2V69 | pdb_00002v69

Crystal structure of Chlamydomonas reinhardtii Rubisco with a large- subunit mutation D473E


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

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
Id2v69i_ Alpha and beta proteins (a+b) RuBisCO, small subunit RuBisCO, small subunit RuBisCO, small subunit automated matches (Chlamydomonas reinhardtii ) [TaxId: 3055 ], SCOPe (2.08)
Jd2v69j_ Alpha and beta proteins (a+b) RuBisCO, small subunit RuBisCO, small subunit RuBisCO, small subunit automated matches (Chlamydomonas reinhardtii ) [TaxId: 3055 ], SCOPe (2.08)
Pd2v69p_ Alpha and beta proteins (a+b) RuBisCO, small subunit RuBisCO, small subunit RuBisCO, small subunit automated matches (Chlamydomonas reinhardtii ) [TaxId: 3055 ], SCOPe (2.08)
Od2v69o_ Alpha and beta proteins (a+b) RuBisCO, small subunit RuBisCO, small subunit RuBisCO, small subunit automated matches (Chlamydomonas reinhardtii ) [TaxId: 3055 ], SCOPe (2.08)
Nd2v69n_ Alpha and beta proteins (a+b) RuBisCO, small subunit RuBisCO, small subunit RuBisCO, small subunit automated matches (Chlamydomonas reinhardtii ) [TaxId: 3055 ], SCOPe (2.08)
Md2v69m_ Alpha and beta proteins (a+b) RuBisCO, small subunit RuBisCO, small subunit RuBisCO, small subunit automated matches (Chlamydomonas reinhardtii ) [TaxId: 3055 ], SCOPe (2.08)
Ld2v69l_ Alpha and beta proteins (a+b) RuBisCO, small subunit RuBisCO, small subunit RuBisCO, small subunit automated matches (Chlamydomonas reinhardtii ) [TaxId: 3055 ], SCOPe (2.08)
Kd2v69k_ Alpha and beta proteins (a+b) RuBisCO, small subunit RuBisCO, small subunit RuBisCO, small subunit automated matches (Chlamydomonas reinhardtii ) [TaxId: 3055 ], SCOPe (2.08)
Ad2v69a1 Alpha and beta proteins (a/b) TIM beta/alpha-barrel RuBisCo, C-terminal domain RuBisCo, large subunit, C-terminal domain automated matches (Chlamydomonas reinhardtii ) [TaxId: 3055 ], SCOPe (2.08)
Ad2v69a2 Alpha and beta proteins (a+b) Ferredoxin-like RuBisCO, large subunit, small (N-terminal) domain automated matches automated matches (Chlamydomonas reinhardtii ) [TaxId: 3055 ], SCOPe (2.08)
Bd2v69b1 Alpha and beta proteins (a/b) TIM beta/alpha-barrel RuBisCo, C-terminal domain RuBisCo, large subunit, C-terminal domain automated matches (Chlamydomonas reinhardtii ) [TaxId: 3055 ], SCOPe (2.08)
Bd2v69b2 Alpha and beta proteins (a+b) Ferredoxin-like RuBisCO, large subunit, small (N-terminal) domain automated matches automated matches (Chlamydomonas reinhardtii ) [TaxId: 3055 ], SCOPe (2.08)
Dd2v69d1 Alpha and beta proteins (a/b) TIM beta/alpha-barrel RuBisCo, C-terminal domain RuBisCo, large subunit, C-terminal domain automated matches (Chlamydomonas reinhardtii ) [TaxId: 3055 ], SCOPe (2.08)
Dd2v69d2 Alpha and beta proteins (a+b) Ferredoxin-like RuBisCO, large subunit, small (N-terminal) domain automated matches automated matches (Chlamydomonas reinhardtii ) [TaxId: 3055 ], SCOPe (2.08)
Gd2v69g1 Alpha and beta proteins (a/b) TIM beta/alpha-barrel RuBisCo, C-terminal domain RuBisCo, large subunit, C-terminal domain automated matches (Chlamydomonas reinhardtii ) [TaxId: 3055 ], SCOPe (2.08)
Gd2v69g2 Alpha and beta proteins (a+b) Ferredoxin-like RuBisCO, large subunit, small (N-terminal) domain automated matches automated matches (Chlamydomonas reinhardtii ) [TaxId: 3055 ], SCOPe (2.08)
Hd2v69h1 Alpha and beta proteins (a/b) TIM beta/alpha-barrel RuBisCo, C-terminal domain RuBisCo, large subunit, C-terminal domain automated matches (Chlamydomonas reinhardtii ) [TaxId: 3055 ], SCOPe (2.08)
Hd2v69h2 Alpha and beta proteins (a+b) Ferredoxin-like RuBisCO, large subunit, small (N-terminal) domain automated matches automated matches (Chlamydomonas reinhardtii ) [TaxId: 3055 ], SCOPe (2.08)
Fd2v69f1 Alpha and beta proteins (a/b) TIM beta/alpha-barrel RuBisCo, C-terminal domain RuBisCo, large subunit, C-terminal domain automated matches (Chlamydomonas reinhardtii ) [TaxId: 3055 ], SCOPe (2.08)
Fd2v69f2 Alpha and beta proteins (a+b) Ferredoxin-like RuBisCO, large subunit, small (N-terminal) domain automated matches automated matches (Chlamydomonas reinhardtii ) [TaxId: 3055 ], SCOPe (2.08)
Ed2v69e1 Alpha and beta proteins (a/b) TIM beta/alpha-barrel RuBisCo, C-terminal domain RuBisCo, large subunit, C-terminal domain automated matches (Chlamydomonas reinhardtii ) [TaxId: 3055 ], SCOPe (2.08)
Ed2v69e2 Alpha and beta proteins (a+b) Ferredoxin-like RuBisCO, large subunit, small (N-terminal) domain automated matches automated matches (Chlamydomonas reinhardtii ) [TaxId: 3055 ], SCOPe (2.08)
Cd2v69c1 Alpha and beta proteins (a/b) TIM beta/alpha-barrel RuBisCo, C-terminal domain RuBisCo, large subunit, C-terminal domain automated matches (Chlamydomonas reinhardtii ) [TaxId: 3055 ], SCOPe (2.08)
Cd2v69c2 Alpha and beta proteins (a+b) Ferredoxin-like RuBisCO, large subunit, small (N-terminal) domain automated matches automated matches (Chlamydomonas reinhardtii ) [TaxId: 3055 ], SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ISCOP2B SuperfamilyRuBisCO, small subunit 8035897 3001622 SCOP2B (2022-06-29)
JSCOP2B SuperfamilyRuBisCO, small subunit 8035897 3001622 SCOP2B (2022-06-29)
PSCOP2B SuperfamilyRuBisCO, small subunit 8035897 3001622 SCOP2B (2022-06-29)
OSCOP2B SuperfamilyRuBisCO, small subunit 8035897 3001622 SCOP2B (2022-06-29)
NSCOP2B SuperfamilyRuBisCO, small subunit 8035897 3001622 SCOP2B (2022-06-29)
MSCOP2B SuperfamilyRuBisCO, small subunit 8035897 3001622 SCOP2B (2022-06-29)
LSCOP2B SuperfamilyRuBisCO, small subunit 8035897 3001622 SCOP2B (2022-06-29)
KSCOP2B SuperfamilyRuBisCO, small subunit 8035897 3001622 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyRuBisCO, large subunit, small (N-terminal) domain 8035891 3001258 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyRuBisCo, C-terminal domain 8035888 3000552 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyRuBisCo, C-terminal domain 8035888 3000552 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyRuBisCO, large subunit, small (N-terminal) domain 8035891 3001258 SCOP2B (2022-06-29)
DSCOP2B SuperfamilyRuBisCo, C-terminal domain 8035888 3000552 SCOP2B (2022-06-29)
DSCOP2B SuperfamilyRuBisCO, large subunit, small (N-terminal) domain 8035891 3001258 SCOP2B (2022-06-29)
GSCOP2B SuperfamilyRuBisCO, large subunit, small (N-terminal) domain 8035891 3001258 SCOP2B (2022-06-29)
GSCOP2B SuperfamilyRuBisCo, C-terminal domain 8035888 3000552 SCOP2B (2022-06-29)
HSCOP2B SuperfamilyRuBisCo, C-terminal domain 8035888 3000552 SCOP2B (2022-06-29)
HSCOP2B SuperfamilyRuBisCO, large subunit, small (N-terminal) domain 8035891 3001258 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyRuBisCO, large subunit, small (N-terminal) domain 8035891 3001258 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyRuBisCo, C-terminal domain 8035888 3000552 SCOP2B (2022-06-29)
ESCOP2B SuperfamilyRuBisCo, C-terminal domain 8035888 3000552 SCOP2B (2022-06-29)
ESCOP2B SuperfamilyRuBisCO, large subunit, small (N-terminal) domain 8035891 3001258 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyRuBisCO, large subunit, small (N-terminal) domain 8035891 3001258 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyRuBisCo, C-terminal domain 8035888 3000552 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
IOKR_DC_1_Ce2v69I1 A: a/b three-layered sandwichesX: ETN0001 domain-likeH: Rpp14/Pop5-likeT: Rpp14/Pop5-likeF: OKR_DC_1_CECOD (v294.1)
JOKR_DC_1_Ce2v69J1 A: a/b three-layered sandwichesX: ETN0001 domain-likeH: Rpp14/Pop5-likeT: Rpp14/Pop5-likeF: OKR_DC_1_CECOD (v294.1)
POKR_DC_1_Ce2v69P1 A: a/b three-layered sandwichesX: ETN0001 domain-likeH: Rpp14/Pop5-likeT: Rpp14/Pop5-likeF: OKR_DC_1_CECOD (v294.1)
OOKR_DC_1_Ce2v69O1 A: a/b three-layered sandwichesX: ETN0001 domain-likeH: Rpp14/Pop5-likeT: Rpp14/Pop5-likeF: OKR_DC_1_CECOD (v294.1)
NOKR_DC_1_Ce2v69N1 A: a/b three-layered sandwichesX: ETN0001 domain-likeH: Rpp14/Pop5-likeT: Rpp14/Pop5-likeF: OKR_DC_1_CECOD (v294.1)
MOKR_DC_1_Ce2v69M1 A: a/b three-layered sandwichesX: ETN0001 domain-likeH: Rpp14/Pop5-likeT: Rpp14/Pop5-likeF: OKR_DC_1_CECOD (v294.1)
LOKR_DC_1_Ce2v69L1 A: a/b three-layered sandwichesX: ETN0001 domain-likeH: Rpp14/Pop5-likeT: Rpp14/Pop5-likeF: OKR_DC_1_CECOD (v294.1)
KOKR_DC_1_Ce2v69K1 A: a/b three-layered sandwichesX: ETN0001 domain-likeH: Rpp14/Pop5-likeT: Rpp14/Pop5-likeF: OKR_DC_1_CECOD (v294.1)
ARNase_P_Rpp14e2v69A1 A: a/b three-layered sandwichesX: ETN0001 domain-likeH: Rpp14/Pop5-likeT: Rpp14/Pop5-likeF: RNase_P_Rpp14ECOD (v294.1)
ADUF711e2v69A2 A: a/b three-layered sandwichesX: HTHH: HTHT: winged helix domainF: DUF711ECOD (v294.1)
BRNase_P_Rpp14e2v69B1 A: a/b three-layered sandwichesX: ETN0001 domain-likeH: Rpp14/Pop5-likeT: Rpp14/Pop5-likeF: RNase_P_Rpp14ECOD (v294.1)
BDUF711e2v69B2 A: a/b three-layered sandwichesX: HTHH: HTHT: winged helix domainF: DUF711ECOD (v294.1)
DRNase_P_Rpp14e2v69D1 A: a/b three-layered sandwichesX: ETN0001 domain-likeH: Rpp14/Pop5-likeT: Rpp14/Pop5-likeF: RNase_P_Rpp14ECOD (v294.1)
DDUF711e2v69D2 A: a/b three-layered sandwichesX: HTHH: HTHT: winged helix domainF: DUF711ECOD (v294.1)
GRNase_P_Rpp14e2v69G1 A: a/b three-layered sandwichesX: ETN0001 domain-likeH: Rpp14/Pop5-likeT: Rpp14/Pop5-likeF: RNase_P_Rpp14ECOD (v294.1)
GDUF711e2v69G2 A: a/b three-layered sandwichesX: HTHH: HTHT: winged helix domainF: DUF711ECOD (v294.1)
HRNase_P_Rpp14e2v69H1 A: a/b three-layered sandwichesX: ETN0001 domain-likeH: Rpp14/Pop5-likeT: Rpp14/Pop5-likeF: RNase_P_Rpp14ECOD (v294.1)
HDUF711e2v69H2 A: a/b three-layered sandwichesX: HTHH: HTHT: winged helix domainF: DUF711ECOD (v294.1)
FRNase_P_Rpp14e2v69F1 A: a/b three-layered sandwichesX: ETN0001 domain-likeH: Rpp14/Pop5-likeT: Rpp14/Pop5-likeF: RNase_P_Rpp14ECOD (v294.1)
FDUF711e2v69F2 A: a/b three-layered sandwichesX: HTHH: HTHT: winged helix domainF: DUF711ECOD (v294.1)
ERNase_P_Rpp14e2v69E1 A: a/b three-layered sandwichesX: ETN0001 domain-likeH: Rpp14/Pop5-likeT: Rpp14/Pop5-likeF: RNase_P_Rpp14ECOD (v294.1)
EDUF711e2v69E2 A: a/b three-layered sandwichesX: HTHH: HTHT: winged helix domainF: DUF711ECOD (v294.1)
CRNase_P_Rpp14e2v69C1 A: a/b three-layered sandwichesX: ETN0001 domain-likeH: Rpp14/Pop5-likeT: Rpp14/Pop5-likeF: RNase_P_Rpp14ECOD (v294.1)
CDUF711e2v69C2 A: a/b three-layered sandwichesX: HTHH: HTHT: winged helix domainF: DUF711ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
I3.30.190.10 Alpha Beta 2-Layer Sandwich Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase Ribulose bisphosphate carboxylase, small subunitCATH (4.3.0)
J3.30.190.10 Alpha Beta 2-Layer Sandwich Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase Ribulose bisphosphate carboxylase, small subunitCATH (4.3.0)
P3.30.190.10 Alpha Beta 2-Layer Sandwich Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase Ribulose bisphosphate carboxylase, small subunitCATH (4.3.0)
O3.30.190.10 Alpha Beta 2-Layer Sandwich Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase Ribulose bisphosphate carboxylase, small subunitCATH (4.3.0)
N3.30.190.10 Alpha Beta 2-Layer Sandwich Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase Ribulose bisphosphate carboxylase, small subunitCATH (4.3.0)
M3.30.190.10 Alpha Beta 2-Layer Sandwich Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase Ribulose bisphosphate carboxylase, small subunitCATH (4.3.0)
L3.30.190.10 Alpha Beta 2-Layer Sandwich Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase Ribulose bisphosphate carboxylase, small subunitCATH (4.3.0)
K3.30.190.10 Alpha Beta 2-Layer Sandwich Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase Ribulose bisphosphate carboxylase, small subunitCATH (4.3.0)
A3.30.70.150 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits RuBisCO large subunit, N-terminal domainCATH (4.3.0)
A3.20.20.110 Alpha Beta Alpha-Beta Barrel TIM Barrel Ribulose bisphosphate carboxylase, large subunit, C-terminal domainCATH (4.3.0)
B3.30.70.150 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits RuBisCO large subunit, N-terminal domainCATH (4.3.0)
B3.20.20.110 Alpha Beta Alpha-Beta Barrel TIM Barrel Ribulose bisphosphate carboxylase, large subunit, C-terminal domainCATH (4.3.0)
D3.30.70.150 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits RuBisCO large subunit, N-terminal domainCATH (4.3.0)
D3.20.20.110 Alpha Beta Alpha-Beta Barrel TIM Barrel Ribulose bisphosphate carboxylase, large subunit, C-terminal domainCATH (4.3.0)
G3.30.70.150 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits RuBisCO large subunit, N-terminal domainCATH (4.3.0)
G3.20.20.110 Alpha Beta Alpha-Beta Barrel TIM Barrel Ribulose bisphosphate carboxylase, large subunit, C-terminal domainCATH (4.3.0)
H3.30.70.150 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits RuBisCO large subunit, N-terminal domainCATH (4.3.0)
H3.20.20.110 Alpha Beta Alpha-Beta Barrel TIM Barrel Ribulose bisphosphate carboxylase, large subunit, C-terminal domainCATH (4.3.0)
F3.30.70.150 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits RuBisCO large subunit, N-terminal domainCATH (4.3.0)
F3.20.20.110 Alpha Beta Alpha-Beta Barrel TIM Barrel Ribulose bisphosphate carboxylase, large subunit, C-terminal domainCATH (4.3.0)
E3.30.70.150 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits RuBisCO large subunit, N-terminal domainCATH (4.3.0)
E3.20.20.110 Alpha Beta Alpha-Beta Barrel TIM Barrel Ribulose bisphosphate carboxylase, large subunit, C-terminal domainCATH (4.3.0)
C3.30.70.150 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits RuBisCO large subunit, N-terminal domainCATH (4.3.0)
C3.20.20.110 Alpha Beta Alpha-Beta Barrel TIM Barrel Ribulose bisphosphate carboxylase, large subunit, C-terminal domainCATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
I, J, K, L, M
PF00101Ribulose bisphosphate carboxylase, small chain (RuBisCO_small)Ribulose bisphosphate carboxylase, small chainDomain
A, B, C, D, E
PF02788Ribulose bisphosphate carboxylase large chain, N-terminal domain (RuBisCO_large_N)Ribulose bisphosphate carboxylase large chain, N-terminal domainThe N-terminal domain of RuBisCO large chain adopts a ferredoxin-like fold. Domain
A, B, C, D, E
PF00016Ribulose bisphosphate carboxylase large chain, catalytic domain (RuBisCO_large)Ribulose bisphosphate carboxylase large chain, catalytic domainThe 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

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
I, J, K, L, M
RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1
A, B, C, D, E
RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN

Protein Modification Annotation

Modified Residue(s)
ChainResidue(s)Description
I, J, K, L, M
MME Parent Component: MET

RESIDAA0064

PSI-MOD :  N-methyl-L-methionine MOD:00073
A, B, C, D, E
HYP Parent Component: PRO

RESIDAA0064 , AA0030

PSI-MOD :  N-methyl-L-methionine MOD:00073 , 4-hydroxy-L-proline MOD:00039
A, B, C, D, E
KCX Parent Component: LYS

RESIDAA0064 , AA0030

A, B, C, D, E
SMC Parent Component: CYS

RESIDAA0064 , AA0030 , AA0234

PSI-MOD :  N-methyl-L-methionine MOD:00073 , 4-hydroxy-L-proline MOD:00039 , S-methyl-L-cysteine MOD:00239