3H8S | pdb_00003h8s

Structure of D19N T4 RNase H in the presence of divalent magnesium

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	d3h8sa2	All alpha proteins	SAM domain-like	5' to 3' exonuclease, C-terminal subdomain	5' to 3' exonuclease, C-terminal subdomain	T4 RNase H	Bacteriophage T4 (Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
A	d3h8sa1	Alpha and beta proteins (a/b)	PIN domain-like	PIN domain-like	5' to 3' exonuclease catalytic domain	T4 RNase H	Bacteriophage T4 (Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	5' to 3' exonuclease, C-terminal subdomain	8037730	3000537	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PIN domain-like	8044457	3001041	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	PBP	e3h8sA2	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Immunoglobulin-related	T: PEBP-like	F: PBP	ECOD (v294.1)
A	APG6	e3h8sA3	A: a/b three-layered sandwiches	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.1010	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	5'-nuclease	CATH (4.3.0)
A	1.10.150.20	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	PF02739	5'-3' exonuclease, N-terminal resolvase-like domain (5_3_exonuc_N)	5'-3' exonuclease, N-terminal resolvase-like domain		Domain
A	PF09293	T4 RNase H, C terminal (RNaseH_C)	T4 RNase H, C terminal	Members of this family are found in T4 RNaseH ribonuclease, and adopt a SAM domain-like fold, consisting of a bundle of four/five helices. These residues may have a role in providing a docking site for other proteins or enzymes in the replication for ...	Members of this family are found in T4 RNaseH ribonuclease, and adopt a SAM domain-like fold, consisting of a bundle of four/five helices. These residues may have a role in providing a docking site for other proteins or enzymes in the replication fork [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Ribonuclease H	DNA binding binding nucleic acid binding 5'-flap endonuclease activity endonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity DNA nuclease activity DNA endonuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA nuclease activity flap endonuclease activity DNA endonuclease activity, producing 5'-phosphomonoesters DNA binding binding nucleic acid binding 5'-flap endonuclease activity endonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity DNA nuclease activity DNA endonuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA nuclease activity flap endonuclease activity DNA endonuclease activity, producing 5'-phosphomonoesters catalytic activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism catalytic activity, acting on RNA RNA-DNA hybrid ribonuclease activity RNA nuclease activity RNA endonuclease activity 5'-3' RNA exonuclease activity 5'-3' exonuclease activity RNA exonuclease activity, producing 5'-phosphomonoesters RNA exonuclease activity exonuclease activity	DNA-templated DNA replication lagging strand elongation primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA strand elongation DNA replication DNA replication, Okazaki fragment processing metabolic process cellular process DNA strand elongation involved in DNA replication macromolecule metabolic process DNA replication, removal of RNA primer DNA-templated DNA replication lagging strand elongation primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA strand elongation DNA replication DNA replication, Okazaki fragment processing metabolic process cellular process DNA strand elongation involved in DNA replication macromolecule metabolic process DNA replication, removal of RNA primer catabolic process RNA metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleic acid catabolic process RNA catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR002421	5'-3' exonuclease	Domain
A	IPR036276	Ribonuclease H, C-terminal	Domain
A	IPR038969	Flap endonuclease	Family
A	IPR029060	PIN-like domain superfamily	Homologous Superfamily
A	IPR036279	5'-3' exonuclease, C-terminal domain superfamily	Homologous Superfamily
A	IPR008918	Helix-hairpin-helix motif, class 2	Conserved Site
A	IPR020046	5'-3' exonuclease, alpha-helical arch, N-terminal	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.