2FAQ | pdb_00002faq

Crystal Structure of Pseudomonas aeruginosa LigD polymerase domain with ATP and Manganese

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	SH3_9	e2faqB1	A: alpha bundles	X: Lipocalins/Streptavidin	H: SAM/DNA-glycosylase	T: SAM domain-like	F: SH3_9	ECOD (develop294)
A		e2faqA2	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F:	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.90.920.10	Alpha Beta	Alpha-Beta Complex	DNA primase, PRIM domain	DNA primase, PRIM domain	CATH (4.3.0)
A	3.90.920.10	Alpha Beta	Alpha-Beta Complex	DNA primase, PRIM domain	DNA primase, PRIM domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF21686	LigD, primase-polymerase domain (LigD_Prim-Pol)	LigD, primase-polymerase domain	This entry represents the primase-polymerase domain (Prim-Pol) of bacterial LigD proteins, such as LigD from Pseudomonas aeruginosa and Mycobacterium tuberculosis. LigD, together with Ku protein, is required for nonhomologous end-joining (NHEJ)-media ...	This entry represents the primase-polymerase domain (Prim-Pol) of bacterial LigD proteins, such as LigD from Pseudomonas aeruginosa and Mycobacterium tuberculosis. LigD, together with Ku protein, is required for nonhomologous end-joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). This domain belongs to the archaeal/eukaryal primase (AEP) superfamily and mediates several nucleotidyl transferase activities, including DNA-dependent RNA primase, terminal transferase and DNA-dependent DNA/RNA gap-filling polymerase activities [1-5].	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 DNA-templated DNA replication DNA replication, synthesis of primer 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 DNA-templated DNA replication DNA replication, synthesis of primer RNA metabolic process RNA biosynthetic process DNA replication DNA recombination cellular response to stimulus double-strand break repair response to stimulus double-strand break repair via nonhomologous end joining cellular response to stress DNA damage response response to stress DNA repair	-

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.