Annotations: 2NV1

Structure of the synthase subunit Pdx1 (YaaD) of PLP synthase from Bacillus subtilis

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)
F	d2nv1f_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	PdxS-like	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
E	d2nv1e_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	PdxS-like	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
D	d2nv1d_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	PdxS-like	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
C	d2nv1c_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	PdxS-like	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d2nv1b_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	PdxS-like	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
A	d2nv1a_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	PdxS-like	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8085956	3000216	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8085956	3000216	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8085956	3000216	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8085956	3000216	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8085956	3000216	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8085956	3000216	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)
F	ACR_tran	e2nv1F1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: ACR_tran	ECOD (v295.2)
E	ACR_tran	e2nv1E1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: ACR_tran	ECOD (v295.2)
D	ACR_tran	e2nv1D1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: ACR_tran	ECOD (v295.2)
C	ACR_tran	e2nv1C1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: ACR_tran	ECOD (v295.2)
B	ACR_tran	e2nv1B1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: ACR_tran	ECOD (v295.2)
A	Homeodomain	e2nv1A1	A: alpha arrays	X: Globin-like	H: Globin-like	T: Globin-like	F: Homeodomain	ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
E	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
D	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
C	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
B	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
A	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF01680	SOR/SNZ family (SOR_SNZ)	SOR/SNZ family	Members of this family are enzymes involved in a new pathway of pyridoxine/pyridoxal 5-phosphate biosynthesis [1]. This family was formerly known as UPF0019.	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	Pyridoxal biosynthesis lyase pdxS	amine-lyase activity lyase activity catalytic activity carbon-nitrogen lyase activity identical protein binding protein binding binding pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity	vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process pyridine-containing compound biosynthetic process vitamin biosynthetic process pyridoxine biosynthetic process vitamin metabolic process pyridoxine metabolic process biosynthetic process pyridine-containing compound metabolic process vitamin B6 metabolic process metabolic process cellular process small molecule metabolic process vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process pyridine-containing compound biosynthetic process vitamin biosynthetic process pyridoxine biosynthetic process vitamin metabolic process pyridoxine metabolic process biosynthetic process pyridine-containing compound metabolic process vitamin B6 metabolic process metabolic process cellular process small molecule metabolic process pyridoxal 5'-phosphate biosynthetic process aldehyde biosynthetic process aldehyde metabolic process organophosphate metabolic process organophosphate biosynthetic process pyridoxal 5'-phosphate metabolic process phosphorus metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR011060	Ribulose-phosphate binding barrel	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR001852	Pyridoxal 5'-phosphate synthase subunit PdxS/SNZ	Family
A, B, C, D, E A, B, C, D, E, F	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR033755	PdxS/SNZ N-terminal domain	Domain