Reviewed, UniProtKB/Swiss-Prot O85040 (RBL1_HALNC)

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
Ordered Locus Names:	Hneap_0922

Organism

Halothiobacillus neapolitanus (strain ATCC 23641 / c2) (Thiobacillus neapolitanus)

Taxonomic identifier

555778 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Chromatiales › Halothiobacillaceae › Halothiobacillus

Protein attributes

Sequence length	473 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. Both reactions occur simultaneously and in competition at the same active site By similarity. 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 By similarity. HAMAP MF_01338
Subunit structure	Heterohexadecamer of 8 large chains and 8 small chains By similarity. HAMAP MF_01338
Induction	Produced when grown in air or in air supplemented with 5% CO2. 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" By similarity. HAMAP MF_01338
Sequence similarities	Belongs to the RuBisCO large chain family. Type I subfamily.

Ontologies

Keywords
Biological process	Calvin cycle Carbon dioxide fixation
Ligand	Magnesium Metal-binding
Molecular function	Lyase Monooxygenase Oxidoreductase
Technical term	3D-structure
Gene Ontology (GO)
Biological process	oxidation reduction 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 – 473

473

Ribulose bisphosphate carboxylase large chain HAMAP MF_01338

PRO_0000062660

Sites

Active site

168

1

Proton acceptor By similarity

Active site

287

1

Proton acceptor By similarity

Metal binding

194

1

Magnesium; via carbamate group By similarity

Metal binding

196

1

Magnesium By similarity

Metal binding

197

1

Magnesium By similarity

Binding site

116

1

Substrate; in homodimeric partner By similarity

Binding site

166

1

Substrate By similarity

Binding site

170

1

Substrate By similarity

Binding site

288

1

Substrate By similarity

Binding site

320

1

Substrate By similarity

Binding site

372

1

Substrate By similarity

Site

327

1

Transition state stabilizer By similarity

Amino acid modifications

Modified residue

194

1

N6-carboxylysine By similarity

Secondary structure

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473

Helix Strand Turn

Details...

Beta strand

28 – 37

10

Helix

43 – 53

11

Turn

54 – 56

3

Helix

63 – 67

5

Turn

70 – 72

3

Beta strand

76 – 83

8

Beta strand

86 – 96

11

Helix

98 – 100

3

Helix

106 – 114

9

Helix

117 – 119

3

Beta strand

123 – 132

10

Helix

135 – 138

4

Helix

148 – 155

8

Beta strand

162 – 166

5

Beta strand

170 – 172

3

Helix

175 – 187

13

Beta strand

191 – 194

4

Beta strand

200 – 202

3

Helix

207 – 225

19

Beta strand

230 – 234

5

Helix

240 – 253

14

Beta strand

257 – 261

5

Turn

262 – 265

4

Helix

267 – 280

14

Beta strand

283 – 287

5

Helix

291 – 295

5

Beta strand

300 – 302

3

Helix

304 – 314

11

Beta strand

317 – 320

4

Helix

329 – 331

3

Helix

333 – 343

11

Beta strand

345 – 347

3

Helix

351 – 353

3

Beta strand

368 – 374

7

Helix

377 – 379

3

Helix

380 – 387

8

Beta strand

389 – 394

6

Helix

397 – 400

4

Helix

406 – 425

20

Turn

430 – 433

4

Helix

434 – 442

9

Helix

446 – 455

10

Sequences

	Sequence		Length	Mass (Da)
	O85040-1 [UniParc]. Last modified November 1, 1998. Version 1. Checksum: B84D2EDE46CAF7D8	FASTA	473	52,636
	10 20 30 40 50 60 MAVKKYSAGV KEYRQTYWMP EYTPLDSDIL ACFKITPQPG VDREEAAAAV AAESSTGTWT 70 80 90 100 110 120 TVWTDLLTDM DYYKGRAYRI EDVPGDDAAF YAFIAYPIDL FEEGSVVNVF TSLVGNVFGF 130 140 150 160 170 180 KAVRGLRLED VRFPLAYVKT CGGPPHGIQV ERDKMNKYGR PLLGCTIKPK LGLSAKNYGR 190 200 210 220 230 240 AVYECLRGGL DFTKDDENIN SQPFMRWRDR FLFVQDATET AEAQTGERKG HYLNVTAPTP 250 260 270 280 290 300 EEMYKRAEFA KEIGAPIIMH DYITGGFTAN TGLAKWCQDN GVLLHIHRAM HAVIDRNPNH 310 320 330 340 350 360 GIHFRVLTKI LRLSGGDHLH TGTVVGKLEG DRASTLGWID LLRESFIPED RSRGIFFDQD 370 380 390 400 410 420 WGSMPGVFAV ASGGIHVWHM PALVNIFGDD SVLQFGGGTL GHPWGNAAGA AANRVALEAC 430 440 450 460 470 VEARNQGRDI EKEGKEILTA AAQHSPELKI AMETWKEIKF EFDTVDKLDT QNR

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Insertion mutation of the form I cbbL gene encoding ribulose bisphosphate carboxylase/oxygenase (RuBisCO) in Thiobacillus neapolitanus results in expression of form II RuBisCO, loss of carboxysomes, and an increased CO2 requirement for growth." Baker S.H., Jin S., Aldrich H.C., Howard G.T., Shively J.M. J. Bacteriol. 180:4133-4139(1998) [PubMed: 9696760] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], EXPRESSION.
[2]	"Complete sequence of Halothiobacillus neapolitanus c2." Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Tice H., Bruce D., Goodwin L., Pitluck S., Davenport K., Brettin T., Detter J.C., Han C., Tapia R., Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N. , Kerfeld C., Cannon G., Heinhort S. Submitted (OCT-2009) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]	"The structure of Halothiobacillus neapolitanus Rubisco." Kerfeld C.A., Sawaya M.R., Pashkov I., Cannon G., Williams E., Tran K., Yeates T.O. Submitted (APR-2005) to the PDB data bank Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AF038430 Genomic DNA. Translation: AAC32549.1.
CP001801 Genomic DNA. Translation: ACX95765.1.

RefSeq

YP_003262812.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1SVD	X-ray	1.80	A	1-473	[»]

ModBase

Search...

Genome annotation databases

GeneID

8534063.

Enzyme and pathway databases

BRENDA

4.1.1.39. 1673.

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

RBL1_HALNC

Accession

Primary (citable) accession number: O85040
Secondary accession number(s): D0KZ92

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 22, 2005
Last sequence update:	November 1, 1998
Last modified:	January 19, 2010
This is version 54 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)