3N9B | pdb_00003n9b

Crystal Structure of the P. aeruginosa LigD phosphoesterase domain

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
B	SCOP2 Family	LigD phosphoesterase-like	8048543	4006141	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	NHEJ phosphoesterases-like	8092049	3002555	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	NHEJ phosphoesterases-like	8092049	3002555	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)
B	LigD_N	e3n9bB1	A: beta barrels	X: Oncogene product-like	H: LigD phosphoesterase domain (From Topology)	T: LigD phosphoesterase domain	F: LigD_N	ECOD (1.6)
A	LigD_N	e3n9bA1	A: beta barrels	X: Oncogene product-like	H: LigD phosphoesterase domain (From Topology)	T: LigD phosphoesterase domain	F: LigD_N	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF13298	DNA Ligase D 3'-phosphoesterase domain (LigD_N)	DNA Ligase D 3'-phosphoesterase domain	This entry represents a 3'-phosphoesterase domain of a multidomain, multifunctional DNA ligase, LigD, which is involved along with bacterial Ku protein in non-homologous end joining [1]- the less common of two general mechanisms of repairing doubl ...	This entry represents a 3'-phosphoesterase domain of a multidomain, multifunctional DNA ligase, LigD, which is involved along with bacterial Ku protein in non-homologous end joining [1]- the less common of two general mechanisms of repairing double-stranded breaks in DNA sequences.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Probable ATP-dependent DNA ligase	catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding hydrolase activity, acting on ester bonds nuclease activity catalytic activity, acting on RNA RNA exonuclease activity RNA nuclease activity hydrolase activity exonuclease activity ligase activity, forming phosphoric ester bonds DNA ligase (ATP) activity DNA ligase activity ligase activity cation binding metal ion binding	primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process DNA biosynthetic process cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process DNA biosynthetic process cellular response to stimulus response to stimulus cellular response to stress DNA damage response response to stress DNA repair DNA recombination	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR033651	LigD polymerase domain, PaeLigD-type	Domain
A, B	IPR014143	DNA ligase D	Domain
A, B	IPR052171	Non-homologous end joining protein LigD	Family
A, B	IPR012310	DNA ligase, ATP-dependent, central	Domain
A, B	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A, B	IPR014144	DNA ligase D, 3'-phosphoesterase domain	Domain
A, B	IPR012309	DNA ligase, ATP-dependent, C-terminal	Domain
A, B	IPR014146	DNA ligase D, ligase domain	Domain
A, B	IPR014145	DNA ligase D, polymerase 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.