2PAR | pdb_00002par

Crystal structure of the 5'-deoxynucleotidase YfbR mutant E72A complexed with Co(2+) and TMP

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	d2para_	All alpha proteins	HD-domain/PDEase-like	HD-domain/PDEase-like	HD domain	5'-nucleotidase YfbR	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d2parb_	All alpha proteins	HD-domain/PDEase-like	HD-domain/PDEase-like	HD domain	5'-nucleotidase YfbR	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	HD-domain/PDEase-like	8043853	3000943	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	HD-domain/PDEase-like	8043853	3000943	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	Me-amine-dh_H	e2parA1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Me-amine-dh_H	ECOD (develop294)
B	Me-amine-dh_H	e2parB1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Me-amine-dh_H	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.3210.10	Mainly Alpha	Orthogonal Bundle	Hypothetical protein af1432	Hypothetical protein af1432	CATH (4.3.0)
B	1.10.3210.10	Mainly Alpha	Orthogonal Bundle	Hypothetical protein af1432	Hypothetical protein af1432	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01966	HD domain (HD)	HD domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	5'-deoxynucleotidase YfbR	cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding phosphoric ester hydrolase activity 5'-deoxynucleotidase activity hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity catalytic activity nucleoside phosphate binding cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding phosphoric ester hydrolase activity 5'-deoxynucleotidase activity hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity catalytic activity nucleoside phosphate binding nucleotide binding heterocyclic compound binding identical protein binding protein binding	pyrimidine deoxyribonucleotide metabolic process deoxyribose phosphate biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process pyrimidine deoxyribonucleoside monophosphate metabolic process nucleobase-containing compound metabolic process deoxyribonucleotide biosynthetic process pyrimidine deoxyribonucleotide biosynthetic process deoxyribonucleotide metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process deoxyribonucleoside monophosphate biosynthetic process small molecule metabolic process pyrimidine deoxyribonucleotide metabolic process deoxyribose phosphate biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process pyrimidine deoxyribonucleoside monophosphate metabolic process nucleobase-containing compound metabolic process deoxyribonucleotide biosynthetic process pyrimidine deoxyribonucleotide biosynthetic process deoxyribonucleotide metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process deoxyribonucleoside monophosphate biosynthetic process small molecule metabolic process pyrimidine deoxyribonucleoside monophosphate biosynthetic process pyrimidine-containing compound biosynthetic process phosphorus metabolic process nucleoside monophosphate metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process pyrimidine nucleoside monophosphate metabolic process pyrimidine-containing compound metabolic process 2'-deoxyribonucleotide metabolic process 2'-deoxyribonucleotide biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process nucleotide metabolic process dUMP biosynthetic process nucleoside monophosphate biosynthetic process dUMP metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process metabolic process cellular process pyrimidine nucleoside monophosphate biosynthetic process pyrimidine nucleotide biosynthetic process pyrimidine-containing compound salvage pyrimidine nucleotide salvage nucleotide salvage metabolic compound salvage pyrimidine deoxyribonucleotide salvage	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR003607	HD/PDEase domain	Domain
A, B	IPR022971	5'-deoxynucleotidase YfbR	Family
A, B	IPR006674	HD domain	Domain
A, B	IPR039356	5'-deoxynucleotidase YfbR/HDDC2	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.