Ribulose bisphosphate carboxylase large chain precursor

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Reviewed, UniProtKB/Swiss-Prot P00875 (RBL_SPIOL)

Last modified June 16, 2009. Version 103. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Web resources · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

Recommended name:
    Ribulose bisphosphate carboxylase large chain
      Short name=RuBisCO large subunit
    EC=4.1.1.39

Gene names

Name:

rbcL

Encoded on

Plastid; Chloroplast

Organism

Spinacia oleracea (Spinach)

Taxonomic identifier

3562 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › Caryophyllales › Amaranthaceae › Spinacia

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Protein attributes

Sequence length	475 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Function	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. HAMAP MF_01338
Catalytic activity	2 3-phospho-D-glycerate + 2 H⁺ = D-ribulose 1,5-bisphosphate + CO₂ + H₂O. HAMAP MF_01338 3-phospho-D-glycerate + 2-phosphoglycolate = D-ribulose 1,5-bisphosphate + O₂. HAMAP MF_01338
Cofactor	Binds 1 magnesium ion per subunit. HAMAP MF_01338
Subunit structure	Heterohexadecamer of 8 large chains and 8 small chains; disulfide-linked. The disulfide link is formed within the large subunit homodimers. HAMAP MF_01338
Subcellular location	Plastid › chloroplast. HAMAP MF_01338
Post-translational modification	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.
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". HAMAP MF_01338
Sequence similarities	Belongs to the RuBisCO large chain family. Type I subfamily.

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Ontologies

Keywords
Biological process	Calvin cycle Carbon dioxide fixation Photorespiration Photosynthesis
Cellular component	Chloroplast Plastid
Ligand	Magnesium Metal-binding
Molecular function	Lyase Monooxygenase Oxidoreductase
PTM	Acetylation Disulfide bond
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological process	oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW photorespiration Inferred from electronic annotation. Source: UniProtKB-KW reductive pentose-phosphate cycle Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	chloroplast Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW monooxygenase activity Inferred from electronic annotation. Source: UniProtKB-KW ribulose-bisphosphate carboxylase activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Propeptide

1 – 2

Ref.3

PRO_0000031415

Chain

3 – 475

473

Ribulose bisphosphate carboxylase large chain HAMAP MF_01338

PRO_0000031416

Sites

Active site

175

Proton acceptor Ref.5

Active site

294

Proton acceptor Ref.5

Metal binding

201

Magnesium; via carbamate group HAMAP MF_01338

Metal binding

203

Magnesium HAMAP MF_01338

Metal binding

204

Magnesium HAMAP MF_01338

Binding site

123

Substrate; in homodimeric partner HAMAP MF_01338

Binding site

173

Substrate HAMAP MF_01338

Binding site

177

Substrate HAMAP MF_01338

Binding site

295

Substrate HAMAP MF_01338

Binding site

327

Substrate HAMAP MF_01338

Binding site

379

Substrate HAMAP MF_01338

Site

Not N6-methylated HAMAP MF_01338

Site

334

Transition state stabilizer HAMAP MF_01338

Amino acid modifications

Modified residue

N-acetylproline HAMAP MF_01338

Modified residue

201

N6-carboxylysine HAMAP MF_01338

Disulfide bond

247

Interchain; in linked form HAMAP MF_01338

Experimental info

Sequence conflict

E → G in CAB88737. Ref.2

Secondary structure

475

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

P00875-1 [UniParc].

Last modified July 21, 1986. Version 1.
Checksum: 484FFFFD36BB1238
Show »

FASTA

475

52,740

        10         20         30         40         50         60 
MSPQTETKAS VEFKAGVKDY KLTYYTPEYE TLDTDILAAF RVSPQPGVPP EEAGAAVAAE 

        70         80         90        100        110        120 
SSTGTWTTVW TDGLTNLDRY KGRCYHIEPV AGEENQYICY VAYPLDLFEE GSVTNMFTSI 

       130        140        150        160        170        180 
VGNVFGFKAL RALRLEDLRI PVAYVKTFQG PPHGIQVERD KLNKYGRPLL GCTIKPKLGL 

       190        200        210        220        230        240 
SAKNYGRAVY ECLRGGLDFT KDDENVNSQP FMRWRDRFLF CAEALYKAQA ETGEIKGHYL 

       250        260        270        280        290        300 
NATAGTCEDM MKRAVFAREL GVPIVMHDYL TGGFTANTTL SHYCRDNGLL LHIHRAMHAV 

       310        320        330        340        350        360 
IDRQKNHGMH FRVLAKALRL SGGDHIHSGT VVGKLEGERD ITLGFVDLLR DDYTEKDRSR 

       370        380        390        400        410        420 
GIYFTQSWVS TPGVLPVASG GIHVWHMPAL TEIFGDDSVL QFGGGTLGHP WGNAPGAVAN 

       430        440        450        460        470 
RVALEACVQA RNEGRDLARE GNTIIREATK WSPELAAACE VWKEIKFEFP AMDTV

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[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: 6269077] [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: 11292076] [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: 2928307] [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: 3422748] [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: 637859] [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: 2118958] [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: 8648644] [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: 8955130] [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: 9092835] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
[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: 9034362] [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: 14596800] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).

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Web resources

Protein Spotlight

The Plant Kingdom's sloth - Issue 38 of September 2003

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Cross-references

Sequence databases

V00168 Genomic DNA. Translation: CAA23473.1.
AJ400848 Genomic DNA. Translation: CAB88737.1.

PIR

RKSPL. A01094.
A28965.

RefSeq

NP_054944.1.

3D structure databases

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	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:27641N.

Genome annotation databases

GeneID

2715621.

Enzyme and pathway databases

BRENDA

4.1.1.39. 286.

Family and domain databases

HAMAP

MF_01338.
[Tree]

InterPro

IPR000685. RuBisCO_lsu_C.
IPR017443. RuBisCO_lsu_fd_N.
IPR017444. RuBisCO_lsu_N.
[Graphical view]

Gene3D

G3DSA:3.20.20.110. RuBisCO_large. 1 hit.
G3DSA:3.30.70.150. RuBisCO_large. 1 hit.

Pfam

PF00016. RuBisCO_large. 1 hit.
PF02788. RuBisCO_large_N. 1 hit.
[Graphical view]

PROSITE

PS00157. RUBISCO_LARGE. 1 hit.
[Graphical view]

ProtoNet

Search...

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Entry information

Entry name

RBL_SPIOL

Accession

Primary (citable) accession number: P00875
Secondary accession number(s): Q9M3L8

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	July 21, 1986
Last modified:	June 16, 2009
This is version 103 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)

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Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families