Reviewed, UniProtKB/Swiss-Prot P00876 (RBL_TOBAC)

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
Synonyms:	rbcA

Encoded on

Plastid; Chloroplast

Organism

Nicotiana tabacum (Common tobacco)

Taxonomic identifier

4097 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › asterids › lamiids › Solanales › Solanaceae › Nicotianoideae › Nicotianeae › Nicotiana

Protein attributes

Sequence length	477 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 bonds reported in 3RUB and 4RUB may be the result of oxidation during crystallization. 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 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

HAMAP MF_01338

PRO_0000031427

Chain

3 – 477

475

Ribulose bisphosphate carboxylase large chain HAMAP MF_01338

PRO_0000031428

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 HAMAP MF_01338

Modified residue

14

1

N6,N6,N6-trimethyllysine Ref.4

Modified residue

201

1

N6-carboxylysine HAMAP MF_01338

Disulfide bond

247

Interchain; in linked form HAMAP MF_01338

Natural variations

Natural variant

394

1

F → V

Natural variant

405

1

G → M

Experimental info

Sequence conflict

284

1

C → G AA sequence Ref.3

Sequence conflict

377

1

V → E in AAD15025. Ref.1

Secondary structure

1

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477

Helix Strand Turn

Details...

Helix

21 – 24

4

Beta strand

36 – 44

9

Helix

50 – 60

11

Turn

61 – 63

3

Helix

70 – 73

4

Helix

77 – 80

4

Beta strand

83 – 89

7

Beta strand

91 – 95

5

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

Beta strand

151 – 153

3

Helix

155 – 162

8

Beta strand

169 – 173

5

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

Helix

338 – 350

13

Beta strand

352 – 354

3

Helix

358 – 360

3

Beta strand

375 – 381

7

Helix

384 – 386

3

Helix

387 – 394

8

Beta strand

399 – 403

5

Turn

404 – 408

5

Helix

413 – 432

20

Helix

437 – 450

14

Helix

453 – 458

6

Helix

460 – 466

7

Sequences

	Sequence		Length	Mass (Da)
	P00876-1 [UniParc]. Last modified June 1, 2001. Version 2. Checksum: 232D54E42263198F	FASTA	477	52,898
	10 20 30 40 50 60 MSPQTETKAS VGFKAGVKEY KLTYYTPEYQ TKDTDILAAF RVTPQPGVPP EEAGAAVAAE 70 80 90 100 110 120 SSTGTWTTVW TDGLTSLDRY KGRCYRIERV VGEKDQYIAY VAYPLDLFEE GSVTNMFTSI 130 140 150 160 170 180 VGNVFGFKAL RALRLEDLRI PPAYVKTFQG PPHGIQVERD KLNKYGRPLL GCTIKPKLGL 190 200 210 220 230 240 SAKNYGRAVY ECLRGGLDFT KDDENVNSQP FMRWRDRFLF CAEALYKAQA ETGEIKGHYL 250 260 270 280 290 300 NATAGTCEEM IKRAVFAREL GVPIVMHDYL TGGFTANTSL AHYCRDNGLL LHIHRAMHAV 310 320 330 340 350 360 IDRQKNHGIH FRVLAKALRM SGGDHIHSGT VVGKLEGERD ITLGFVDLLR DDFVEQDRSR 370 380 390 400 410 420 GIYFTQDWVS LPGVLPVASG GIHVWHMPAL TEIFGDDSVL QFGGGTLGHP WGNAPGAVAN 430 440 450 460 470 RVALEACVKA RNEGRDLAQE GNEIIREACK WSPELAAACE VWKEIVFNFA AVDVLDK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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: 7160620] [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: 16453699] [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: 2928307] [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: 3681999] [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: 1512238] [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: 10801357] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.45 ANGSTROMS) OF 3-477.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

J01450 Genomic DNA. Translation: AAD15025.1.
Z00044 Genomic DNA. Translation: CAA77361.1.

PIR

RKNTL. A01095.

RefSeq

NP_054507.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ModBase

Search...

Genome annotation databases

GeneID

800513.

Enzyme and pathway databases

BRENDA

4.1.1.39. 298.

Family and domain databases

HAMAP

MF_01338. RuBisCO_L_type1.
[Tree]

InterPro

IPR020878. RuBisCo_large_chain_AS.
IPR020888. RuBisCO_lsu.
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_TOBAC

Accession

Primary (citable) accession number: P00876
Secondary accession number(s): Q32716

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	June 1, 2001
Last modified:	January 19, 2010
This is version 95 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

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