1HO1

CRYSTAL STRUCTURE OF PYRIDOXINE 5'-PHOSPHATE SYNTHASE

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
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1ho1a_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Pyridoxine 5'-phosphate synthase	Pyridoxine 5'-phosphate synthase	Pyridoxine 5'-phosphate synthase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1ho1b_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Pyridoxine 5'-phosphate synthase	Pyridoxine 5'-phosphate synthase	Pyridoxine 5'-phosphate synthase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1ho1c_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Pyridoxine 5'-phosphate synthase	Pyridoxine 5'-phosphate synthase	Pyridoxine 5'-phosphate synthase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d1ho1d_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Pyridoxine 5'-phosphate synthase	Pyridoxine 5'-phosphate synthase	Pyridoxine 5'-phosphate synthase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Pyridoxine 5'-phosphate synthase	8032714	3000586	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Pyridoxine 5'-phosphate synthase	8032714	3000586	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Pyridoxine 5'-phosphate synthase	8032714	3000586	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Pyridoxine 5'-phosphate synthase	8032714	3000586	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)
A	PdxJ	e1ho1A1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PdxJ	ECOD (1.6)
B	PdxJ	e1ho1B1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PdxJ	ECOD (1.6)
C	PdxJ	e1ho1C1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PdxJ	ECOD (1.6)
D	PdxJ	e1ho1D1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PdxJ	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	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)
C	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF03740	Pyridoxal phosphate biosynthesis protein PdxJ (PdxJ)	Pyridoxal phosphate biosynthesis protein PdxJ	Members of this family belong to the PdxJ family that catalyses the condensation of 1-deoxy-d-xylulose-5-phosphate (DXP) and 1-amino-3-oxo-4-(phosphohydroxy)propan-2-one to form pyridoxine 5'-phosphate (PNP). This reaction is involved in de novo synt ...	Members of this family belong to the PdxJ family that catalyses the condensation of 1-deoxy-d-xylulose-5-phosphate (DXP) and 1-amino-3-oxo-4-(phosphohydroxy)propan-2-one to form pyridoxine 5'-phosphate (PNP). This reaction is involved in de novo synthesis of pyridoxine (vitamin B6) and pyridoxal phosphate [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	PYRIDOXINE 5'-PHOSPHATE SYNTHASE	transferase activity, transferring nitrogenous groups pyridoxine 5'-phosphate synthase activity transferase activity catalytic activity identical protein binding protein binding binding	vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process organic hydroxy compound metabolic process pyridine-containing compound biosynthetic process vitamin biosynthetic process pyridoxine biosynthetic process vitamin metabolic process pyridoxine metabolic process biosynthetic process organic hydroxy compound biosynthetic process pyridine-containing compound metabolic process metabolic process cellular process vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process organic hydroxy compound metabolic process pyridine-containing compound biosynthetic process vitamin biosynthetic process pyridoxine biosynthetic process vitamin metabolic process pyridoxine metabolic process biosynthetic process organic hydroxy compound biosynthetic process pyridine-containing compound metabolic process metabolic process cellular process vitamin B6 metabolic process small molecule metabolic process water-soluble vitamin metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR036130	Pyridoxine 5'-phosphate synthase	Homologous Superfamily
A, B, C, D	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A, B, C, D	IPR004569	Pyridoxal phosphate (active vitamin B6) biosynthesis PdxJ	Family

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	pyridoxine 5'-phosphate synthase M-CSA #243	Pyridoxine 5'-phosphate synthase (PdxJ) catalyses the complicated ring closure reaction between the two acyclic compounds 1-deoxy-D-xylulose-5-phosphate (DXP) and 3-amino-2-oxopropyl phosphate (AAP) to form pyridoxine 5'-phosphate (PNP) and inorganic phosphate. The product of the PdxJ reaction is then oxidised by PdxH to form pyridoxal 5'-phosphate (PLP). PLP is the active form of vitamin B6 (pyridoxine or pyridoxal), a versatile catalyst, acting as a coenzyme in a multitude of reactions, including decarboxylations, deaminations and transaminations.	Defined by 9 residues: ASN:A-8 [auth A-9]HIS:A-11 [auth A-12]HIS:A-44 [auth A-45]ARG:A-46 [auth A-47]ARG:A-50 [auth A-51]GLU:A-71 [auth A-72]THR:A-102 [auth A-103]GLU:A-152 [auth A-153]HIS:A-192 [auth A-193] Some residues are not modelled and lack atomic coordinates. Visualization is not available. Some residues are not modelled and lack atomic coordinates. Structure Motif searching is not available. EC: 2.6.99.2 (UniProt)

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.