2YBV | pdb_00002ybv

STRUCTURE OF RUBISCO FROM THERMOSYNECHOCOCCUS ELONGATUS

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d2ybvb_	Alpha and beta proteins (a+b)	RuBisCO, small subunit	RuBisCO, small subunit	RuBisCO, small subunit	automated matches	(Thermosynechococcus vestitus BP-1 ) [TaxId: 197221 ],	SCOPe (2.08)
D	d2ybvd_	Alpha and beta proteins (a+b)	RuBisCO, small subunit	RuBisCO, small subunit	RuBisCO, small subunit	automated matches	(Thermosynechococcus vestitus BP-1 ) [TaxId: 197221 ],	SCOPe (2.08)
F	d2ybvf_	Alpha and beta proteins (a+b)	RuBisCO, small subunit	RuBisCO, small subunit	RuBisCO, small subunit	automated matches	(Thermosynechococcus vestitus BP-1 ) [TaxId: 197221 ],	SCOPe (2.08)
L	d2ybvl_	Alpha and beta proteins (a+b)	RuBisCO, small subunit	RuBisCO, small subunit	RuBisCO, small subunit	automated matches	(Thermosynechococcus vestitus BP-1 ) [TaxId: 197221 ],	SCOPe (2.08)
N	d2ybvn_	Alpha and beta proteins (a+b)	RuBisCO, small subunit	RuBisCO, small subunit	RuBisCO, small subunit	automated matches	(Thermosynechococcus vestitus BP-1 ) [TaxId: 197221 ],	SCOPe (2.08)
P	d2ybvp_	Alpha and beta proteins (a+b)	RuBisCO, small subunit	RuBisCO, small subunit	RuBisCO, small subunit	automated matches	(Thermosynechococcus vestitus BP-1 ) [TaxId: 197221 ],	SCOPe (2.08)
J	d2ybvj_	Alpha and beta proteins (a+b)	RuBisCO, small subunit	RuBisCO, small subunit	RuBisCO, small subunit	automated matches	(Thermosynechococcus vestitus BP-1 ) [TaxId: 197221 ],	SCOPe (2.08)
H	d2ybvh_	Alpha and beta proteins (a+b)	RuBisCO, small subunit	RuBisCO, small subunit	RuBisCO, small subunit	automated matches	(Thermosynechococcus vestitus BP-1 ) [TaxId: 197221 ],	SCOPe (2.08)
A	d2ybva2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	RuBisCo, large subunit, C-terminal domain	automated matches	(Thermosynechococcus vestitus BP-1 ) [TaxId: 197221 ],	SCOPe (2.08)
A	d2ybva1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Thermosynechococcus vestitus BP-1 ) [TaxId: 197221 ],	SCOPe (2.08)
C	d2ybvc2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	RuBisCo, large subunit, C-terminal domain	automated matches	(Thermosynechococcus vestitus BP-1 ) [TaxId: 197221 ],	SCOPe (2.08)
C	d2ybvc1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Thermosynechococcus vestitus BP-1 ) [TaxId: 197221 ],	SCOPe (2.08)
E	d2ybve2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	RuBisCo, large subunit, C-terminal domain	automated matches	(Thermosynechococcus vestitus BP-1 ) [TaxId: 197221 ],	SCOPe (2.08)
E	d2ybve1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Thermosynechococcus vestitus BP-1 ) [TaxId: 197221 ],	SCOPe (2.08)
G	d2ybvg2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	RuBisCo, large subunit, C-terminal domain	automated matches	(Thermosynechococcus vestitus BP-1 ) [TaxId: 197221 ],	SCOPe (2.08)
G	d2ybvg1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Thermosynechococcus vestitus BP-1 ) [TaxId: 197221 ],	SCOPe (2.08)
M	d2ybvm2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	RuBisCo, large subunit, C-terminal domain	automated matches	(Thermosynechococcus vestitus BP-1 ) [TaxId: 197221 ],	SCOPe (2.08)
M	d2ybvm1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Thermosynechococcus vestitus BP-1 ) [TaxId: 197221 ],	SCOPe (2.08)
O	d2ybvo2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	RuBisCo, large subunit, C-terminal domain	automated matches	(Thermosynechococcus vestitus BP-1 ) [TaxId: 197221 ],	SCOPe (2.08)
O	d2ybvo1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Thermosynechococcus vestitus BP-1 ) [TaxId: 197221 ],	SCOPe (2.08)
K	d2ybvk2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	RuBisCo, large subunit, C-terminal domain	automated matches	(Thermosynechococcus vestitus BP-1 ) [TaxId: 197221 ],	SCOPe (2.08)
K	d2ybvk1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Thermosynechococcus vestitus BP-1 ) [TaxId: 197221 ],	SCOPe (2.08)
I	d2ybvi2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	RuBisCo, large subunit, C-terminal domain	automated matches	(Thermosynechococcus vestitus BP-1 ) [TaxId: 197221 ],	SCOPe (2.08)
I	d2ybvi1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Thermosynechococcus vestitus BP-1 ) [TaxId: 197221 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	RuBisCO, small subunit	8069974	4001455	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	RuBisCO, small subunit	8069975	3001622	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	RuBisCO, small subunit	8069975	3001622	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	RuBisCO, small subunit	8069975	3001622	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	RuBisCO, small subunit	8069975	3001622	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	RuBisCO, small subunit	8069975	3001622	SCOP2B (2022-06-29)
P	SCOP2B Superfamily	RuBisCO, small subunit	8069975	3001622	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	RuBisCO, small subunit	8069975	3001622	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	RuBisCO, small subunit	8069975	3001622	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	Peptidase_M49	e2ybvB2	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Peptidase_M49	ECOD (develop294)
D	Peptidase_M49	e2ybvD2	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Peptidase_M49	ECOD (develop294)
F	Peptidase_M49	e2ybvF2	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Peptidase_M49	ECOD (develop294)
L	Peptidase_M49	e2ybvL2	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Peptidase_M49	ECOD (develop294)
N	Peptidase_M49	e2ybvN2	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Peptidase_M49	ECOD (develop294)
P	Peptidase_M49	e2ybvP2	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Peptidase_M49	ECOD (develop294)
J	Peptidase_M49	e2ybvJ2	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Peptidase_M49	ECOD (develop294)
H	Peptidase_M49	e2ybvH2	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Peptidase_M49	ECOD (develop294)
A	N-glycanase_C	e2ybvA3	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: N-glycanase_C	ECOD (develop294)
C	RuBisCO_large_N	e2ybvC3	A: alpha bundles	X: Fusion glycoprotein F2	H: HTH	T: winged helix domain	F: RuBisCO_large_N	ECOD (develop294)
E	RuBisCO_large_N	e2ybvE3	A: alpha bundles	X: Fusion glycoprotein F2	H: HTH	T: winged helix domain	F: RuBisCO_large_N	ECOD (develop294)
G	RuBisCO_large_N	e2ybvG3	A: alpha bundles	X: Fusion glycoprotein F2	H: HTH	T: winged helix domain	F: RuBisCO_large_N	ECOD (develop294)
M	RuBisCO_large_N	e2ybvM3	A: alpha bundles	X: Fusion glycoprotein F2	H: HTH	T: winged helix domain	F: RuBisCO_large_N	ECOD (develop294)
O	RuBisCO_large_N	e2ybvO3	A: alpha bundles	X: Fusion glycoprotein F2	H: HTH	T: winged helix domain	F: RuBisCO_large_N	ECOD (develop294)
K	RuBisCO_large_N	e2ybvK3	A: alpha bundles	X: Fusion glycoprotein F2	H: HTH	T: winged helix domain	F: RuBisCO_large_N	ECOD (develop294)
I	RuBisCO_large_N	e2ybvI3	A: alpha bundles	X: Fusion glycoprotein F2	H: HTH	T: winged helix domain	F: RuBisCO_large_N	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.190.10	Alpha Beta	2-Layer Sandwich	Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase	Ribulose bisphosphate carboxylase, small subunit	CATH (4.3.0)
D	3.30.190.10	Alpha Beta	2-Layer Sandwich	Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase	Ribulose bisphosphate carboxylase, small subunit	CATH (4.3.0)
F	3.30.190.10	Alpha Beta	2-Layer Sandwich	Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase	Ribulose bisphosphate carboxylase, small subunit	CATH (4.3.0)
L	3.30.190.10	Alpha Beta	2-Layer Sandwich	Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase	Ribulose bisphosphate carboxylase, small subunit	CATH (4.3.0)
N	3.30.190.10	Alpha Beta	2-Layer Sandwich	Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase	Ribulose bisphosphate carboxylase, small subunit	CATH (4.3.0)
P	3.30.190.10	Alpha Beta	2-Layer Sandwich	Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase	Ribulose bisphosphate carboxylase, small subunit	CATH (4.3.0)
J	3.30.190.10	Alpha Beta	2-Layer Sandwich	Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase	Ribulose bisphosphate carboxylase, small subunit	CATH (4.3.0)
H	3.30.190.10	Alpha Beta	2-Layer Sandwich	Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase	Ribulose bisphosphate carboxylase, small subunit	CATH (4.3.0)
A	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (4.3.0)
A	3.20.20.110	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain	CATH (4.3.0)
C	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (4.3.0)
C	3.20.20.110	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain	CATH (4.3.0)
E	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (4.3.0)
E	3.20.20.110	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain	CATH (4.3.0)
G	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (4.3.0)
G	3.20.20.110	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain	CATH (4.3.0)
M	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (4.3.0)
M	3.20.20.110	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain	CATH (4.3.0)
O	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (4.3.0)
O	3.20.20.110	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain	CATH (4.3.0)
K	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (4.3.0)
K	3.20.20.110	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain	CATH (4.3.0)
I	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (4.3.0)
I	3.20.20.110	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H, J B, D, F, H, J, L, N, P	PF00101	Ribulose bisphosphate carboxylase, small chain (RuBisCO_small)	Ribulose bisphosphate carboxylase, small chain		Domain
A, C, E, G, I A, C, E, G, I, K, M, O	PF02788	Ribulose bisphosphate carboxylase large chain, N-terminal domain (RuBisCO_large_N)	Ribulose bisphosphate carboxylase large chain, N-terminal domain	The N-terminal domain of RuBisCO large chain adopts a ferredoxin-like fold.	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	PF00016	Ribulose bisphosphate carboxylase large chain, catalytic domain (RuBisCO_large)	Ribulose bisphosphate carboxylase large chain, catalytic domain	The C-terminal domain of RuBisCO large chain is the catalytic domain adopting a TIM barrel fold.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H, J B, D, F, H, J, L, N, P	RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL SUBUNIT	ribulose-bisphosphate carboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity	metabolic compound salvage biosynthetic process metabolic process cellular process photorespiration carbohydrate metabolic process photosynthesis reductive pentose-phosphate cycle carbohydrate biosynthetic process photosynthesis, dark reaction primary metabolic process carbon fixation	intracellular organelle bacterial microcompartment cellular anatomical structure intracellular anatomical structure organelle carboxysome membraneless organelle intracellular membraneless organelle
A, C, E, G, I A, C, E, G, I, K, M, O	RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding ribulose-bisphosphate carboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity monooxygenase activity oxidoreductase activity	metabolic compound salvage biosynthetic process metabolic process cellular process photorespiration carbohydrate metabolic process photosynthesis reductive pentose-phosphate cycle carbohydrate biosynthetic process photosynthesis, dark reaction primary metabolic process carbon fixation	intracellular organelle bacterial microcompartment cellular anatomical structure intracellular anatomical structure organelle carboxysome membraneless organelle intracellular membraneless organelle cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H, J B, D, F, H, J, L, N, P	IPR036385	Ribulose bisphosphate carboxylase, small subunit superfamily	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L, N, P	IPR024681	Ribulose bisphosphate carboxylase, small subunit	Family
B, D, F, H, J B, D, F, H, J, L, N, P	IPR000894	Ribulose bisphosphate carboxylase small subunit, domain	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR020888	Ribulose bisphosphate carboxylase large subunit, type I	Family
A, C, E, G, I A, C, E, G, I, K, M, O	IPR036376	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O	IPR020878	Ribulose bisphosphate carboxylase, large chain, active site	Active Site
A, C, E, G, I A, C, E, G, I, K, M, O	IPR000685	Ribulose bisphosphate carboxylase, large subunit, C-terminal	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR033966	RuBisCO	Family
A, C, E, G, I A, C, E, G, I, K, M, O	IPR017443	Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR036422	RuBisCO large subunit, N-terminal domain superfamily	Homologous Superfamily