SMART: RuBisCO_small domain annotation

RuBisCO_small Ribulose bisphosphate carboxylase, small chain

SMART accession number:	SM00961
Description:	RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) is a bifunctional enzyme that catalyses both the carboxylation and oxygenation of ribulose-1,5-bisphosphate (RuBP), thus fixing carbon dioxide as the first step of the Calvin cycle. RuBisCO is the major protein in the stroma of chloroplasts, and in higher plants exists as a complex of 8 large and 8 small subunits. The function of the small subunit is unknown (PUBMED:3012537). While the large subunit is coded for by a single gene, the small subunit is coded for by several different genes, which are distributed in a tissue specific manner. They are transcriptionally regulated by light receptor phytochrome (PUBMED:3010233), which results in RuBisCO being more abundant during the day when it is required.
Interpro abstract (IPR000894):	RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) is a bifunctional enzyme that catalyses both the carboxylation and oxygenation of ribulose-1,5-bisphosphate (RuBP), thus fixing carbon dioxide as the first step of the Calvin cycle. RuBisCO is the major protein in the stroma of chloroplasts, and in higher plants exists as a complex of 8 large and 8 small subunits. The function of the small subunit is unknown [ (PUBMED:3012537) ]. While the large subunit is coded for by a single gene, the small subunit is coded for by several different genes, which are distributed in a tissue specific manner. They are transcriptionally regulated by light receptor phytochrome [ (PUBMED:3010233) ], which results in RuBisCO being more abundant during the day when it is required. The RuBisCo small subunit consists of a central four-stranded beta-sheet, with two helices packed against it [ (PUBMED:1512238) ].
Family alignment:	View or

There are 2883 RuBisCO_small domains in 2176 proteins in SMART's nrdb database.

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Evolution (species in which this domain is found)
Taxonomic distribution of proteins containing RuBisCO_small domain.
This tree includes only several representative species. The complete taxonomic breakdown of all proteins with RuBisCO_small domain is also avaliable.

Click on the protein counts, or double click on taxonomic names to display all proteins containing RuBisCO_small domain in the selected taxonomic class.
Cellular role (predicted cellular role)
Cellular role: metabolism
Literature (relevant references for this domain)
Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.
- Pichersky E, Bernatzky R, Tanksley SD, Cashmore AR
- Evidence for selection as a mechanism in the concerted evolution ofLycopersicon esculentum (tomato) genes encoding the small subunit ofribulose-1,5-bisphosphate carboxylase/oxygenase.
- Proc Natl Acad Sci U S A. 1986; 83: 3880-4
- Display abstract
- The nuclear gene sequences encoding RBCS, the small subunit ofribulose-1,5-bisphosphate carboxylase/oxygenase (EC 4.1.1.39) from severalplants show extensive interspecific divergence but little intraspecificdivergence, suggesting that these genes are evolving in concert within agenome. In this study, the nucleotide sequences of two tomato(Lycopersicon esculentum) RBCS genes and a cDNA clone containing theentire coding region of a third tomato RBCS gene were determined. Thethree genes, designated Rbcs-1, Rbcs-2A, and Rbcs-3A, each belong to adifferent one of the three RBCS loci in the tomato genome. The nucleotidesequence of Rbcs-1 differs from that of Rbcs-2A and Rbcs-3A by 13.9% and13.1%, respectively. Rbcs-2A and Rbcs-3A differ from each other by 10.7%.A recently published RBCS gene sequence from tobacco (Nicotiana tabacum)[Mazur, B. J. & Chui, C.-F. (1985) Nucleic Acids Res. 13, 2373-2386]differs by 10.6% and 11.3% from Rbcs-2A and Rbcs-3A, respectively, and by15.0% from Rbcs-1. Thus the tobacco gene seems to be phylogenetically asclosely related to the tomato genes Rbcs-2A and Rbcs-3A as the latter twoare to each other, and more closely related to them than Rbcs-1 is.However, the mature part of the polypeptide encoded by the tobacco RBCSgene differs by five and six amino acids from the corresponding region inthe polypeptides encoded by Rbcs-2A and Rbcs-3A, respectively, while thesetwo tomato RBCS polypeptides differ from each other in the mature part bya single amino acid. Rbcs-1, whose nucleotide sequence shows higherdivergence from both the tobacco RBCS gene and Rbcs-2A and Rbcs-3A,encodes a polypeptide whose mature part differs by eight amino acids fromthe corresponding region in the tobacco polypeptide but only by three andfour amino acids from the corresponding regions of Rbcs-2A- andRbcs-3A-encoded polypeptides, respectively. Thus, it appears that in thetomato selection has maintained near uniformity of the coding informationin the portion of the RBCS genes encoding the mature polypeptides.
- Tumer NE, Clark WG, Tabor GJ, Hironaka CM, Fraley RT, Shah DM
- The genes encoding the small subunit of ribulose-1,5-bisphosphatecarboxylase are expressed differentially in petunia leaves.
- Nucleic Acids Res. 1986; 14: 3325-42
- Display abstract
- We have isolated five members of the multigene family encoding the smallsubunit (rbcS) of ribulose-1,5-bisphosphate carboxylase in petunia andexamined their expression in petunia leaves. Of the five rbcS genes, two(ssu11A and ssu8) are expressed at high levels in petunia leaves. Northernanalysis using gene specific oligonucleotide probes revealed that ssu11Aaccounts for 40% of the total rbcS transcripts in petunia leaves whilessu8 accounts for 4 to 5% of the total rbcS transcripts. Structuralcomparisons of ssu8 and ssu11A revealed that the coding sequence of ssu8is interrupted by three introns, while the coding sequence of ssu11A isinterrupted by two introns. The positions of the first two introns areidentical, the third intron in ssu8 is located in a highly conservedregion of the protein. The 5' and 3' flanking sequences of ssu11A arehighly homologous to the 5' and 3' flanking sequences of ssu8. S1 nucleasemapping was used to locate the start of transcription of ssu8 and ssu11Aand showed that ssu8 mRNA leader differs in sequence from the ssu11A mRNAleader.
Structure (3D structures containing this domain)

3D Structures of RuBisCO_small domains in PDB

PDB code	Main view	Title
1aa1		ACTIVATED SPINACH RUBISCO IN COMPLEX WITH THE PRODUCT 3-PHOSPHOGLYCERATE
1aus		ACTIVATED UNLIGANDED SPINACH RUBISCO
1bwv		Activated Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase (RUBISCO) Complexed with the Reaction Intermediate Analogue 2-Carboxyarabinitol 1,5-Bisphosphate
1bxn		THE CRYSTAL STRUCTURE OF RUBISCO FROM ALCALIGENES EUTROPHUS TO 2.7 ANGSTROMS.
1ej7		CRYSTAL STRUCTURE OF UNACTIVATED TOBACCO RUBISCO WITH BOUND PHOSPHATE IONS
1gk8		Rubisco from Chlamydomonas reinhardtii
1ir1		Crystal Structure of Spinach Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with CO2, Mg2+ and 2-Carboxyarabinitol-1,5-Bisphosphate
1ir2		Crystal Structure of Activated Ribulose-1,5-bisphosphate Carboxylase/oxygenase (Rubisco) from Green alga, Chlamydomonas reinhardtii Complexed with 2-Carboxyarabinitol-1,5-bisphosphate (2-CABP)
1iwa		RUBISCO FROM GALDIERIA PARTITA
1rbl		STRUCTURE DETERMINATION AND REFINEMENT OF RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE FROM SYNECHOCOCCUS PCC6301
1rbo		SPINACH RUBISCO IN COMPLEX WITH THE INHIBITOR 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
1rco		SPINACH RUBISCO IN COMPLEX WITH THE INHIBITOR D-XYLULOSE-2,2-DIOL-1,5-BISPHOSPHATE
1rcx		NON-ACTIVATED SPINACH RUBISCO IN COMPLEX WITH ITS SUBSTRATE RIBULOSE-1,5-BISPHOSPHATE
1rlc		CRYSTAL STRUCTURE OF THE UNACTIVATED RIBULOSE 1, 5-BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE COMPLEXED WITH A TRANSITION STATE ANALOG, 2-CARBOXY-D-ARABINITOL 1,5-BISPHOSPHATE
1rld		SOLID-STATE PHASE TRANSITION IN THE CRYSTAL STRUCTURE OF RIBULOSE 1,5-BIPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE
1rsc		STRUCTURE OF AN EFFECTOR INDUCED INACTIVATED STATE OF RIBULOSE BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE: THE BINARY COMPLEX BETWEEN ENZYME AND XYLULOSE BISPHOSPHATE
1rxo		ACTIVATED SPINACH RUBISCO IN COMPLEX WITH ITS SUBSTRATE RIBULOSE-1,5-BISPHOSPHATE AND CALCIUM
1svd		The structure of Halothiobacillus neapolitanus RuBisCo
1upm		ACTIVATED SPINACH RUBISCO COMPLEXED WITH 2-CARBOXYARABINITOL 2 BISPHOSPHAT AND CA2+.
1upp		SPINACH RUBISCO IN COMPLEX WITH 2-CARBOXYARABINITOL 2 BISPHOSPHATE and Calcium.
1uw9		L290F-A222T chlamydomonas Rubisco mutant
1uwa		L290F mutant rubisco from chlamydomonas
1uzd		Chlamydomonas,Spinach Chimeric Rubisco
1uzh		A CHIMERIC CHLAMYDOMONAS, SPINACH RUBISCO ENZYME
1wdd		Crystal Structure of Activated Rice Rubisco Complexed with 2-Carboxyarabinitol-1,5-bisphosphate
2v63		Crystal structure of Rubisco from Chlamydomonas reinhardtii with a large-subunit V331A mutation
2v67		Crystal structure of Chlamydomonas reinhardtii Rubisco with a large- subunit supressor mutation T342I
2v68		Crystal structure of Chlamydomonas reinhardtii Rubisco with large- subunit mutations V331A, T342I
2v69		Crystal structure of Chlamydomonas reinhardtii Rubisco with a large- subunit mutation D473E
2v6a		Crystal structure of Chlamydomonas reinhardtii Rubisco with large- subunit mutations V331A, G344S
2vdh		Crystal structure of Chlamydomonas reinhardtii Rubisco with a large- subunit C172S mutation
2vdi		Crystal structure of Chlamydomonas reinhardtii Rubisco with a large- subunit C192S mutation
2ybv		STRUCTURE OF RUBISCO FROM THERMOSYNECHOCOCCUS ELONGATUS
3axk		Structure of rice Rubisco in complex with NADP(H)
3axm		Structure of rice Rubisco in complex with 6PG
3rub		CRYSTAL STRUCTURE OF THE UNACTIVATED FORM OF RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE FROM TOBACCO REFINED AT 2.0-ANGSTROMS RESOLUTION
3zxw		STRUCTURE OF ACTIVATED RUBISCO FROM THERMOSYNECHOCOCCUS ELONGATUS COMPLEXED WITH 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
4f0h		UNACTIVATED RUBISCO with OXYGEN BOUND
4f0k		UNACTIVATED RUBISCO with MAGNESIUM AND CARBON DIOXIDE BOUND
4f0m		UNACTIVATED RUBISCO with MAGNESIUM AND A WATER MOLECULE BOUND
4hhh		Structure of Pisum sativum Rubisco
4mkv		Structure of Pisum sativum Rubisco with ABA
4rub		A CRYSTAL FORM OF RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE FROM NICOTIANA TABACUM IN THE ACTIVATED STATE
8ruc		ACTIVATED SPINACH RUBISCO COMPLEXED WITH 2-CARBOXYARABINITOL BISPHOSPHATE

Links (links to other resources describing this domain)
INTERPRO IPR000894
PFAM RuBisCO_small

INTERPRO	IPR000894
PFAM	RuBisCO_small

RuBisCO_small

Taxonomic distribution of proteins containing RuBisCO_small domain.

3D Structures of RuBisCO_small domains in PDB