O93627 (RBL_PYRKO) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Ribulose bisphosphate carboxylase
Short name=RuBisCO
EC=4.1.1.39

Gene names

Name:	rbcL
Ordered Locus Names:	TK2290

Organism

Pyrococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Thermococcus kodakaraensis (strain KOD1)) [Reference proteome] [HAMAP]

Taxonomic identifier

69014 [NCBI]

Taxonomic lineage

cellular organisms › Archaea › Euryarchaeota › Thermococci › Thermococcales › Thermococcaceae › Thermococcus › Thermococcus kodakarensis

Protein attributes

Sequence length	444 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)

Catalytic activity	2 3-phospho-D-glycerate + 2 H+ = D-ribulose 1,5-bisphosphate + CO2 + H2O. HAMAP-Rule MF_01133 3-phospho-D-glycerate + 2-phosphoglycolate = D-ribulose 1,5-bisphosphate + O2. HAMAP-Rule MF_01133
Cofactor	Binds 1 magnesium ion per subunit. Ref.5
Subunit structure	Homodecamer, consisting of fiver dimer units which form a ring-like pentagonal structure. This arrangement is essential for its high thermostability. Composed solely of large subunits. Ref.4 Ref.5
Miscellaneous	The basic functional RuBisCO is composed of a large chain homodimer in a "head-to-tail" conformation By similarity. HAMAP-Rule MF_01133
Sequence similarities	Belongs to the RuBisCO large chain family. Type III subfamily.
Biophysicochemical properties	Temperature dependence: Optimum temperature is 90 degrees Celsius. Highly thermostable. HAMAP-Rule MF_01133

Ontologies

Keywords
Biological process	Carbon dioxide fixation
Ligand	Magnesium Metal-binding
Molecular function	Lyase Monooxygenase Oxidoreductase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	carbon fixation Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	magnesium ion binding Inferred from electronic annotation. Source: HAMAP 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

Initiator methionine

1

1

Removed Ref.1 Ref.3

Chain

2 – 444

443

Ribulose bisphosphate carboxylase HAMAP-Rule MF_01133

PRO_0000062678

Sites

Active site

163

1

Proton acceptor

Active site

281

1

Proton acceptor

Metal binding

189

1

Magnesium; via carbamate group

Metal binding

191

1

Magnesium

Metal binding

192

1

Magnesium

Binding site

111

1

Substrate; in homodimeric partner

Binding site

165

1

Substrate

Binding site

282

1

Substrate

Binding site

314

1

Substrate

Binding site

367

1

Substrate

Site

322

1

Transition state stabilizer

Amino acid modifications

Modified residue

189

1

N6-carboxylysine HAMAP-Rule MF_01133

Experimental info

Mutagenesis

63

1

E → S: Decrease in activity and in thermostability. Large decrease in activity; forms dimers; when associated with S-66 and S-69. Ref.4

Mutagenesis

66

1

R → S: Large decrease in activity and in thermostability. Large decrease in activity; forms dimers; when associated with S-63 and S-69. Ref.4

Mutagenesis

69

1

D → S: Slight decrease in activity; no change in thermostability. Large decrease in activity; forms dimers; when associated with S-63 and S-66. Ref.4

Secondary structure

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444

Helix Strand Turn

Details...

Helix

10 – 12

3

Turn

21 – 23

3

Beta strand

24 – 33

10

Helix

39 – 49

11

Turn

50 – 52

3

Helix

64 – 70

7

Beta strand

73 – 79

7

Beta strand

81 – 83

3

Beta strand

85 – 92

8

Helix

93 – 95

3

Helix

101 – 108

8

Helix

111 – 114

4

Beta strand

118 – 127

10

Helix

130 – 133

4

Helix

142 – 150

9

Beta strand

157 – 160

4

Beta strand

163 – 166

4

Helix

170 – 182

13

Beta strand

187 – 189

3

Helix

202 – 220

19

Beta strand

225 – 229

5

Helix

234 – 247

14

Beta strand

251 – 255

5

Helix

256 – 259

4

Helix

261 – 274

14

Beta strand

277 – 281

5

Turn

283 – 285

3

Helix

286 – 289

4

Beta strand

294 – 296

3

Helix

298 – 308

11

Beta strand

311 – 314

4

Beta strand

320 – 323

4

Helix

327 – 338

12

Beta strand

340 – 342

3

Beta strand

363 – 369

7

Helix

372 – 374

3

Helix

376 – 382

7

Beta strand

384 – 389

6

Helix

392 – 395

4

Helix

401 – 415

15

Helix

421 – 425

5

Helix

429 – 438

10

Sequences

	Sequence		Length	Mass (Da)
	O93627 [UniParc]. Last modified January 23, 2007. Version 5. Checksum: 6E3AFF37367DD7FE	FASTA	444	49,713
	10 20 30 40 50 60 MVEKFDTIYD YYVDKGYEPS KKRDIIAVFR VTPAEGYTIE QAAGAVAAES STGTWTTLYP 70 80 90 100 110 120 WYEQERWADL SAKAYDFHDM GDGSWIVRIA YPFHAFEEAN LPGLLASIAG NIFGMKRVKG 130 140 150 160 170 180 LRLEDLYFPE KLIREFDGPA FGIEGVRKML EIKDRPIYGV VPKPKVGYSP EEFEKLAYDL 190 200 210 220 230 240 LSNGADYMKD DENLTSPWYN RFEERAEIMA KIIDKVENET GEKKTWFANI TADLLEMEQR 250 260 270 280 290 300 LEVLADLGLK HAMVDVVITG WGALRYIRDL AADYGLAIHG HRAMHAAFTR NPYHGISMFV 310 320 330 340 350 360 LAKLYRLIGI DQLHVGTAGA GKLEGGKWDV IQNARILRES HYKPDENDVF HLEQKFYSIK 370 380 390 400 410 420 AAFPTSSGGL HPGNIQPVIE ALGTDIVLQL GGGTLGHPDG PAAGARAVRQ AIDAIMQGIP 430 440 LDEYAKTHKE LARALEKWGH VTPV

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Presence of a structurally novel type ribulose-bisphosphate carboxylase/oxygenase in the hyperthermophilic archaeon, Pyrococcus kodakaraensis KOD1." Ezaki S., Maeda N., Kishimoto T., Atomi H., Imanaka T. J. Biol. Chem. 274:5078-5082(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-12, CHARACTERIZATION. Strain: ATCC BAA-918 / JCM 12380 / KOD1.
[2]	"Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes." Fukui T., Atomi H., Kanai T., Matsumi R., Fujiwara S., Imanaka T. Genome Res. 15:352-363(2005) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC BAA-918 / JCM 12380 / KOD1.
[3]	"Ribulose bisphosphate carboxylase/oxygenase from the hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1 is composed solely of large subunits and forms a pentagonal structure." Maeda N., Kitano K., Fukui T., Ezaki S., Atomi H., Miki K., Imanaka T. J. Mol. Biol. 293:57-66(1999) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-12, CHARACTERIZATION, CRYSTALLIZATION. Strain: ATCC BAA-918 / JCM 12380 / KOD1.
[4]	"The unique pentagonal structure of an archaeal Rubisco is essential for its high thermostability." Maeda N., Kanai T., Atomi H., Imanaka T. J. Biol. Chem. 277:31656-31662(2002) [PubMed] [Europe PMC] [Abstract] Cited for: SUBUNIT, MUTAGENESIS OF GLU-63; ARG-66 AND ASP-69. Strain: ATCC BAA-918 / JCM 12380 / KOD1.
[5]	"Crystal structure of a novel-type archaeal rubisco with pentagonal symmetry." Kitano K., Maeda N., Fukui T., Atomi H., Imanaka T., Miki K. Structure 9:473-481(2001) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS), COFACTOR, SUBUNIT. Strain: ATCC BAA-918 / JCM 12380 / KOD1.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AB018555 Genomic DNA. Translation: BAA33863.1.
AP006878 Genomic DNA. Translation: BAD86479.1.

RefSeq

YP_184703.1. NC_006624.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1GEH	X-ray	2.80	A/B/C/D/E	1-444	[»]
3A12	X-ray	2.30	A/B/C/D/E/F/G/H/I/J	1-444	[»]
3A13	X-ray	2.34	A/B/C/D/E/F/G/H/I/J	1-444	[»]
3KDN	X-ray	2.09	A/B/C/D/E/F/G/H/I/J	1-444	[»]
3KDO	X-ray	2.36	A/B/C/D/E/F/G/H/I/J	1-444	[»]

ProteinModelPortal

O93627.

SMR

O93627. Positions 12-443.

ModBase

Search...

Protein-protein interaction databases

MINT

MINT-8377356.

STRING

69014.TK2290.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

BAD86479; BAD86479; TK2290.

GeneID

3234791.

KEGG

tko:TK2290.

Phylogenomic databases

eggNOG

COG1850.

HOGENOM

HOG000230831.

KO

K01601.

OMA

HRAMHAA.

ProtClustDB

PRK04208.

Enzyme and pathway databases

BioCyc

MetaCyc:MONOMER-13272.
TKOD69014:GH72-2342-MONOMER.

Family and domain databases

Gene3D

3.20.20.110. 1 hit.
3.30.70.150. 1 hit.

HAMAP

MF_01133. RuBisCO_L_type3.

InterPro

IPR017712. RuBisCO_III.
IPR000685. RuBisCO_lsu_C.
IPR017443. RuBisCO_lsu_fd_N.
IPR017444. RuBisCO_lsu_N.
[Graphical view]

Pfam

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

SUPFAM

SSF51649. RuBisCO_large. 1 hit.
SSF54966. RuBisCO_large. 1 hit.

TIGRFAMs

TIGR03326. rubisco_III. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

O93627.

Entry information

Entry name

RBL_PYRKO

Accession

Primary (citable) accession number: O93627

Entry history

Integrated into UniProtKB/Swiss-Prot:	September 26, 2003
Last sequence update:	January 23, 2007
Last modified:	May 29, 2013
This is version 102 of the entry and version 5 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program