Reviewed, UniProtKB/Swiss-Prot P00877 (RBL_CHLRE)

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

Chlamydomonas reinhardtii

Taxonomic identifier

3055 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Chlorophyta › Chlorophyceae › Chlamydomonadales › Chlamydomonadaceae › Chlamydomonas

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.

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 bond reported in 1IR2 may be the result of oxidation during crystallization. The electron density found in the position of Thr-471 (Ref.6 only) suggests it is either O-methylthreonine, or Ile, which may be produced by RNA editing. HAMAP MF_01338
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.

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 Hydroxylation Methylation
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...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Propeptide

1 – 2

2

Ref.3

PRO_0000031175

Chain

3 – 475

473

Ribulose bisphosphate carboxylase large chain HAMAP MF_01338

PRO_0000031176

Sites

Active site

175

1

Proton acceptor HAMAP MF_01338

Active site

294

1

Proton acceptor HAMAP MF_01338

Metal binding

201

1

Magnesium; via carbamate group HAMAP MF_01338

Metal binding

203

1

Magnesium HAMAP MF_01338

Metal binding

204

1

Magnesium HAMAP MF_01338

Binding site

123

1

Substrate; in homodimeric partner HAMAP MF_01338

Binding site

173

1

Substrate HAMAP MF_01338

Binding site

177

1

Substrate HAMAP MF_01338

Binding site

295

1

Substrate HAMAP MF_01338

Binding site

327

1

Substrate HAMAP MF_01338

Binding site

379

1

Substrate HAMAP MF_01338

Site

334

1

Transition state stabilizer HAMAP MF_01338

Amino acid modifications

Modified residue

3

1

N-acetylproline Ref.3

Modified residue

104

1

4-hydroxyproline HAMAP MF_01338

Modified residue

151

1

4-hydroxyproline HAMAP MF_01338

Modified residue

201

1

N6-carboxylysine HAMAP MF_01338

Modified residue

256

1

S-methylcysteine HAMAP MF_01338

Modified residue

369

1

S-methylcysteine HAMAP MF_01338

Disulfide bond

247

Interchain; in linked form HAMAP MF_01338

Natural variations

Natural variant

46

1

L → P in strain: 137c and CC-503. HAMAP MF_01338

Secondary structure

1

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475

Helix Strand Turn

Details...

Helix

21 – 24

4

Beta strand

36 – 44

9

Helix

50 – 60

11

Turn

61 – 63

3

Helix

70 – 74

5

Helix

77 – 80

4

Beta strand

83 – 89

7

Beta strand

97 – 103

7

Helix

105 – 107

3

Helix

113 – 121

9

Helix

124 – 126

3

Beta strand

130 – 139

10

Helix

142 – 145

4

Helix

155 – 162

8

Beta strand

169 – 171

3

Beta strand

175 – 178

4

Helix

182 – 194

13

Beta strand

198 – 201

4

Beta strand

207 – 209

3

Helix

214 – 232

19

Beta strand

237 – 241

5

Helix

247 – 260

14

Beta strand

263 – 268

6

Helix

269 – 272

4

Helix

274 – 287

14

Beta strand

290 – 294

5

Helix

298 – 302

5

Beta strand

305 – 309

5

Helix

311 – 321

11

Beta strand

324 – 327

4

Beta strand

331 – 335

5

Helix

339 – 350

12

Beta strand

352 – 354

3

Helix

358 – 360

3

Beta strand

375 – 381

7

Helix

384 – 386

3

Helix

387 – 394

8

Beta strand

396 – 401

6

Helix

404 – 407

4

Helix

413 – 432

20

Helix

437 – 451

15

Helix

453 – 462

10

Sequences

	Sequence		Length	Mass (Da)
	P00877-1 [UniParc]. Last modified July 21, 1986. Version 1. Checksum: 5A9BFD394CF7D4D4	FASTA	475	52,543
	10 20 30 40 50 60 MVPQTETKAG AGFKAGVKDY RLTYYTPDYV VRDTDILAAF RMTPQLGVPP EECGAAVAAE 70 80 90 100 110 120 SSTGTWTTVW TDGLTSLDRY KGRCYDIEPV PGEDNQYIAY VAYPIDLFEE GSVTNMFTSI 130 140 150 160 170 180 VGNVFGFKAL RALRLEDLRI PPAYVKTFVG PPHGIQVERD KLNKYGRGLL GCTIKPKLGL 190 200 210 220 230 240 SAKNYGRAVY ECLRGGLDFT KDDENVNSQP FMRWRDRFLF VAEAIYKAQA ETGEVKGHYL 250 260 270 280 290 300 NATAGTCEEM MKRAVCAKEL GVPIIMHDYL TGGFTANTSL AIYCRDNGLL LHIHRAMHAV 310 320 330 340 350 360 IDRQRNHGIH FRVLAKALRM SGGDHLHSGT VVGKLEGERE VTLGFVDLMR DDYVEKDRSR 370 380 390 400 410 420 GIYFTQDWCS MPGVMPVASG GIHVWHMPAL VEIFGDDACL QFGGGTLGHP WGNAPGAAAN 430 440 450 460 470 RVALEACTQA RNEGRDLARE GGDVIRSACK WSPELAAACE VWKEIKFEFD TIDKL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Sequence of the chloroplast DNA region of Chlamydomonas reinhardii containing the gene of the large subunit of ribulose bisphosphate carboxylase and parts of its flanking genes." Dron M., Rahire M., Rochaix J.-D. J. Mol. Biol. 162:775-793(1982) [PubMed: 6302265] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Nucleotide diversity in the chloroplast genome of Chlamydomonas reinhardtii." United States Department of Energy Joint Genome Institute Smith D.R. Submitted (OCT-2008) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: CC-503.
[3]	"Posttranslational modifications in the amino-terminal region of the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase from several plant species." Houtz R.L., Poneleit L., Jones S.B., Royer M., Stults J.T. Plant Physiol. 98:1170-1174(1992) [PubMed: 16668742] [Abstract] Cited for: PROTEIN SEQUENCE OF 3-14, ACETYLATION AT PRO-3.
[4]	"The Chlamydomonas reinhardtii plastid chromosome: islands of genes in a sea of repeats." Maul J.E., Lilly J.W., Cui L., dePamphilis C.W., Miller W., Harris E.H., Stern D.B. Plant Cell 14:2659-2679(2002) [PubMed: 12417694] [Abstract] Cited for: IDENTIFICATION, COMPLETE PLASTID GENOME.
[5]	"First crystal structure of Rubisco from a green alga, Chlamydomonas reinhardtii." Taylor T.C., Backlund A., Bjorhall K., Spreitzer R.J., Andersson I. J. Biol. Chem. 276:48159-48164(2001) [PubMed: 11641402] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS) IN COMPLEX WITH THE TRANSITION-STATE ANALOG 2-CABP. Strain: 2137.
[6]	"Crystal structure of activated ribulose-1,5-bisphosphate carboxylase/oxygenase from green alga Chlamydomonas reinhardtii complexed with 2-carboxyarabinitol-1,5-bisphosphate." Mizohata E., Matsumura H., Okano Y., Kumei M., Takuma H., Onodera J., Kato K., Shibata N., Inoue T., Yokota A., Kai Y. J. Mol. Biol. 316:679-691(2002) [PubMed: 11866526] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH THE TRANSITION-STATE ANALOG 2-CABP. Strain: 137c / CC-125.

Cross-references

Sequence databases

EMBLGenBankDDBJ

J01399 Genomic DNA. Translation: AAA84449.1.
FJ423446 Genomic DNA. Translation: ACJ50136.1.
BK000554 Genomic DNA. Translation: DAA00950.1.

PIR

RKKML. A01097.

RefSeq

NP_958405.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1GK8	X-ray	1.40	A/C/E/G	1-475	[»]
1IR2	X-ray	1.84	A/B/C/D/E/F/G/H/S/T/U/V/W/X/Y/Z	1-475	[»]
1UW9	X-ray	2.05	A/B/E/H/K/O/R/V	1-475	[»]
1UWA	X-ray	2.30	A/B/E/H/K/O/R/V	1-475	[»]
1UZD	X-ray	2.40	A/B/E/H/K/O/R/V	1-475	[»]
1UZH	X-ray	2.20	A/B/E/H/K/O/R/V	1-475	[»]
2V63	X-ray	1.80	A/B/C/D/E/F/G/H	1-475	[»]
2V67	X-ray	2.00	A/B/C/D/E/F/G/H	1-475	[»]
2V68	X-ray	2.30	A/B/C/D/E/F/G/H	1-475	[»]
2V69	X-ray	2.80	A/B/C/D/E/F/G/H	1-475	[»]
2V6A	X-ray	1.50	A/B/C/D/E/F/G/H	1-475	[»]
2VDH	X-ray	2.30	A/B/C/D/E/F/G/H	1-475	[»]
2VDI	X-ray	2.65	A/B/C/D/E/F/G/H	1-475	[»]

ModBase

Search...

Proteomic databases

PRIDE

P00877.

Genome annotation databases

GeneID

2717040.

KEGG

cre:ChreCp049.

Enzyme and pathway databases

BRENDA

4.1.1.39. 144.

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...

Entry information

Entry name

RBL_CHLRE

Accession

Primary (citable) accession number: P00877
Secondary accession number(s): B7U1I9

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	July 21, 1986
Last modified:	June 16, 2009
This is version 93 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)