDAi4.1.1.39 4460

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
Ordered Locus Names:LOC_Osp1g00420
ORF Names:Nip064
Encoded oniPlastid; Chloroplast
OrganismiOryza sativa subsp. japonica (Rice)
Taxonomic identifieri39947 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaLiliopsidaPoalesPoaceaeBOP cladeOryzoideaeOryzeaeOryzinaeOryzaOryza sativa
Proteomesi

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Chloroplast Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertion Graphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Chloroplast, Plastid

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
PropeptideiPRO_00002901011 – 2By similarity2
ChainiPRO_00002901023 – 477Ribulose bisphosphate carboxylase large chainAdd BLAST475

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei3N-acetylprolineBy similarity1
Modified residuei201N6-carboxylysine1 Publication1
Disulfide bondi247Interchain; in linked formBy similarity

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 bond reported in 1WDD may be the result of oxidation during crystallization.By similarity

Keywords - PTMi

Acetylation, Disulfide bond

Proteomic databases

PaxDbiP0C512

Expressioni

Gene expression databases

GenevisibleiP0C512 OS

Interactioni

Subunit structurei

Heterohexadecamer of 8 large chains and 8 small chains (PubMed:22609438); disulfide-linked. The disulfide link is formed within the large subunit homodimers.1 Publication

Protein-protein interaction databases

STRINGi39947.LOC_Osp1g00420.1

Structurei

Secondary structure

1477
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi21 – 24Combined sources4
Beta strandi35 – 44Combined sources10
Helixi50 – 60Combined sources11
Turni61 – 63Combined sources3
Helixi70 – 74Combined sources5
Helixi77 – 80Combined sources4
Beta strandi83 – 89Combined sources7
Beta strandi91 – 93Combined sources3
Beta strandi97 – 103Combined sources7
Helixi105 – 107Combined sources3
Helixi113 – 121Combined sources9
Helixi124 – 126Combined sources3
Beta strandi130 – 139Combined sources10
Helixi142 – 145Combined sources4
Helixi155 – 162Combined sources8
Beta strandi169 – 171Combined sources3
Beta strandi175 – 178Combined sources4
Helixi182 – 194Combined sources13
Beta strandi198 – 201Combined sources4
Beta strandi207 – 209Combined sources3
Helixi214 – 232Combined sources19
Beta strandi237 – 241Combined sources5
Helixi247 – 260Combined sources14
Beta strandi263 – 268Combined sources6
Helixi269 – 272Combined sources4
Helixi274 – 287Combined sources14
Beta strandi290 – 294Combined sources5
Helixi298 – 302Combined sources5
Beta strandi305 – 309Combined sources5
Helixi311 – 321Combined sources11
Beta strandi324 – 327Combined sources4
Beta strandi331 – 335Combined sources5
Helixi339 – 350Combined sources12
Beta strandi352 – 354Combined sources3
Helixi358 – 360Combined sources3
Beta strandi375 – 381Combined sources7
Helixi384 – 386Combined sources3
Helixi387 – 394Combined sources8
Beta strandi396 – 401Combined sources6
Helixi404 – 407Combined sources4
Helixi413 – 432Combined sources20
Helixi437 – 449Combined sources13
Helixi453 – 462Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1WDDX-ray1.35A/E1-477[»]
3AXKX-ray1.90A/B1-477[»]
3AXMX-ray1.65A/B/C/D/E/F/G/H1-477[»]
ProteinModelPortaliP0C512
SMRiP0C512
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0C512

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni173 – 177Substrate bindingCombined sources1 Publication5
Regioni201 – 204Substrate bindingCombined sources1 Publication4
Regioni294 – 295Substrate bindingCombined sources2
Regioni379 – 381Substrate bindingCombined sources1 Publication3

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG410IIVP Eukaryota
COG1850 LUCA
InParanoidiP0C512
KOiK01601

Family and domain databases

CDDicd08212 RuBisCO_large_I, 1 hit
Gene3Di3.20.20.110, 1 hit
3.30.70.150, 1 hit
HAMAPiMF_01338 RuBisCO_L_type1, 1 hit
InterProiView protein in InterPro
IPR033966 RuBisCO
IPR020878 RuBisCo_large_chain_AS
IPR000685 RuBisCO_lsu_C
IPR036376 RuBisCO_lsu_C_sf
IPR017443 RuBisCO_lsu_fd_N
IPR036422 RuBisCO_lsu_N_sf
IPR020888 RuBisCO_lsuI
PfamiView protein in Pfam
PF00016 RuBisCO_large, 1 hit
PF02788 RuBisCO_large_N, 1 hit
SFLDiSFLDS00014 RuBisCO, 1 hit
SUPFAMiSSF51649 SSF51649, 1 hit
SSF54966 SSF54966, 1 hit
PROSITEiView protein in PROSITE
PS00157 RUBISCO_LARGE, 1 hit

Sequencei

Sequence statusi: Complete.

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

P0C512-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSPQTETKAS VGFKAGVKDY KLTYYTPEYE TKDTDILAAF RVTPQPGVPP
60 70 80 90 100
EEAGAAVAAE SSTGTWTTVW TDGLTSLDRY KGRCYHIEPV VGEDNQYIAY
110 120 130 140 150
VAYPLDLFEE GSVTNMFTSI VGNVFGFKAL RALRLEDLRI PPTYSKTFQG
160 170 180 190 200
PPHGIQVERD KLNKYGRPLL GCTIKPKLGL SAKNYGRACY ECLRGGLDFT
210 220 230 240 250
KDDENVNSQP FMRWRDRFVF CAEAIYKSQA ETGEIKGHYL NATAGTCEEM
260 270 280 290 300
IKRAVFAREL GVPIVMHDYL TGGFTANTSL AHYCRDNGLL LHIHRAMHAV
310 320 330 340 350
IDRQKNHGMH FRVLAKALRM SGGDHIHAGT VVGKLEGERE MTLGFVDLLR
360 370 380 390 400
DDFIEKDRAR GIFFTQDWVS MPGVIPVASG GIHVWHMPAL TEIFGDDSVL
410 420 430 440 450
QFGGGTLGHP WGNAPGAAAN RVALEACVQA RNEGRDLARE GNEIIRSACK
460 470
WSPELAAACE IWKAIKFEFE PVDKLDS
Length:477
Mass (Da):52,881
Last modified:June 12, 2007 - v1
Checksum:i8EECF4F8F1F0A8F9
GO

Sequence cautioni

The sequence AAS46127 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D00207 Genomic DNA Translation: BAA00147.1
X15901 Genomic DNA Translation: CAA34004.1
AY522330 Genomic DNA Translation: AAS46127.1 Different initiation.
PIRiJQ0231 RKRZL
RefSeqiNP_039391.1, NC_001320.1
YP_009305312.1, NC_031333.1

Genome annotation databases

EnsemblPlantsiCAA34004; CAA34004; CAA34004
GeneIDi29141378
3131463
GrameneiCAA34004; CAA34004; CAA34004
KEGGiosa:3131463

Similar proteinsi

Entry informationi

Entry nameiRBL_ORYSJ
AccessioniPrimary (citable) accession number: P0C512
Secondary accession number(s): P12089, Q6QY04, Q6QY68
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 12, 2007
Last sequence update: June 12, 2007
Last modified: May 23, 2018
This is version 80 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Oryza sativa (rice)
    Index of Oryza sativa entries and their corresponding gene designations
  3. SIMILARITY comments
    Index of protein domains and families

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