3PKY | pdb_00003pky

Polymerase Domain from Mycobacterium tuberculosis Ligase D in complex with DNA, UTP 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		e3pkyB2	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F:	ECOD (v294.1)
A	CHS5_N	e3pkyA1	A: a/b three-layered sandwiches	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: CHS5_N	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.70.3300	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
A	3.30.70.3300	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		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	Putative DNA ligase-like protein	ligase activity, forming phosphoric ester bonds catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid catalytic activity DNA ligase activity ligase activity binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding DNA ligase (ATP) activity DNA exonuclease activity 3'-5' exonuclease activity ligase activity, forming phosphoric ester bonds catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid catalytic activity DNA ligase activity ligase activity binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding DNA ligase (ATP) activity DNA exonuclease activity 3'-5' exonuclease activity hydrolase activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity single-stranded DNA exodeoxyribonuclease activity nuclease activity hydrolase activity, acting on ester bonds 3'-5'-DNA exonuclease activity exonuclease activity single-stranded DNA 3'-5' DNA exonuclease activity cation binding manganese ion binding transition metal ion binding ion binding metal ion binding DNA-directed DNA polymerase activity DNA polymerase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups magnesium ion binding adenyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding carbohydrate derivative binding ribonucleotide binding DNA binding nucleic acid binding DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA RNA polymerase activity	DNA-templated DNA replication DNA replication, synthesis of primer RNA metabolic process primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA replication biosynthetic process metabolic process DNA-templated DNA replication DNA replication, synthesis of primer RNA metabolic process primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA replication biosynthetic process metabolic process cellular process macromolecule metabolic process DNA recombination cellular response to stimulus double-strand break repair response to stimulus cellular response to stress DNA damage response response to stress DNA repair double-strand break repair via nonhomologous end joining	cell periphery cellular anatomical structure plasma membrane membrane
C	DNA 5'-D(PGPCPGPGP*C)-3'	-	-	-
D	DNA 5'-D(GCPCPGPCPAPAPCPGPCPAPCP*G)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR052171	Non-homologous end joining protein LigD	Family
A, B	IPR012310	DNA ligase, ATP-dependent, central	Domain
A, B	IPR014146	DNA ligase D, ligase domain	Domain
A, B	IPR014145	DNA ligase D, polymerase domain	Domain
A, B	IPR033649	LigD polymerase domain, MtLigD-type	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

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.