9CCA | pdb_00009cca

Cryo-EM structure of a designed pyridoxal phosphate (PLP) synthase fused to a designed circumsporozoite protein antigen from Plasmodium falciparum (CSP-P1-CSP and CSP-P2-CSP)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
X	SCOP2B Superfamily	Class I glutamine amidotransferase-like	8036862	3001405	SCOP2B (2022-06-29)
W	SCOP2B Superfamily	Class I glutamine amidotransferase-like	8036862	3001405	SCOP2B (2022-06-29)
V	SCOP2B Superfamily	Class I glutamine amidotransferase-like	8036862	3001405	SCOP2B (2022-06-29)
U	SCOP2B Superfamily	Class I glutamine amidotransferase-like	8036862	3001405	SCOP2B (2022-06-29)
T	SCOP2B Superfamily	Class I glutamine amidotransferase-like	8036862	3001405	SCOP2B (2022-06-29)
S	SCOP2B Superfamily	Class I glutamine amidotransferase-like	8036862	3001405	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Class I glutamine amidotransferase-like	8036862	3001405	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Class I glutamine amidotransferase-like	8036862	3001405	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Class I glutamine amidotransferase-like	8036862	3001405	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Class I glutamine amidotransferase-like	8036862	3001405	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Class I glutamine amidotransferase-like	8036862	3001405	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Class I glutamine amidotransferase-like	8036862	3001405	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
G, H, I, J, K G, H, I, J, K, L, S, T, U, V, W, X	PF01174	SNO glutamine amidotransferase family (SNO)	SNO glutamine amidotransferase family	This family and its amidotransferase domain was first described in [1]. It is predicted that members of this family are involved in the pyridoxine biosynthetic pathway, based on the proximity and co-regulation of the corresponding genes and physical ...	This family and its amidotransferase domain was first described in [1]. It is predicted that members of this family are involved in the pyridoxine biosynthetic pathway, based on the proximity and co-regulation of the corresponding genes and physical interaction between the members of Pfam:PF01174 and Pfam:PF01680 [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, M, N, O, P, Q, R	Circumsporozoite protein,Pyridoxal 5'-phosphate synthase subunit Pdx1	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides glutaminase activity hydrolase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds amine-lyase activity lyase activity pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity carbon-nitrogen lyase activity identical protein binding protein binding binding host cell surface binding heparan sulfate proteoglycan binding hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides glutaminase activity hydrolase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds amine-lyase activity lyase activity pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity carbon-nitrogen lyase activity identical protein binding protein binding binding host cell surface binding heparan sulfate proteoglycan binding proteoglycan binding carbohydrate derivative binding	vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process pyridine-containing compound biosynthetic process vitamin biosynthetic process aldehyde biosynthetic process aldehyde metabolic process vitamin metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process pyridoxal phosphate biosynthetic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process pyridine-containing compound biosynthetic process vitamin biosynthetic process aldehyde biosynthetic process aldehyde metabolic process vitamin metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process pyridoxal phosphate biosynthetic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process metabolic process cellular process vitamin B6 metabolic process small molecule metabolic process phosphorus metabolic process pyridoxal phosphate metabolic process response to oxidative stress response to singlet oxygen response to stimulus response to stress response to chemical response to oxygen-containing compound response to reactive oxygen species pyridoxine biosynthetic process pyridoxine metabolic process amino acid metabolic process primary metabolic process biological process involved in interspecies interaction between organisms symbiont entry into host biological process involved in interaction with host biological process involved in symbiotic interaction symbiont entry into host cell viral process viral life cycle entry into host cell by a symbiont-containing vacuole	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell surface membrane side of membrane cell periphery plasma membrane
G, H, I, J, K G, H, I, J, K, L, S, T, U, V, W, X	Circumsporozoite protein,Pyridoxal 5'-phosphate synthase subunit PDX2	host cell surface binding binding protein binding heparan sulfate proteoglycan binding proteoglycan binding carbohydrate derivative binding hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides glutaminase activity hydrolase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds amine-lyase activity lyase activity pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity host cell surface binding binding protein binding heparan sulfate proteoglycan binding proteoglycan binding carbohydrate derivative binding hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides glutaminase activity hydrolase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds amine-lyase activity lyase activity pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity carbon-nitrogen lyase activity	biological process involved in interspecies interaction between organisms symbiont entry into host biological process involved in interaction with host biological process involved in symbiotic interaction symbiont entry into host cell viral process viral life cycle entry into host cell by a symbiont-containing vacuole response to oxidative stress response to singlet oxygen response to stimulus response to stress response to chemical response to oxygen-containing compound biological process involved in interspecies interaction between organisms symbiont entry into host biological process involved in interaction with host biological process involved in symbiotic interaction symbiont entry into host cell viral process viral life cycle entry into host cell by a symbiont-containing vacuole response to oxidative stress response to singlet oxygen response to stimulus response to stress response to chemical response to oxygen-containing compound response to reactive oxygen species vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process pyridine-containing compound biosynthetic process vitamin biosynthetic process vitamin metabolic process biosynthetic process pyridine-containing compound metabolic process vitamin B6 metabolic process metabolic process cellular process small molecule metabolic process aldehyde biosynthetic process aldehyde metabolic process organophosphate metabolic process organophosphate biosynthetic process pyridoxal phosphate biosynthetic process phosphate-containing compound metabolic process phosphorus metabolic process pyridoxal phosphate metabolic process pyridoxine metabolic process	cell surface cellular anatomical structure membrane side of membrane cell periphery plasma membrane intracellular anatomical structure cytoplasm cytosol protein-containing complex catalytic complex glutaminase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, M, N, O, P, Q, R	IPR001852	Pyridoxal 5'-phosphate synthase subunit PdxS/SNZ	Family
A, B, C, D, E A, B, C, D, E, F, M, N, O, P, Q, R	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, M, N, O, P, Q, R	IPR033755	PdxS/SNZ N-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F, M, N, O, P, Q, R	IPR011060	Ribulose-phosphate binding barrel	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, M, N, O, P, Q, R	IPR000884	Thrombospondin type-1 (TSP1) repeat	Repeat
A, B, C, D, E A, B, C, D, E, F, M, N, O, P, Q, R	IPR003067	Plasmodium circumsporozoite protein	Family
A, B, C, D, E A, B, C, D, E, F, M, N, O, P, Q, R	IPR051860	Plasmodium Circumsporozoite Invasion Protein	Family
A, B, C, D, E A, B, C, D, E, F, M, N, O, P, Q, R	IPR036383	Thrombospondin type-1 repeat superfamily	Homologous Superfamily
G, H, I, J, K G, H, I, J, K, L, S, T, U, V, W, X	IPR000884	Thrombospondin type-1 (TSP1) repeat	Repeat
G, H, I, J, K G, H, I, J, K, L, S, T, U, V, W, X	IPR003067	Plasmodium circumsporozoite protein	Family
G, H, I, J, K G, H, I, J, K, L, S, T, U, V, W, X	IPR051860	Plasmodium Circumsporozoite Invasion Protein	Family
G, H, I, J, K G, H, I, J, K, L, S, T, U, V, W, X	IPR036383	Thrombospondin type-1 repeat superfamily	Homologous Superfamily
G, H, I, J, K G, H, I, J, K, L, S, T, U, V, W, X	IPR029062	Class I glutamine amidotransferase-like	Homologous Superfamily
G, H, I, J, K G, H, I, J, K, L, S, T, U, V, W, X	IPR002161	Pyridoxal 5'-phosphate synthase subunit PdxT/SNO	Family
G, H, I, J, K G, H, I, J, K, L, S, T, U, V, W, X	IPR021196	PdxT/SNO family, conserved site	Conserved Site

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.