RBL_ORYSJ
ID RBL_ORYSJ Reviewed; 477 AA.
AC P0C512; P12089; Q6QY04; Q6QY68;
DT 12-JUN-2007, integrated into UniProtKB/Swiss-Prot.
DT 12-JUN-2007, sequence version 1.
DT 03-AUG-2022, entry version 100.
DE RecName: Full=Ribulose bisphosphate carboxylase large chain;
DE Short=RuBisCO large subunit;
DE EC=4.1.1.39;
DE Flags: Precursor;
GN Name=rbcL; OrderedLocusNames=LOC_Osp1g00420; ORFNames=Nip064;
OS Oryza sativa subsp. japonica (Rice).
OG Plastid; Chloroplast.
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RA Nishizawa Y., Hirai A.;
RT "Nucleotide sequence and expression of the gene for the large subunit of
RT rice ribulose 1,5-bisphosphate carboxylase.";
RL Jpn. J. Genet. 62:389-395(1987).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=2770692; DOI=10.1007/bf02464880;
RA Hiratsuka J., Shimada H., Whittier R., Ishibashi T., Sakamoto M., Mori M.,
RA Kondo C., Honji Y., Sun C.-R., Meng B.-Y., Li Y.-Q., Kanno A.,
RA Nishizawa Y., Hirai A., Shinozaki K., Sugiura M.;
RT "The complete sequence of the rice (Oryza sativa) chloroplast genome:
RT intermolecular recombination between distinct tRNA genes accounts for a
RT major plastid DNA inversion during the evolution of the cereals.";
RL Mol. Gen. Genet. 217:185-194(1989).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15122023; DOI=10.1104/pp.103.031245;
RA Tang J., Xia H., Cao M., Zhang X., Zeng W., Hu S., Tong W., Wang J.,
RA Wang J., Yu J., Yang H., Zhu L.;
RT "A comparison of rice chloroplast genomes.";
RL Plant Physiol. 135:412-420(2004).
RN [4]
RP PROTEIN SEQUENCE [LARGE SCALE ANALYSIS] OF 41-48; 180-186 AND 320-327, AND
RP IDENTIFICATION BY MASS SPECTROMETRY.
RC STRAIN=cv. Nipponbare;
RX PubMed=16758443; DOI=10.1002/pmic.200600043;
RA Nozu Y., Tsugita A., Kamijo K.;
RT "Proteomic analysis of rice leaf, stem and root tissues during growth
RT course.";
RL Proteomics 6:3665-3670(2006).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (1.35 ANGSTROMS) OF ACTIVATED HOLOENZYME IN COMPLEX
RP WITH MAGNESIUM AND NADP; 6-PHOSPHOGLUCONATE OR TRANSITION-STATE ANALOG
RP 2-CABP, SUBUNIT, AND CARBOXYLATION AT LYS-201.
RC STRAIN=cv. Notohikari; TISSUE=Leaf;
RX PubMed=22609438; DOI=10.1016/j.jmb.2012.05.014;
RA Matsumura H., Mizohata E., Ishida H., Kogami A., Ueno T., Makino A.,
RA Inoue T., Yokota A., Mae T., Kai Y.;
RT "Crystal structure of rice Rubisco and implications for activation induced
RT by positive effectors NADPH and 6-phosphogluconate.";
RL J. Mol. Biol. 422:75-86(2012).
CC -!- FUNCTION: RuBisCO catalyzes two reactions: the carboxylation of D-
CC ribulose 1,5-bisphosphate, the primary event in carbon dioxide
CC fixation, as well as the oxidative fragmentation of the pentose
CC substrate in the photorespiration process. Both reactions occur
CC simultaneously and in competition at the same active site.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2 (2R)-3-phosphoglycerate + 2 H(+) = CO2 + D-ribulose 1,5-
CC bisphosphate + H2O; Xref=Rhea:RHEA:23124, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:16526, ChEBI:CHEBI:57870,
CC ChEBI:CHEBI:58272; EC=4.1.1.39;
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-ribulose 1,5-bisphosphate + O2 = (2R)-3-phosphoglycerate +
CC 2-phosphoglycolate + 2 H(+); Xref=Rhea:RHEA:36631, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:15379, ChEBI:CHEBI:57870, ChEBI:CHEBI:58033,
CC ChEBI:CHEBI:58272;
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:22609438};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000269|PubMed:22609438};
CC -!- SUBUNIT: Heterohexadecamer of 8 large chains and 8 small chains
CC (PubMed:22609438); disulfide-linked. The disulfide link is formed
CC within the large subunit homodimers. {ECO:0000269|PubMed:22609438}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast.
CC -!- PTM: The disulfide bond which can form between Cys-247 in the large
CC chain dimeric partners within the hexadecamer appears to be associated
CC with oxidative stress and protein turnover (By similarity). The
CC disulfide bond reported in 1WDD may be the result of oxidation during
CC crystallization. {ECO:0000250|UniProtKB:P11383}.
CC -!- MISCELLANEOUS: The basic functional RuBisCO is composed of a large
CC chain homodimer in a 'head-to-tail' conformation. In form I RuBisCO
CC this homodimer is arranged in a barrel-like tetramer with the small
CC subunits forming a tetrameric 'cap' on each end of the 'barrel'.
CC -!- MISCELLANEOUS: NADPH and 6-phosphogluconate function as positive
CC effectors to promote enzyme activation. {ECO:0000305|PubMed:22609438}.
CC -!- SIMILARITY: Belongs to the RuBisCO large chain family. Type I
CC subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAS46127.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; D00207; BAA00147.1; -; Genomic_DNA.
DR EMBL; X15901; CAA34004.1; -; Genomic_DNA.
DR EMBL; AY522330; AAS46127.1; ALT_INIT; Genomic_DNA.
DR PIR; JQ0231; RKRZL.
DR RefSeq; NP_039391.1; NC_001320.1.
DR RefSeq; YP_009305312.1; NC_031333.1.
DR PDB; 1WDD; X-ray; 1.35 A; A/E=1-477.
DR PDB; 3AXK; X-ray; 1.90 A; A/B=1-477.
DR PDB; 3AXM; X-ray; 1.65 A; A/B/C/D/E/F/G/H=1-477.
DR PDBsum; 1WDD; -.
DR PDBsum; 3AXK; -.
DR PDBsum; 3AXM; -.
DR AlphaFoldDB; P0C512; -.
DR SMR; P0C512; -.
DR STRING; 4530.OS10T0356000-00; -.
DR PaxDb; P0C512; -.
DR PRIDE; P0C512; -.
DR GeneID; 29141378; -.
DR GeneID; 3131463; -.
DR KEGG; osa:3131463; -.
DR eggNOG; ENOG502QTI9; Eukaryota.
DR InParanoid; P0C512; -.
DR OrthoDB; 474428at2759; -.
DR BRENDA; 4.1.1.39; 4460.
DR EvolutionaryTrace; P0C512; -.
DR PRO; PR:P0C512; -.
DR Proteomes; UP000059680; Chloroplast.
DR Genevisible; P0C512; OS.
DR GO; GO:0009507; C:chloroplast; IEA:UniProtKB-SubCell.
DR GO; GO:0009536; C:plastid; IC:Gramene.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0004497; F:monooxygenase activity; IEA:UniProtKB-KW.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0016984; F:ribulose-bisphosphate carboxylase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0009853; P:photorespiration; IEA:UniProtKB-KW.
DR GO; GO:0019253; P:reductive pentose-phosphate cycle; IEA:UniProtKB-UniRule.
DR CDD; cd08212; RuBisCO_large_I; 1.
DR Gene3D; 3.20.20.110; -; 1.
DR Gene3D; 3.30.70.150; -; 1.
DR HAMAP; MF_01338; RuBisCO_L_type1; 1.
DR InterPro; IPR033966; RuBisCO.
DR InterPro; IPR020878; RuBisCo_large_chain_AS.
DR InterPro; IPR000685; RuBisCO_lsu_C.
DR InterPro; IPR036376; RuBisCO_lsu_C_sf.
DR InterPro; IPR017443; RuBisCO_lsu_fd_N.
DR InterPro; IPR036422; RuBisCO_lsu_N_sf.
DR InterPro; IPR020888; RuBisCO_lsuI.
DR PANTHER; PTHR42704; PTHR42704; 1.
DR Pfam; PF00016; RuBisCO_large; 1.
DR Pfam; PF02788; RuBisCO_large_N; 1.
DR SFLD; SFLDS00014; RuBisCO; 1.
DR SUPFAM; SSF51649; SSF51649; 1.
DR SUPFAM; SSF54966; SSF54966; 1.
DR PROSITE; PS00157; RUBISCO_LARGE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Calvin cycle; Carbon dioxide fixation;
KW Chloroplast; Direct protein sequencing; Disulfide bond; Lyase; Magnesium;
KW Metal-binding; Monooxygenase; NADP; Nucleotide-binding; Oxidoreductase;
KW Photorespiration; Photosynthesis; Plastid; Reference proteome.
FT PROPEP 1..2
FT /evidence="ECO:0000250"
FT /id="PRO_0000290101"
FT CHAIN 3..477
FT /note="Ribulose bisphosphate carboxylase large chain"
FT /id="PRO_0000290102"
FT ACT_SITE 175
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01338"
FT ACT_SITE 294
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01338"
FT BINDING 60
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:22609438,
FT ECO:0007744|PDB:3AXK"
FT BINDING 65
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:22609438,
FT ECO:0007744|PDB:1WDD"
FT BINDING 68
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:22609438,
FT ECO:0007744|PDB:3AXK"
FT BINDING 123
FT /ligand="substrate"
FT /note="in homodimeric partner"
FT /evidence="ECO:0000269|PubMed:22609438,
FT ECO:0007744|PDB:1WDD, ECO:0007744|PDB:3AXM"
FT BINDING 127
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:22609438,
FT ECO:0007744|PDB:3AXK"
FT BINDING 173..177
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:22609438,
FT ECO:0007744|PDB:1WDD"
FT BINDING 175
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:22609438,
FT ECO:0007744|PDB:3AXK"
FT BINDING 201..204
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:22609438,
FT ECO:0007744|PDB:1WDD"
FT BINDING 201
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /note="via carbamate group"
FT /evidence="ECO:0000269|PubMed:22609438,
FT ECO:0007744|PDB:1WDD, ECO:0007744|PDB:3AXK,
FT ECO:0007744|PDB:3AXM"
FT BINDING 203
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:22609438,
FT ECO:0007744|PDB:1WDD, ECO:0007744|PDB:3AXK,
FT ECO:0007744|PDB:3AXM"
FT BINDING 204
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:22609438,
FT ECO:0007744|PDB:1WDD, ECO:0007744|PDB:3AXK,
FT ECO:0007744|PDB:3AXM"
FT BINDING 294..295
FT /ligand="substrate"
FT /evidence="ECO:0007744|PDB:1WDD"
FT BINDING 295..298
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:22609438,
FT ECO:0007744|PDB:3AXK"
FT BINDING 327
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:22609438,
FT ECO:0007744|PDB:1WDD"
FT BINDING 334
FT /ligand="substrate"
FT /evidence="ECO:0007744|PDB:1WDD"
FT BINDING 379..381
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:22609438,
FT ECO:0007744|PDB:1WDD"
FT BINDING 381
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:22609438,
FT ECO:0007744|PDB:3AXK"
FT BINDING 404..405
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:22609438"
FT SITE 334
FT /note="Transition state stabilizer"
FT MOD_RES 3
FT /note="N-acetylproline"
FT /evidence="ECO:0000250"
FT MOD_RES 201
FT /note="N6-carboxylysine"
FT /evidence="ECO:0000269|PubMed:22609438"
FT DISULFID 247
FT /note="Interchain; in linked form"
FT /evidence="ECO:0000250"
FT HELIX 21..24
FT /evidence="ECO:0007829|PDB:1WDD"
FT STRAND 35..44
FT /evidence="ECO:0007829|PDB:1WDD"
FT HELIX 50..60
FT /evidence="ECO:0007829|PDB:1WDD"
FT TURN 61..63
FT /evidence="ECO:0007829|PDB:1WDD"
FT HELIX 70..74
FT /evidence="ECO:0007829|PDB:1WDD"
FT HELIX 77..80
FT /evidence="ECO:0007829|PDB:1WDD"
FT STRAND 83..89
FT /evidence="ECO:0007829|PDB:1WDD"
FT STRAND 91..93
FT /evidence="ECO:0007829|PDB:3AXK"
FT STRAND 97..103
FT /evidence="ECO:0007829|PDB:1WDD"
FT HELIX 105..107
FT /evidence="ECO:0007829|PDB:1WDD"
FT HELIX 113..121
FT /evidence="ECO:0007829|PDB:1WDD"
FT HELIX 124..126
FT /evidence="ECO:0007829|PDB:1WDD"
FT STRAND 130..139
FT /evidence="ECO:0007829|PDB:1WDD"
FT HELIX 142..145
FT /evidence="ECO:0007829|PDB:1WDD"
FT HELIX 155..162
FT /evidence="ECO:0007829|PDB:1WDD"
FT STRAND 169..171
FT /evidence="ECO:0007829|PDB:1WDD"
FT STRAND 175..178
FT /evidence="ECO:0007829|PDB:1WDD"
FT HELIX 182..194
FT /evidence="ECO:0007829|PDB:1WDD"
FT STRAND 198..201
FT /evidence="ECO:0007829|PDB:1WDD"
FT STRAND 207..209
FT /evidence="ECO:0007829|PDB:1WDD"
FT HELIX 214..232
FT /evidence="ECO:0007829|PDB:1WDD"
FT STRAND 237..241
FT /evidence="ECO:0007829|PDB:1WDD"
FT HELIX 247..260
FT /evidence="ECO:0007829|PDB:1WDD"
FT STRAND 263..268
FT /evidence="ECO:0007829|PDB:1WDD"
FT HELIX 269..272
FT /evidence="ECO:0007829|PDB:1WDD"
FT HELIX 274..287
FT /evidence="ECO:0007829|PDB:1WDD"
FT STRAND 290..294
FT /evidence="ECO:0007829|PDB:1WDD"
FT HELIX 298..302
FT /evidence="ECO:0007829|PDB:1WDD"
FT STRAND 305..309
FT /evidence="ECO:0007829|PDB:1WDD"
FT HELIX 311..321
FT /evidence="ECO:0007829|PDB:1WDD"
FT STRAND 324..327
FT /evidence="ECO:0007829|PDB:1WDD"
FT STRAND 331..335
FT /evidence="ECO:0007829|PDB:1WDD"
FT HELIX 339..350
FT /evidence="ECO:0007829|PDB:1WDD"
FT STRAND 352..354
FT /evidence="ECO:0007829|PDB:1WDD"
FT HELIX 358..360
FT /evidence="ECO:0007829|PDB:1WDD"
FT STRAND 375..381
FT /evidence="ECO:0007829|PDB:1WDD"
FT HELIX 384..386
FT /evidence="ECO:0007829|PDB:1WDD"
FT HELIX 387..394
FT /evidence="ECO:0007829|PDB:1WDD"
FT STRAND 396..401
FT /evidence="ECO:0007829|PDB:1WDD"
FT HELIX 404..407
FT /evidence="ECO:0007829|PDB:1WDD"
FT HELIX 413..432
FT /evidence="ECO:0007829|PDB:1WDD"
FT HELIX 437..449
FT /evidence="ECO:0007829|PDB:1WDD"
FT HELIX 453..462
FT /evidence="ECO:0007829|PDB:1WDD"
SQ SEQUENCE 477 AA; 52881 MW; 8EECF4F8F1F0A8F9 CRC64;
MSPQTETKAS VGFKAGVKDY KLTYYTPEYE TKDTDILAAF RVTPQPGVPP EEAGAAVAAE
SSTGTWTTVW TDGLTSLDRY KGRCYHIEPV VGEDNQYIAY VAYPLDLFEE GSVTNMFTSI
VGNVFGFKAL RALRLEDLRI PPTYSKTFQG PPHGIQVERD KLNKYGRPLL GCTIKPKLGL
SAKNYGRACY ECLRGGLDFT KDDENVNSQP FMRWRDRFVF CAEAIYKSQA ETGEIKGHYL
NATAGTCEEM IKRAVFAREL GVPIVMHDYL TGGFTANTSL AHYCRDNGLL LHIHRAMHAV
IDRQKNHGMH FRVLAKALRM SGGDHIHAGT VVGKLEGERE MTLGFVDLLR DDFIEKDRAR
GIFFTQDWVS MPGVIPVASG GIHVWHMPAL TEIFGDDSVL QFGGGTLGHP WGNAPGAAAN
RVALEACVQA RNEGRDLARE GNEIIRSACK WSPELAAACE IWKAIKFEFE PVDKLDS
