2G07

X-ray structure of mouse pyrimidine 5'-nucleotidase type 1, phospho-enzyme intermediate analog with Beryllium fluoride

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)
B	d2g07b_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	Pyrimidine 5'-nucleotidase (UMPH-1)	Cytosolic 5'-nucleotidase III	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d2g07a_	Alpha and beta proteins (a/b)	HAD-like	HAD-like	Pyrimidine 5'-nucleotidase (UMPH-1)	Cytosolic 5'-nucleotidase III	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	HAD-like	8033545	3001890	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	HAD-like	8033545	3001890	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)
B	UMPH-1	e2g07B1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: UMPH-1	ECOD (1.6)
A	UMPH-1	e2g07A1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: UMPH-1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
B	1.10.150.340	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
A	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
A	1.10.150.340	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF05822	Pyrimidine 5'-nucleotidase (UMPH-1) (UMPH-1)	Pyrimidine 5'-nucleotidase (UMPH-1)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Cytosolic 5'-nucleotidase III	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding phosphoric ester hydrolase activity nucleotidase activity hydrolase activity, acting on ester bonds XMP 5'-nucleosidase activity phosphatase activity hydrolase activity 5'-nucleotidase activity catalytic activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding phosphoric ester hydrolase activity nucleotidase activity hydrolase activity, acting on ester bonds XMP 5'-nucleosidase activity phosphatase activity hydrolase activity 5'-nucleotidase activity catalytic activity nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding transferase activity	pyrimidine ribonucleotide catabolic process ribose phosphate metabolic process ribonucleotide catabolic process pyrimidine ribonucleoside monophosphate catabolic process CMP catabolic process catabolic process pyrimidine-containing compound catabolic process organophosphate catabolic process carbohydrate derivative metabolic process nucleoside phosphate catabolic process pyrimidine nucleotide metabolic process nucleobase-containing compound metabolic process pyrimidine nucleotide catabolic process ribonucleotide metabolic process ribonucleoside monophosphate metabolic process pyrimidine ribonucleotide catabolic process ribose phosphate metabolic process ribonucleotide catabolic process pyrimidine ribonucleoside monophosphate catabolic process CMP catabolic process catabolic process pyrimidine-containing compound catabolic process organophosphate catabolic process carbohydrate derivative metabolic process nucleoside phosphate catabolic process pyrimidine nucleotide metabolic process nucleobase-containing compound metabolic process pyrimidine nucleotide catabolic process ribonucleotide metabolic process ribonucleoside monophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process small molecule metabolic process ribonucleoside monophosphate catabolic process phosphorus metabolic process nucleoside monophosphate metabolic process pyrimidine ribonucleotide metabolic process nucleotide catabolic process pyrimidine nucleoside monophosphate catabolic process nucleoside phosphate metabolic process pyrimidine nucleoside monophosphate metabolic process carbohydrate derivative catabolic process pyrimidine-containing compound metabolic process pyrimidine ribonucleoside monophosphate metabolic process nucleoside monophosphate catabolic process primary metabolic process nucleotide metabolic process nucleobase-containing compound catabolic process CMP metabolic process organophosphate metabolic process metabolic process cellular process pyrimidine deoxyribonucleotide catabolic process pyrimidine deoxyribonucleoside monophosphate catabolic process deoxyribonucleoside monophosphate catabolic process deoxyribonucleotide catabolic process pyrimidine deoxyribonucleotide metabolic process deoxyribose phosphate catabolic process pyrimidine deoxyribonucleoside monophosphate metabolic process deoxyribonucleotide metabolic process dUMP catabolic process 2'-deoxyribonucleotide metabolic process deoxyribose phosphate metabolic process deoxyribonucleoside monophosphate metabolic process dUMP metabolic process dCMP catabolic process dCMP metabolic process dTMP catabolic process dTMP metabolic process glycosyl compound metabolic process nucleoside metabolic process purine-containing compound metabolic process adenosine metabolic process purine nucleoside metabolic process ribonucleoside metabolic process purine ribonucleoside metabolic process UMP metabolic process UMP catabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol nucleus membrane-enclosed lumen intracellular organelle lumen nuclear body nucleoplasm membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol nucleus membrane-enclosed lumen intracellular organelle lumen nuclear body nucleoplasm organelle lumen nuclear lumen endoplasmic reticulum endomembrane system

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR023214	HAD superfamily	Homologous Superfamily
A, B	IPR036412	HAD-like superfamily	Homologous Superfamily
A, B	IPR006434	Pyrimidine 5'-nucleotidase, eukaryotic	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.