Reviewed, UniProtKB/Swiss-Prot P00880 (RBL_SYNP6)

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:	cbbL
Synonyms:	rbcA, rbcL
Ordered Locus Names:	syc0130_c

Organism

Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1) (Anacystis nidulans) [Complete proteome] [HAMAP]

Taxonomic identifier

269084 [NCBI]

Taxonomic lineage

Bacteria › Cyanobacteria › Chroococcales › Synechococcus

Protein attributes

Sequence length	472 AA.
Sequence status	Complete.
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
Post-translational modification	The disulfide bond which can form in the large chain dimeric partners within the hexadecamer appears to be associated with oxidative stress and protein turnover By similarity. Note this disulfide bond has not been seen in these crystal structures. 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.
Biophysicochemical properties	Kinetic parameters: The CO2/O2 specificity factor (tau) is 39. KM=39 µM for ribulose 1,5-bisphosphate Ref.6 KM=173 µM for CO2 Vmax=2.5 µmol/min/mg enzyme with CO2 as substrate

Ontologies

Keywords
Biological process	Calvin cycle Carbon dioxide fixation Photorespiration Photosynthesis
Ligand	Magnesium Metal-binding
Molecular function	Lyase Monooxygenase Oxidoreductase
PTM	Disulfide bond
Technical term	3D-structure Complete proteome 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	plastid Inferred from electronic annotation. Source: InterPro
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

Chain

1 – 472

472

Ribulose bisphosphate carboxylase large chain HAMAP MF_01338

PRO_0000062651

Sites

Active site

172

1

Proton acceptor HAMAP MF_01338

Active site

291

1

Proton acceptor HAMAP MF_01338

Metal binding

198

1

Magnesium; via carbamate group HAMAP MF_01338

Metal binding

200

1

Magnesium HAMAP MF_01338

Metal binding

201

1

Magnesium HAMAP MF_01338

Binding site

120

1

Substrate; in homodimeric partner HAMAP MF_01338

Binding site

170

1

Substrate HAMAP MF_01338

Binding site

174

1

Substrate HAMAP MF_01338

Binding site

292

1

Substrate HAMAP MF_01338

Binding site

324

1

Substrate HAMAP MF_01338

Binding site

376

1

Substrate HAMAP MF_01338

Site

331

1

Transition state stabilizer HAMAP MF_01338

Amino acid modifications

Modified residue

198

1

N6-carboxylysine HAMAP MF_01338

Experimental info

Sequence conflict

38 – 39

2

RF → PV Ref.1

Sequence conflict

353

1

A → R Ref.1

Secondary structure

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472

Helix Strand Turn

Details...

Helix

18 – 21

4

Beta strand

32 – 41

10

Helix

47 – 57

11

Turn

58 – 60

3

Beta strand

63 – 65

3

Helix

67 – 71

5

Helix

74 – 77

4

Beta strand

80 – 86

7

Beta strand

94 – 100

7

Helix

102 – 104

3

Helix

110 – 118

9

Helix

121 – 123

3

Beta strand

127 – 136

10

Helix

139 – 142

4

Helix

152 – 159

8

Beta strand

166 – 168

3

Beta strand

172 – 175

4

Helix

179 – 191

13

Beta strand

195 – 198

4

Beta strand

204 – 206

3

Helix

211 – 229

19

Beta strand

234 – 238

5

Helix

244 – 256

13

Beta strand

260 – 265

6

Helix

266 – 269

4

Helix

271 – 284

14

Beta strand

287 – 291

5

Helix

295 – 299

5

Beta strand

302 – 306

5

Helix

308 – 318

11

Beta strand

321 – 324

4

Beta strand

328 – 332

5

Helix

336 – 347

12

Beta strand

349 – 351

3

Helix

355 – 357

3

Beta strand

372 – 378

7

Helix

381 – 383

3

Helix

384 – 391

8

Beta strand

396 – 398

3

Helix

401 – 404

4

Helix

410 – 430

21

Helix

434 – 448

15

Helix

450 – 459

10

Sequences

	Sequence		Length	Mass (Da)
	P00880-1 [UniParc]. Last modified February 15, 2005. Version 2. Checksum: CDD8519AA9D493C9	FASTA	472	52,448
	10 20 30 40 50 60 MPKTQSAAGY KAGVKDYKLT YYTPDYTPKD TDLLAAFRFS PQPGVPADEA GAAIAAESST 70 80 90 100 110 120 GTWTTVWTDL LTDMDRYKGK CYHIEPVQGE ENSYFAFIAY PLDLFEEGSV TNILTSIVGN 130 140 150 160 170 180 VFGFKAIRSL RLEDIRFPVA LVKTFQGPPH GIQVERDLLN KYGRPMLGCT IKPKLGLSAK 190 200 210 220 230 240 NYGRAVYECL RGGLDFTKDD ENINSQPFQR WRDRFLFVAD AIHKSQAETG EIKGHYLNVT 250 260 270 280 290 300 APTCEEMMKR AEFAKELGMP IIMHDFLTAG FTANTTLAKW CRDNGVLLHI HRAMHAVIDR 310 320 330 340 350 360 QRNHGIHFRV LAKCLRLSGG DHLHSGTVVG KLEGDKASTL GFVDLMREDH IEADRSRGVF 370 380 390 400 410 420 FTQDWASMPG VLPVASGGIH VWHMPALVEI FGDDSVLQFG GGTLGHPWGN APGATANRVA 430 440 450 460 470 LEACVQARNE GRDLYREGGD ILREAGKWSP ELAAALDLWK EIKFEFETMD KL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The nucleotide sequence for the large subunit of ribulose 1,5-bisphosphate carboxylase from a unicellular cyanobacterium, Synechococcus PCC6301." Reichelt B.Y., Delaney S.F. DNA 2:121-129(1983) [PubMed: 6307620] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Molecular cloning and sequence analysis of the cyanobacterial gene for the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase." Shinozaki K., Yamada C., Takahata N., Sugiura M. Proc. Natl. Acad. Sci. U.S.A. 80:4050-4054(1983) [PubMed: 16593333] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"Genes for the large and small subunits of ribulose-1,5-bisphosphate carboxylase/oxygenase constitute a single operon in a cyanobacterium Anacystis nidulans 6301." Shinozaki K., Sugiura M. Mol. Gen. Genet. 200:27-32(1985) Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[4]	"Complete nucleotide sequence of the freshwater unicellular cyanobacterium Synechococcus elongatus PCC 6301 chromosome: gene content and organization." Sugita C., Ogata K., Shikata M., Jikuya H., Takano J., Furumichi M., Kanehisa M., Omata T., Sugiura M., Sugita M. Photosyn. Res. 93:55-67(2007) [PubMed: 17211581] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]	"High substrate specificity factor ribulose bisphosphate carboxylase/oxygenase from eukaryotic marine algae and properties of recombinant cyanobacterial RubiSCO containing 'algal' residue modifications." Read B.A., Tabita F.R. Arch. Biochem. Biophys. 312:210-218(1994) [PubMed: 8031129] [Abstract] Cited for: PROTEIN SEQUENCE OF 333-342.
[6]	"Closely related form I ribulose bisphosphate carboxylase/oxygenase molecules that possess different CO2/O2 substrate specificities." Horken K.M., Tabita F.R. Arch. Biochem. Biophys. 361:183-194(1999) [PubMed: 9882445] [Abstract] Cited for: KINETIC CHARACTERIZATION.
[7]	"The X-ray structure of Synechococcus ribulose-bisphosphate carboxylase/oxygenase-activated quaternary complex at 2.2-A resolution." Newman J., Gutteridge S. J. Biol. Chem. 268:25876-25886(1993) [PubMed: 8245022] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
[8]	"Structure of an effector-induced inactivated state of ribulose 1,5-bisphosphate carboxylase/oxygenase: the binary complex between enzyme and xylulose 1,5-bisphosphate." Newman J., Gutteridge S. Structure 2:495-502(1994) [PubMed: 7922027] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

K00486 Genomic DNA. No translation available.
X03220 Genomic DNA. Translation: CAA26972.1.
AP008231 Genomic DNA. Translation: BAD78320.1.

PIR

RKYCL. A90941.

RefSeq

YP_170840.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1RBL	X-ray	2.20	A/B/C/D/E/F/G/H	6-472	[»]
1RSC	X-ray	2.30	A/B/C/D/E/F/G/H	1-472	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-6210N.

STRING

P00880.

Genome annotation databases

GeneID

3200134.

GenomeReviews

Gene locus syc0130_c in contig AP008231_GR.

KEGG

syc:syc0130_c.

Organism-specific databases

CMR

Search...

Phylogenomic databases

eggNOG

COG1850.

HOGENOM

HBG405441.

OMA

YTPDYTP.

Enzyme and pathway databases

BioCyc

SELO269084:SYC0130_C-MONOMER.

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_SYNP6

Accession

Primary (citable) accession number: P00880

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	February 15, 2005
Last modified:	January 19, 2010
This is version 90 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)