3NH2 | pdb_00003nh2

Crystal structure of RNase T in complex with a stem DNA with a 3' overhang

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	d3nh2a_	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	DnaQ-like 3'-5' exonuclease	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d3nh2f_	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	DnaQ-like 3'-5' exonuclease	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d3nh2e_	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	DnaQ-like 3'-5' exonuclease	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d3nh2b_	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	DnaQ-like 3'-5' exonuclease	automated matches	(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	SCOP2B Superfamily	Ribonuclease H-like	8088746	3000143	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ribonuclease H-like	8088746	3000143	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ribonuclease H-like	8088746	3000143	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribonuclease H-like	8088746	3000143	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	RNase_T	e3nh2A1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: RNase_T	ECOD (1.6)
F	RNase_T	e3nh2F1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: RNase_T	ECOD (1.6)
E	RNase_T	e3nh2E1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: RNase_T	ECOD (1.6)
B	RNase_T	e3nh2B1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: RNase_T	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
F	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
E	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
B	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, E, F	PF00929	Exonuclease (RNase_T)	Exonuclease	This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, E, F	Ribonuclease T	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding nucleic acid binding hydrolase activity, acting on ester bonds nuclease activity catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity hydrolase activity exonuclease activity catalytic activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding nucleic acid binding hydrolase activity, acting on ester bonds nuclease activity catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity hydrolase activity exonuclease activity catalytic activity identical protein binding protein binding protein homodimerization activity protein dimerization activity DNA exonuclease activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity single-stranded DNA exodeoxyribonuclease activity catalytic activity, acting on DNA 3'-5'-DNA exonuclease activity single-stranded DNA 3'-5' DNA exonuclease activity 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters RNA exonuclease activity RNA nuclease activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process response to light stimulus cellular response to radiation response to UV cellular response to environmental stimulus cellular response to light stimulus response to radiation response to abiotic stimulus cellular response to abiotic stimulus cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process response to light stimulus cellular response to radiation response to UV cellular response to environmental stimulus cellular response to light stimulus response to radiation response to abiotic stimulus cellular response to abiotic stimulus cellular response to UV regulation of cellular process negative regulation of biological process RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process negative regulation of cellular process RNA 3'-end processing RNA processing regulatory ncRNA 3'-end processing negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process regulatory ncRNA processing regulatory ncRNA-mediated gene silencing regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process ribonucleoprotein complex biogenesis rRNA processing cellular component biogenesis ribosome biogenesis rRNA 3'-end processing cellular component organization or biogenesis rRNA metabolic process DNA-templated DNA replication DNA-templated DNA replication maintenance of fidelity DNA replication proofreading DNA metabolic process DNA replication DNA repair tRNA metabolic process tRNA processing tRNA 3'-end processing	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol
C, D, G, H	5'-D(PTPTPAPCPAPAP*C)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, E, F	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, B, E, F	IPR005987	Ribonuclease T	Family
A, B, E, F	IPR013520	Ribonuclease H-like domain	Domain
A, B, E, F	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily

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.