5OYA | pdb_00005oya

Unusual posttranslational modifications revealed in crystal structures of diatom Rubisco.

External Resource: Annotation

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d5oyab2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	RuBisCo, large subunit, C-terminal domain	automated matches	(Chaetoceros socialis ) [TaxId: 163503 ],	SCOPe (2.08)
B	d5oyab1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Chaetoceros socialis ) [TaxId: 163503 ],	SCOPe (2.08)
D	d5oyad2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	RuBisCo, large subunit, C-terminal domain	automated matches	(Chaetoceros socialis ) [TaxId: 163503 ],	SCOPe (2.08)
D	d5oyad1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Chaetoceros socialis ) [TaxId: 163503 ],	SCOPe (2.08)
E	d5oyae2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	RuBisCo, large subunit, C-terminal domain	automated matches	(Chaetoceros socialis ) [TaxId: 163503 ],	SCOPe (2.08)
E	d5oyae1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Chaetoceros socialis ) [TaxId: 163503 ],	SCOPe (2.08)
F	d5oyaf2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	RuBisCo, large subunit, C-terminal domain	automated matches	(Chaetoceros socialis ) [TaxId: 163503 ],	SCOPe (2.08)
F	d5oyaf1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Chaetoceros socialis ) [TaxId: 163503 ],	SCOPe (2.08)
G	d5oyag2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	RuBisCo, large subunit, C-terminal domain	automated matches	(Chaetoceros socialis ) [TaxId: 163503 ],	SCOPe (2.08)
G	d5oyag1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Chaetoceros socialis ) [TaxId: 163503 ],	SCOPe (2.08)
H	d5oyah2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	RuBisCo, large subunit, C-terminal domain	automated matches	(Chaetoceros socialis ) [TaxId: 163503 ],	SCOPe (2.08)
H	d5oyah1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Chaetoceros socialis ) [TaxId: 163503 ],	SCOPe (2.08)
A	d5oyaa2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	RuBisCo, large subunit, C-terminal domain	automated matches	(Chaetoceros socialis ) [TaxId: 163503 ],	SCOPe (2.08)
A	d5oyaa1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Chaetoceros socialis ) [TaxId: 163503 ],	SCOPe (2.08)
C	d5oyac2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	RuBisCo, large subunit, C-terminal domain	automated matches	(Chaetoceros socialis ) [TaxId: 163503 ],	SCOPe (2.08)
C	d5oyac1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Chaetoceros socialis ) [TaxId: 163503 ],	SCOPe (2.08)
I	d5oyai_	Alpha and beta proteins (a+b)	RuBisCO, small subunit	RuBisCO, small subunit	automated matches	automated matches	(Chaetoceros socialis ) [TaxId: 163503 ],	SCOPe (2.08)
J	d5oyaj_	Alpha and beta proteins (a+b)	RuBisCO, small subunit	RuBisCO, small subunit	automated matches	automated matches	(Chaetoceros socialis ) [TaxId: 163503 ],	SCOPe (2.08)
K	d5oyak_	Alpha and beta proteins (a+b)	RuBisCO, small subunit	RuBisCO, small subunit	automated matches	automated matches	(Chaetoceros socialis ) [TaxId: 163503 ],	SCOPe (2.08)
L	d5oyal_	Alpha and beta proteins (a+b)	RuBisCO, small subunit	RuBisCO, small subunit	automated matches	automated matches	(Chaetoceros socialis ) [TaxId: 163503 ],	SCOPe (2.08)
M	d5oyam_	Alpha and beta proteins (a+b)	RuBisCO, small subunit	RuBisCO, small subunit	automated matches	automated matches	(Chaetoceros socialis ) [TaxId: 163503 ],	SCOPe (2.08)
N	d5oyan_	Alpha and beta proteins (a+b)	RuBisCO, small subunit	RuBisCO, small subunit	automated matches	automated matches	(Chaetoceros socialis ) [TaxId: 163503 ],	SCOPe (2.08)
O	d5oyao_	Alpha and beta proteins (a+b)	RuBisCO, small subunit	RuBisCO, small subunit	automated matches	automated matches	(Chaetoceros socialis ) [TaxId: 163503 ],	SCOPe (2.08)
P	d5oyap_	Alpha and beta proteins (a+b)	RuBisCO, small subunit	RuBisCO, small subunit	automated matches	automated matches	(Chaetoceros socialis ) [TaxId: 163503 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
I	SCOP2B Superfamily	RuBisCO, small subunit	8095091	3001622	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	RuBisCO, small subunit	8095091	3001622	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	RuBisCO, small subunit	8095091	3001622	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	RuBisCO, small subunit	8095091	3001622	SCOP2B (2022-06-29)
M	SCOP2 Family	RuBisCO, small subunit	8095090	4001455	SCOP2 (2022-06-29)
M	SCOP2 Superfamily	RuBisCO, small subunit	8095091	3001622	SCOP2 (2022-06-29)
N	SCOP2B Superfamily	RuBisCO, small subunit	8095091	3001622	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	RuBisCO, small subunit	8095091	3001622	SCOP2B (2022-06-29)
P	SCOP2B Superfamily	RuBisCO, small subunit	8095091	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	Chlorophyllase2	e5oyaB1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (v294.1)
D	Chlorophyllase2	e5oyaD1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (v294.1)
E	Chlorophyllase2	e5oyaE1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (v294.1)
F	Chlorophyllase2	e5oyaF1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (v294.1)
G	Chlorophyllase2	e5oyaG1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (v294.1)
H	Chlorophyllase2	e5oyaH1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (v294.1)
A	Chlorophyllase2	e5oyaA1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (v294.1)
C	Chlorophyllase2	e5oyaC1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (v294.1)
I	ACPS	e5oyaI1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: ADP-ribosylation	T: ADP-ribosylation	F: ACPS	ECOD (v294.1)
J	Chlorophyllase2	e5oyaJ1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (v294.1)
K	Chlorophyllase2	e5oyaK1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (v294.1)
L	Chlorophyllase2	e5oyaL1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (v294.1)
M	Chlorophyllase2	e5oyaM1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (v294.1)
N	Chlorophyllase2	e5oyaN1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (v294.1)
O	Chlorophyllase2	e5oyaO1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (v294.1)
P	Chlorophyllase2	e5oyaP1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (4.3.0)
B	3.20.20.110	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain	CATH (4.3.0)
D	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (4.3.0)
D	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)
F	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (4.3.0)
F	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)
H	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (4.3.0)
H	3.20.20.110	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain	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)
I	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)
K	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)
M	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)
O	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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, D, E, F A, B, D, E, F, G, H	Rubisco large subunit	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding monooxygenase activity oxidoreductase activity catalytic activity ribulose-bisphosphate carboxylase activity carboxy-lyase activity lyase activity carbon-carbon lyase activity	carbohydrate metabolic process biosynthetic process photosynthesis reductive pentose-phosphate cycle carbohydrate biosynthetic process photosynthesis, dark reaction primary metabolic process metabolic process cellular process carbon fixation	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle
C	Rubisco large subunit	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding monooxygenase activity oxidoreductase activity catalytic activity ribulose-bisphosphate carboxylase activity carboxy-lyase activity lyase activity carbon-carbon lyase activity	carbohydrate metabolic process biosynthetic process photosynthesis reductive pentose-phosphate cycle carbohydrate biosynthetic process photosynthesis, dark reaction primary metabolic process metabolic process cellular process carbon fixation	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle
I, J, K, L, M I, J, K, L, M, N, O, P	Rubisco small subunit	ribulose-bisphosphate carboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity	carbohydrate metabolic process biosynthetic process photosynthesis reductive pentose-phosphate cycle carbohydrate biosynthetic process photosynthesis, dark reaction primary metabolic process metabolic process cellular process carbon fixation	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle chloroplast

InterPro: Protein Family Classification InterPro Database Homepage

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

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, D, E, F A, B, D, E, F, G, H	CSO	Parent Component: CYS RESID: AA0205 PSI-MOD : L-cysteine sulfenic acid MOD:00210
A, B, D, E, F A, B, D, E, F, G, H	HL2	Parent Component: LEU RESID: AA0205
A, B, D, E, F A, B, D, E, F, G, H	HYP	Parent Component: PRO RESID: AA0205 , AA0030 PSI-MOD : L-cysteine sulfenic acid MOD:00210 , 4-hydroxy-L-proline MOD:00039
A, B, D, E, F A, B, D, E, F, G, H	KCX	Parent Component: LYS RESID: AA0205 , AA0030
A, B, D, E, F A, B, D, E, F, G, H	LOH	RESID: AA0205 , AA0030
A, B, D, E, F A, B, D, E, F, G, H	M3L	Parent Component: LYS RESID: AA0205 , AA0030 , AA0074 PSI-MOD : L-cysteine sulfenic acid MOD:00210 , 4-hydroxy-L-proline MOD:00039 , N6,N6,N6-trimethyl-L-lysine MOD:00083
A, B, D, E, F A, B, D, E, F, G, H	SNC	Parent Component: CYS RESID: AA0205 , AA0030 , AA0074
C	CSO	Parent Component: CYS RESID: AA0205 , AA0030 , AA0074 , AA0205 PSI-MOD : L-cysteine sulfenic acid MOD:00210 , 4-hydroxy-L-proline MOD:00039 , N6,N6,N6-trimethyl-L-lysine MOD:00083 , L-cysteine sulfenic acid MOD:00210
C	HL2	Parent Component: LEU RESID: AA0205 , AA0030 , AA0074 , AA0205
C	HYP	Parent Component: PRO RESID: AA0205 , AA0030 , AA0074 , AA0205 , AA0030 PSI-MOD : L-cysteine sulfenic acid MOD:00210 , 4-hydroxy-L-proline MOD:00039 , N6,N6,N6-trimethyl-L-lysine MOD:00083 , L-cysteine sulfenic acid MOD:00210 , 4-hydroxy-L-proline MOD:00039
C	KCX	Parent Component: LYS RESID: AA0205 , AA0030 , AA0074 , AA0205 , AA0030
C	LOH	RESID: AA0205 , AA0030 , AA0074 , AA0205 , AA0030
C	M3L	Parent Component: LYS RESID: AA0205 , AA0030 , AA0074 , AA0205 , AA0030 , AA0074 PSI-MOD : L-cysteine sulfenic acid MOD:00210 , 4-hydroxy-L-proline MOD:00039 , N6,N6,N6-trimethyl-L-lysine MOD:00083 , L-cysteine sulfenic acid MOD:00210 , 4-hydroxy-L-proline MOD:00039 , N6,N6,N6-trimethyl-L-lysine MOD:00083
C	SNC	Parent Component: CYS RESID: AA0205 , AA0030 , AA0074 , AA0205 , AA0030 , AA0074