1M5W

1.96 A Crystal Structure of Pyridoxine 5'-Phosphate Synthase in Complex with 1-deoxy-D-xylulose phosphate

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)
D	d1m5wd_	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)
H	d1m5wh_	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)
A	d1m5wa_	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	d1m5wb_	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	d1m5wc_	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)
E	d1m5we_	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)
F	d1m5wf_	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)
G	d1m5wg_	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)
D	SCOP2B Superfamily	Pyridoxine 5'-phosphate synthase	8032714	3000586	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Pyridoxine 5'-phosphate synthase	8032714	3000586	SCOP2B (2022-06-29)
A	SCOP2 Family	Pyridoxine 5'-phosphate synthase	8020334	4003313	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Pyridoxine 5'-phosphate synthase	8032714	3000586	SCOP2 (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)
E	SCOP2B Superfamily	Pyridoxine 5'-phosphate synthase	8032714	3000586	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Pyridoxine 5'-phosphate synthase	8032714	3000586	SCOP2B (2022-06-29)
G	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)
D	PdxJ	e1m5wD1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PdxJ	ECOD (1.6)
H	PdxJ	e1m5wH1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PdxJ	ECOD (1.6)
A	PdxJ	e1m5wA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PdxJ	ECOD (1.6)
B	PdxJ	e1m5wB1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PdxJ	ECOD (1.6)
C	PdxJ	e1m5wC1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PdxJ	ECOD (1.6)
E	PdxJ	e1m5wE1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PdxJ	ECOD (1.6)
F	PdxJ	e1m5wF1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PdxJ	ECOD (1.6)
G	PdxJ	e1m5wG1	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)
D	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
H	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)
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)
E	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
F	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
G	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, G, H	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, E A, B, C, D, E, F, G, H	Pyridoxal phosphate biosynthetic protein pdxJ	transferase activity, transferring nitrogenous groups pyridoxine 5'-phosphate synthase activity transferase activity catalytic activity identical protein binding protein binding binding	cellular biosynthetic process organic hydroxy compound metabolic process organonitrogen compound biosynthetic process vitamin biosynthetic process pyridoxine biosynthetic process organic substance metabolic process organic substance biosynthetic process pyridine-containing compound metabolic process small molecule metabolic process water-soluble vitamin metabolic process vitamin B6 biosynthetic process organonitrogen compound metabolic process water-soluble vitamin biosynthetic process small molecule biosynthetic process cellular biosynthetic process organic hydroxy compound metabolic process organonitrogen compound biosynthetic process vitamin biosynthetic process pyridoxine biosynthetic process organic substance metabolic process organic substance biosynthetic process pyridine-containing compound metabolic process small molecule metabolic process water-soluble vitamin metabolic process vitamin B6 biosynthetic process organonitrogen compound metabolic process water-soluble vitamin biosynthetic process small molecule biosynthetic process cellular metabolic process pyridine-containing compound biosynthetic process vitamin metabolic process organic cyclic compound metabolic process pyridoxine metabolic process biosynthetic process organic hydroxy compound biosynthetic process organic cyclic compound biosynthetic process metabolic process vitamin B6 metabolic process cellular process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.