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Protein

Ribulose bisphosphate carboxylase large chain

Gene

rbcL

Organism
Oryza sativa subsp. japonica (Rice)
Status
Reviewed-Annotation score: 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+1 PublicationNote: Binds 1 Mg2+ ion per subunit.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei60NADP1 Publication1
Binding sitei68NADP1 Publication1
Binding sitei123Substrate; in homodimeric partner1
Binding sitei127NADP; via amide nitrogen1 Publication1
Binding sitei173Substrate1
Active sitei175Proton acceptor1
Binding sitei175NADP1 Publication1
Binding sitei177Substrate1
Metal bindingi201Magnesium; via carbamate group1 Publication1
Metal bindingi203Magnesium1 Publication1
Metal bindingi204Magnesium1 Publication1
Active sitei294Proton acceptor1
Binding sitei295Substrate1
Binding sitei327Substrate1
Sitei334Transition state stabilizer1
Binding sitei379Substrate1
Binding sitei381NADP; via amide nitrogen1 Publication1

Regions

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

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Lyase, Monooxygenase, Oxidoreductase

Keywords - Biological processi

Calvin cycle, Carbon dioxide fixation, Photorespiration, Photosynthesis

Keywords - Ligandi

Magnesium, 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 cladeOryzoideaeOryzeaeOryzinaeOryza
Proteomesi
  • UP000059680 Componenti: Chloroplast

Subcellular locationi

GO - Cellular componenti

  • chloroplast stroma Source: GO_Central
  • plastid Source: Gramene
  • small ribosomal subunit Source: GO_Central
Complete GO annotation...

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.
PRIDEiP0C512.

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

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.
InterProiIPR033966. RuBisCO.
IPR020878. RuBisCo_large_chain_AS.
IPR000685. RuBisCO_lsu_C.
IPR017443. RuBisCO_lsu_fd_N.
IPR020888. RuBisCO_lsuI.
[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.

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.

Genome annotation databases

GeneIDi3131463.
KEGGiosa:3131463.

Cross-referencesi

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.

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...

Protein-protein interaction databases

STRINGi39947.LOC_Osp1g00420.1.

Proteomic databases

PaxDbiP0C512.
PRIDEiP0C512.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi3131463.
KEGGiosa:3131463.

Phylogenomic databases

eggNOGiENOG410IIVP. Eukaryota.
COG1850. LUCA.
InParanoidiP0C512.
KOiK01601.

Enzyme and pathway databases

BRENDAi4.1.1.39. 4460.

Miscellaneous databases

EvolutionaryTraceiP0C512.
PROiP0C512.

Gene expression databases

GenevisibleiP0C512. OS.

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.
InterProiIPR033966. RuBisCO.
IPR020878. RuBisCo_large_chain_AS.
IPR000685. RuBisCO_lsu_C.
IPR017443. RuBisCO_lsu_fd_N.
IPR020888. RuBisCO_lsuI.
[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]
ProtoNetiSearch...

Entry informationi

Entry nameiRBL_ORYSJ
AccessioniPrimary (citable) accession number: P0C512
Secondary accession number(s): P12089, Q6QY04, Q6QY68
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 12, 2007
Last sequence update: June 12, 2007
Last modified: November 30, 2016
This is version 71 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".
NADPH and 6-phosphogluconate function as positive effectors to promote enzyme activation.1 Publication

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

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.