2I5R | pdb_00002i5r

Structure of small Toprim domain-containing protein from B. stearothermophilus in complex with Mg2+

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)
C	d2i5rc_	Alpha and beta proteins (a/b)	Toprim domain	Toprim domain	Toprim domain	automated matches	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
B	d2i5rb_	Alpha and beta proteins (a/b)	Toprim domain	Toprim domain	Toprim domain	automated matches	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
A	d2i5ra_	Alpha and beta proteins (a/b)	Toprim domain	Toprim domain	Toprim domain	automated matches	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Toprim domain-like	8040760	3000737	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Toprim domain-like	8040760	3000737	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Toprim domain-like	8040760	3000737	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)
C	TOP6A-Spo11_Toprim	e2i5rC1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: TOP6A-Spo11_Toprim	ECOD (develop294)
B	TOP6A-Spo11_Toprim	e2i5rB1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: TOP6A-Spo11_Toprim	ECOD (develop294)
A	TOP6A-Spo11_Toprim	e2i5rA1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: TOP6A-Spo11_Toprim	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.40.1360.10	Alpha Beta	3-Layer(aba) Sandwich	Dna Topoisomerase Vi A Subunit	Chain: A, domain 2	CATH (4.3.0)
B	3.40.1360.10	Alpha Beta	3-Layer(aba) Sandwich	Dna Topoisomerase Vi A Subunit	Chain: A, domain 2	CATH (4.3.0)
A	3.40.1360.10	Alpha Beta	3-Layer(aba) Sandwich	Dna Topoisomerase Vi A Subunit	Chain: A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF01751	Toprim domain (Toprim)	Toprim domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Toprim domain-containing protein	cation binding ion binding binding metal ion binding small molecule binding endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity ribonuclease M5 activity hydrolase activity, acting on ester bonds nuclease activity cation binding ion binding binding metal ion binding small molecule binding endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity ribonuclease M5 activity hydrolase activity, acting on ester bonds nuclease activity RNA endonuclease activity catalytic activity	ribonucleoprotein complex biogenesis RNA metabolic process primary metabolic process rRNA processing gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process biosynthetic process ribonucleoprotein complex biogenesis RNA metabolic process primary metabolic process rRNA processing gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process cellular component organization or biogenesis RNA processing rRNA metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR006171	TOPRIM domain	Domain
A, B, C	IPR034141	Ribonuclease M5-like, TOPRIM domain	Domain

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.

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