4PE8 | pdb_00004pe8

Crystal structure of TatD in complex with trinucleotide DNA

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Metallo-dependent hydrolases	8033933	3000428	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	Pribosyltran	e4pe8A1	A: a/b three-layered sandwiches	X: Middle and GTPase effector domains in dynamin-related proteins	H: Middle and GTPase effector domains in dynamin-related proteins	T: Middle and GTPase effector domains in dynamin-related proteins	F: Pribosyltran	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.20.20.140	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Metal-dependent hydrolases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01026	TatD related DNase (TatD_DNase)	TatD related DNase	This family of proteins are related to a large superfamily of metalloenzymes [1]. TatD, a member of this family has been shown experimentally to be a DNase enzyme.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	DNA (5'-D(GPCP*T)-3')	-	-	-
A	Tat-linked quality control protein TatD	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding catalytic activity, acting on DNA nuclease activity catalytic activity, acting on a nucleic acid catalytic activity DNA nuclease activity DNA exonuclease activity 3'-5' exonuclease activity hydrolase activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding catalytic activity, acting on DNA nuclease activity catalytic activity, acting on a nucleic acid catalytic activity DNA nuclease activity DNA exonuclease activity 3'-5' exonuclease activity hydrolase activity DNA exonuclease activity, producing 5'-phosphomonoesters single-stranded DNA exodeoxyribonuclease activity hydrolase activity, acting on ester bonds 3'-5'-DNA exonuclease activity 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	response to hydrogen peroxide response to oxidative stress response to stimulus response to stress response to chemical response to oxygen-containing compound response to reactive oxygen species	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR018228	Deoxyribonuclease, TatD-related, conserved site	Conserved Site
A	IPR032466	Metal-dependent hydrolase	Homologous Superfamily
A	IPR050891	TatD-type Metallo-dependent Hydrolase	Family
A	IPR001130	3'-5' ssDNA/RNA exonuclease TatD-like	Family
A	IPR024918	3'-5' ssDNA/RNA exonuclease TatD	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.