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)
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)
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)
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)
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)
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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
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)
D	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)
G	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)
F	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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
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)
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)
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)
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)
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)
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)
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)

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)
D	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)
G	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)
F	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)

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	vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process cellular biosynthetic process organic hydroxy compound metabolic process cellular 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 vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process cellular biosynthetic process organic hydroxy compound metabolic process cellular 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 vitamin B6 metabolic process small molecule metabolic process cellular process water-soluble vitamin metabolic 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 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.