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P00876

- RBL_TOBAC

UniProt

P00876 - RBL_TOBAC

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Protein

Ribulose bisphosphate carboxylase large chain

Gene

rbcL

Organism
Nicotiana tabacum (Common tobacco)
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

Binds 1 magnesium ion per subunit.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei123 – 1231Substrate; in homodimeric partner
Binding sitei173 – 1731Substrate
Active sitei175 – 1751Proton acceptor
Binding sitei177 – 1771Substrate
Metal bindingi201 – 2011Magnesium; via carbamate group
Metal bindingi203 – 2031Magnesium
Metal bindingi204 – 2041Magnesium
Active sitei294 – 2941Proton acceptor
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

Enzyme and pathway databases

SABIO-RKP00876.

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
Synonyms:rbcA
Encoded oniPlastid; Chloroplast
OrganismiNicotiana tabacum (Common tobacco)
Taxonomic identifieri4097 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaeasteridslamiidsSolanalesSolanaceaeNicotianoideaeNicotianeaeNicotiana

Subcellular locationi

GO - Cellular componenti

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

Keywords - Cellular componenti

Chloroplast, Plastid

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Propeptidei1 – 221 PublicationPRO_0000031427
Chaini3 – 477475Ribulose bisphosphate carboxylase large chainPRO_0000031428Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei3 – 31N-acetylproline
Modified residuei14 – 141N6,N6,N6-trimethyllysine1 Publication
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 3RUB and 4RUB may be the result of oxidation during crystallization.By similarity

Keywords - PTMi

Acetylation, Disulfide bond, Methylation

Proteomic databases

PRIDEiP00876.

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-42221N.
MINTiMINT-1176576.

Structurei

Secondary structure

1
477
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi21 – 244
Beta strandi36 – 449
Helixi50 – 5910
Turni60 – 623
Helixi71 – 733
Helixi77 – 804
Beta strandi83 – 897
Beta strandi91 – 955
Beta strandi97 – 1037
Helixi105 – 1073
Helixi113 – 1219
Helixi124 – 1263
Beta strandi130 – 13910
Helixi142 – 1454
Beta strandi151 – 1533
Helixi155 – 1628
Beta strandi169 – 1735
Beta strandi175 – 1784
Helixi182 – 19413
Beta strandi198 – 2014
Beta strandi207 – 2093
Beta strandi210 – 2123
Helixi214 – 23219
Beta strandi237 – 2415
Helixi247 – 26014
Beta strandi263 – 2686
Helixi269 – 2724
Helixi274 – 28714
Beta strandi290 – 2945
Helixi298 – 3025
Beta strandi307 – 3093
Helixi311 – 32111
Beta strandi324 – 3274
Beta strandi332 – 3343
Helixi336 – 35015
Beta strandi352 – 3543
Helixi358 – 3603
Beta strandi375 – 3817
Helixi384 – 3863
Helixi387 – 3948
Beta strandi396 – 4038
Turni404 – 4085
Helixi413 – 43220
Helixi437 – 45115
Helixi453 – 46614

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1EJ7X-ray2.45L3-477[»]
1RLCX-ray2.70L1-477[»]
1RLDX-ray2.50A/B22-467[»]
3RUBX-ray2.00L1-477[»]
4RUBX-ray2.70A/B/C/D1-477[»]
ProteinModelPortaliP00876.
SMRiP00876. Positions 9-472.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP00876.

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.

P00876 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSPQTETKAS VGFKAGVKEY KLTYYTPEYQ TKDTDILAAF RVTPQPGVPP
60 70 80 90 100
EEAGAAVAAE SSTGTWTTVW TDGLTSLDRY KGRCYRIERV VGEKDQYIAY
110 120 130 140 150
VAYPLDLFEE GSVTNMFTSI VGNVFGFKAL RALRLEDLRI PPAYVKTFQG
160 170 180 190 200
PPHGIQVERD KLNKYGRPLL GCTIKPKLGL SAKNYGRAVY ECLRGGLDFT
210 220 230 240 250
KDDENVNSQP FMRWRDRFLF CAEALYKAQA ETGEIKGHYL NATAGTCEEM
260 270 280 290 300
IKRAVFAREL GVPIVMHDYL TGGFTANTSL AHYCRDNGLL LHIHRAMHAV
310 320 330 340 350
IDRQKNHGIH FRVLAKALRM SGGDHIHSGT VVGKLEGERD ITLGFVDLLR
360 370 380 390 400
DDFVEQDRSR GIYFTQDWVS LPGVLPVASG GIHVWHMPAL TEIFGDDSVL
410 420 430 440 450
QFGGGTLGHP WGNAPGAVAN RVALEACVKA RNEGRDLAQE GNEIIREACK
460 470
WSPELAAACE VWKEIVFNFA AVDVLDK
Length:477
Mass (Da):52,898
Last modified:June 1, 2001 - v2
Checksum:i232D54E42263198F
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti284 – 2841C → G AA sequence 1 PublicationCurated
Sequence conflicti377 – 3771V → E in AAD15025. (PubMed:7160620)Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti394 – 3941F → V.1 Publication
Natural varianti405 – 4051G → M.1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
J01450 Genomic DNA. Translation: AAD15025.1.
Z00044 Genomic DNA. Translation: CAA77361.1.
PIRiA01095. RKNTL.
RefSeqiNP_054507.1. NC_001879.2.

Genome annotation databases

GeneIDi800513.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
J01450 Genomic DNA. Translation: AAD15025.1 .
Z00044 Genomic DNA. Translation: CAA77361.1 .
PIRi A01095. RKNTL.
RefSeqi NP_054507.1. NC_001879.2.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1EJ7 X-ray 2.45 L 3-477 [» ]
1RLC X-ray 2.70 L 1-477 [» ]
1RLD X-ray 2.50 A/B 22-467 [» ]
3RUB X-ray 2.00 L 1-477 [» ]
4RUB X-ray 2.70 A/B/C/D 1-477 [» ]
ProteinModelPortali P00876.
SMRi P00876. Positions 9-472.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-42221N.
MINTi MINT-1176576.

Proteomic databases

PRIDEi P00876.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

GeneIDi 800513.

Enzyme and pathway databases

SABIO-RK P00876.

Miscellaneous databases

EvolutionaryTracei P00876.

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 nucleotide sequence of the tobacco chloroplast gene for the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase."
    Shinozaki K., Sugiura M.
    Gene 20:91-102(1982) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression."
    Shinozaki K., Ohme M., Tanaka M., Wakasugi T., Hayashida N., Matsubayashi T., Zaita N., Chunwongse J., Obokata J., Yamaguchi-Shinozaki K., Ohto C., Torazawa K., Meng B.-Y., Sugita M., Deno H., Kamogashira T., Yamada K., Kusuda J.
    , Takaiwa F., Kato A., Tohdoh N., Shimada H., Sugiura M.
    EMBO J. 5:2043-2049(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Bright Yellow 4.
  3. "Amino-acid sequence of the large subunit of D-ribulose bisphosphate carboxylase/oxygenase from Nicotiana tabacum."
    Amiri I., Salnikow J., Vater J.
    Biochim. Biophys. Acta 784:116-123(1984)
    Cited for: PROTEIN SEQUENCE OF 5-477, VARIANTS VAL-394 AND MET-405.
  4. "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, METHYLATION AT LYS-14.
  5. "A crystal form of ribulose-1,5-bisphosphate carboxylase/oxygenase from Nicotiana tabacum in the activated state."
    Suh S.W., Cascio D., Chapman M.S., Eisenberg D.
    J. Mol. Biol. 197:363-365(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS).
  6. "Crystal structure of the unactivated form of ribulose-1,5-bisphosphate carboxylase/oxygenase from tobacco refined at 2.0-A resolution."
    Curmi P.M.G., Cascio D., Sweet R.M., Eisenberg D., Schreuder H.
    J. Biol. Chem. 267:16980-16989(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
  7. "The transition between the open and closed states of rubisco is triggered by the inter-phosphate distance of the bound bisphosphate."
    Duff A.P., Andrews T.J., Curmi P.M.G.
    J. Mol. Biol. 298:903-916(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.45 ANGSTROMS) OF 3-477, CARBAMYLATION AT LYS-201.

Entry informationi

Entry nameiRBL_TOBAC
AccessioniPrimary (citable) accession number: P00876
Secondary accession number(s): Q32716
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: June 1, 2001
Last modified: October 29, 2014
This is version 116 of the entry and version 2 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. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3