Crystal structure of designed two-component self-assembling icosahedral cage I52-32


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
Z [auth b]SCOP2B SuperfamilyPTS system fructose IIA component-like 8083013 3000475 SCOP2B (2022-06-29)
TSCOP2B SuperfamilyPTS system fructose IIA component-like 8083013 3000475 SCOP2B (2022-06-29)
S [auth R]SCOP2B SuperfamilyPTS system fructose IIA component-like 8083013 3000475 SCOP2B (2022-06-29)
R [auth S]SCOP2B SuperfamilyPTS system fructose IIA component-like 8083013 3000475 SCOP2B (2022-06-29)
QSCOP2B SuperfamilyPTS system fructose IIA component-like 8083013 3000475 SCOP2B (2022-06-29)
PSCOP2B SuperfamilyPTS system fructose IIA component-like 8083013 3000475 SCOP2B (2022-06-29)
NA [auth n]SCOP2B SuperfamilyPTS system fructose IIA component-like 8083013 3000475 SCOP2B (2022-06-29)
MA [auth l]SCOP2B SuperfamilyPTS system fructose IIA component-like 8083013 3000475 SCOP2B (2022-06-29)
LA [auth m]SCOP2B SuperfamilyPTS system fructose IIA component-like 8083013 3000475 SCOP2B (2022-06-29)
KA [auth k]SCOP2B SuperfamilyPTS system fructose IIA component-like 8083013 3000475 SCOP2B (2022-06-29)
JA [auth j]SCOP2B SuperfamilyPTS system fructose IIA component-like 8083013 3000475 SCOP2B (2022-06-29)
JSCOP2B SuperfamilyPTS system fructose IIA component-like 8083013 3000475 SCOP2B (2022-06-29)
ISCOP2B SuperfamilyPTS system fructose IIA component-like 8083013 3000475 SCOP2B (2022-06-29)
H [auth G]SCOP2B SuperfamilyPTS system fructose IIA component-like 8083013 3000475 SCOP2B (2022-06-29)
G [auth H]SCOP2B SuperfamilyPTS system fructose IIA component-like 8083013 3000475 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyPTS system fructose IIA component-like 8083013 3000475 SCOP2B (2022-06-29)
DA [auth a]SCOP2B SuperfamilyPTS system fructose IIA component-like 8083013 3000475 SCOP2B (2022-06-29)
CA [auth Z]SCOP2B SuperfamilyPTS system fructose IIA component-like 8083013 3000475 SCOP2B (2022-06-29)
BA [auth c]SCOP2B SuperfamilyPTS system fructose IIA component-like 8083013 3000475 SCOP2B (2022-06-29)
AA [auth d]SCOP2B SuperfamilyPTS system fructose IIA component-like 8083013 3000475 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
Z [auth b]Pantoate_ligasee5im4b1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
TPantoate_ligasee5im4T1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
S [auth R]Pantoate_ligasee5im4R1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
R [auth S]Pantoate_ligasee5im4S1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
QPantoate_ligasee5im4Q1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
PPantoate_ligasee5im4P1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
NA [auth n]Pantoate_ligasee5im4n1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
MA [auth l]Pantoate_ligasee5im4l1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
LA [auth m]Pantoate_ligasee5im4m1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
KA [auth k]Pantoate_ligasee5im4k1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
JA [auth j]Pantoate_ligasee5im4j1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
JPantoate_ligasee5im4J1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
IPantoate_ligasee5im4I1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
H [auth G]Pantoate_ligasee5im4G1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
G [auth H]Pantoate_ligasee5im4H1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
FPantoate_ligasee5im4F1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
DA [auth a]Pantoate_ligasee5im4a1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
CA [auth Z]Pantoate_ligasee5im4Z1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
BA [auth c]Pantoate_ligasee5im4c1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
AA [auth d]Pantoate_ligasee5im4d1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
YPantoate_ligasee5im4Y1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
X [auth W]Pantoate_ligasee5im4W1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
W [auth X]Pantoate_ligasee5im4X1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
VPantoate_ligasee5im4V1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
UPantoate_ligasee5im4U1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
OPantoate_ligasee5im4O1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
N [auth M]Pantoate_ligasee5im4M1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
M [auth N]Pantoate_ligasee5im4N1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
LPantoate_ligasee5im4L1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
KPantoate_ligasee5im4K1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
IA [auth i]Pantoate_ligasee5im4i1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
HA [auth g]Pantoate_ligasee5im4g1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
GA [auth h]Pantoate_ligasee5im4h1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
FA [auth f]Pantoate_ligasee5im4f1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
EA [auth e]Pantoate_ligasee5im4e1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
E [auth D]Pantoate_ligasee5im4D1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
D [auth B]Pantoate_ligasee5im4B1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
CPantoate_ligasee5im4C1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
B [auth E]Pantoate_ligasee5im4E1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)
APantoate_ligasee5im4A1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: Pantoate_ligaseECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
Z [auth b]3.40.50.510 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Phosphotransferase system, mannose-type IIA componentCATH (4.3.0)
T3.40.50.510 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Phosphotransferase system, mannose-type IIA componentCATH (4.3.0)
S [auth R]3.40.50.510 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Phosphotransferase system, mannose-type IIA componentCATH (4.3.0)
R [auth S]3.40.50.510 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Phosphotransferase system, mannose-type IIA componentCATH (4.3.0)
Q3.40.50.510 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Phosphotransferase system, mannose-type IIA componentCATH (4.3.0)
P3.40.50.510 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Phosphotransferase system, mannose-type IIA componentCATH (4.3.0)
NA [auth n]3.40.50.510 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Phosphotransferase system, mannose-type IIA componentCATH (4.3.0)
MA [auth l]3.40.50.510 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Phosphotransferase system, mannose-type IIA componentCATH (4.3.0)
LA [auth m]3.40.50.510 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Phosphotransferase system, mannose-type IIA componentCATH (4.3.0)
KA [auth k]3.40.50.510 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Phosphotransferase system, mannose-type IIA componentCATH (4.3.0)
JA [auth j]3.40.50.510 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Phosphotransferase system, mannose-type IIA componentCATH (4.3.0)
J3.40.50.510 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Phosphotransferase system, mannose-type IIA componentCATH (4.3.0)
I3.40.50.510 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Phosphotransferase system, mannose-type IIA componentCATH (4.3.0)
H [auth G]3.40.50.510 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Phosphotransferase system, mannose-type IIA componentCATH (4.3.0)
G [auth H]3.40.50.510 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Phosphotransferase system, mannose-type IIA componentCATH (4.3.0)
F3.40.50.510 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Phosphotransferase system, mannose-type IIA componentCATH (4.3.0)
DA [auth a]3.40.50.510 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Phosphotransferase system, mannose-type IIA componentCATH (4.3.0)
CA [auth Z]3.40.50.510 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Phosphotransferase system, mannose-type IIA componentCATH (4.3.0)
BA [auth c]3.40.50.510 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Phosphotransferase system, mannose-type IIA componentCATH (4.3.0)
AA [auth d]3.40.50.510 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Phosphotransferase system, mannose-type IIA componentCATH (4.3.0)
Y3.40.50.960 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Lumazine/riboflavin synthaseCATH (4.3.0)
X [auth W]3.40.50.960 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Lumazine/riboflavin synthaseCATH (4.3.0)
W [auth X]3.40.50.960 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Lumazine/riboflavin synthaseCATH (4.3.0)
V3.40.50.960 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Lumazine/riboflavin synthaseCATH (4.3.0)
U3.40.50.960 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Lumazine/riboflavin synthaseCATH (4.3.0)
O3.40.50.960 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Lumazine/riboflavin synthaseCATH (4.3.0)
N [auth M]3.40.50.960 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Lumazine/riboflavin synthaseCATH (4.3.0)
M [auth N]3.40.50.960 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Lumazine/riboflavin synthaseCATH (4.3.0)
L3.40.50.960 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Lumazine/riboflavin synthaseCATH (4.3.0)
K3.40.50.960 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Lumazine/riboflavin synthaseCATH (4.3.0)
IA [auth i]3.40.50.960 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Lumazine/riboflavin synthaseCATH (4.3.0)
HA [auth g]3.40.50.960 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Lumazine/riboflavin synthaseCATH (4.3.0)
GA [auth h]3.40.50.960 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Lumazine/riboflavin synthaseCATH (4.3.0)
FA [auth f]3.40.50.960 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Lumazine/riboflavin synthaseCATH (4.3.0)
EA [auth e]3.40.50.960 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Lumazine/riboflavin synthaseCATH (4.3.0)
E [auth D]3.40.50.960 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Lumazine/riboflavin synthaseCATH (4.3.0)
D [auth B]3.40.50.960 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Lumazine/riboflavin synthaseCATH (4.3.0)
C3.40.50.960 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Lumazine/riboflavin synthaseCATH (4.3.0)
B [auth E]3.40.50.960 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Lumazine/riboflavin synthaseCATH (4.3.0)
A3.40.50.960 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Lumazine/riboflavin synthaseCATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF03610PTS system fructose IIA component (EIIA-man)PTS system fructose IIA component- Family
PF008856,7-dimethyl-8-ribityllumazine synthase (DMRL_synthase)6,7-dimethyl-8-ribityllumazine synthaseThis family includes the beta chain of 6,7-dimethyl-8- ribityllumazine synthase EC:2.5.1.9, an enzyme involved in riboflavin biosynthesis. The family also includes a subfamily of distant archaebacterial proteins that may also have the same function f ...This family includes the beta chain of 6,7-dimethyl-8- ribityllumazine synthase EC:2.5.1.9, an enzyme involved in riboflavin biosynthesis. The family also includes a subfamily of distant archaebacterial proteins that may also have the same function for example Swiss:O28856. The family contains a number of different subsets including a family of proteins comprising archaeal lumazine and riboflavin synthases, type I lumazine synthases, and the eubacterial type II lumazine synthases [1]. It has been established that lumazine synthase catalyses the penultimate step in the biosynthesis of riboflavin in plants and microorganisms. The type I lumazine synthases area active in pentameric or icosahedral quaternary assemblies, whereas the type II are decameric [2]. Brucella, a bacterial genus that causes brucellosis, and other Rhizobiales have an atypical riboflavin metabolic pathway. Brucella spp code for both a type-I and a type-II lumazine synthase, and it has been shown that at least one of these two has to be present in order for Brucella to be viable, showing that in the case of Brucella flavin metabolism is implicated in bacterial virulence [3].
Domain
PF008856,7-dimethyl-8-ribityllumazine synthase (DMRL_synthase)6,7-dimethyl-8-ribityllumazine synthaseThis family includes the beta chain of 6,7-dimethyl-8- ribityllumazine synthase EC:2.5.1.9, an enzyme involved in riboflavin biosynthesis. The family also includes a subfamily of distant archaebacterial proteins that may also have the same function f ...This family includes the beta chain of 6,7-dimethyl-8- ribityllumazine synthase EC:2.5.1.9, an enzyme involved in riboflavin biosynthesis. The family also includes a subfamily of distant archaebacterial proteins that may also have the same function for example Swiss:O28856. The family contains a number of different subsets including a family of proteins comprising archaeal lumazine and riboflavin synthases, type I lumazine synthases, and the eubacterial type II lumazine synthases [1]. It has been established that lumazine synthase catalyses the penultimate step in the biosynthesis of riboflavin in plants and microorganisms. The type I lumazine synthases area active in pentameric or icosahedral quaternary assemblies, whereas the type II are decameric [2]. Brucella, a bacterial genus that causes brucellosis, and other Rhizobiales have an atypical riboflavin metabolic pathway. Brucella spp code for both a type-I and a type-II lumazine synthase, and it has been shown that at least one of these two has to be present in order for Brucella to be viable, showing that in the case of Brucella flavin metabolism is implicated in bacterial virulence [3].
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
Phosphotransferase system, mannose/fructose-specific component IIA
6,7-dimethyl-8-ribityllumazine synthase

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR036662Phosphotransferase system, mannose-type IIA component superfamilyHomologous Superfamily
IPR004701Phosphotransferase system, mannose-type IIA componentDomain
IPR051471Bacterial PTS system sugar-specific componentsFamily
IPR033887PTS system mannose/sorbose specific IIA subunitDomain
IPR036467Lumazine/riboflavin synthase superfamilyHomologous Superfamily
IPR034964Lumazine synthaseFamily
IPR002180Lumazine/riboflavin synthaseFamily