3NH1

Crystal structure of RNase T in complex with a preferred ssDNA (TAGG) with two Mg in the active site

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	d3nh1a_	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	d3nh1b_	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)
C	d3nh1c_	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)
D	d3nh1d_	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	SCOP2 Family	DnaQ-like 3'-5' exonuclease	8088745	4000547	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ribonuclease H-like	8088746	3000143	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Ribonuclease H-like	8088746	3000143	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribonuclease H-like	8088746	3000143	SCOP2B (2022-06-29)
D	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	e3nh1A1	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	e3nh1B1	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)
C	RNase_T	e3nh1C1	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)
D	RNase_T	e3nh1D1	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)
B	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
C	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
D	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, C, D	PF00929	Exonuclease (RNase_T)	Exonuclease	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Ribonuclease T	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding organic cyclic compound binding nucleic acid binding nuclease activity hydrolase activity, acting on ester bonds 3'-5' exonuclease activity hydrolase activity exonuclease activity catalytic activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding organic cyclic compound binding nucleic acid binding nuclease activity hydrolase activity, acting on ester bonds 3'-5' exonuclease activity hydrolase activity exonuclease activity catalytic activity identical protein binding protein binding protein homodimerization activity protein dimerization activity DNA exonuclease activity catalytic activity, acting on a nucleic acid DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters 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 regulation of cellular process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process nucleobase-containing compound metabolic process organic substance metabolic process organic substance biosynthetic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of cellular process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process nucleobase-containing compound metabolic process organic substance metabolic process organic substance 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 cellular metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process nucleic acid metabolic process regulatory ncRNA processing regulatory ncRNA-mediated gene silencing regulation of cellular biosynthetic process regulation of gene expression organic cyclic compound metabolic process 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 cellular component organization or biogenesis rRNA metabolic process ncRNA metabolic process nucleic acid catabolic process rRNA 3'-end processing 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	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol
E, F, G, H	5'-D(TPTPAPTPAPGP*G)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, B, C, D	IPR005987	Ribonuclease T	Family
A, B, C, D	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A, B, C, D	IPR013520	Exonuclease, RNase T/DNA polymerase III	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.