1YJ5

Molecular architecture of mammalian polynucleotide kinase, a DNA repair enzyme

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	d1yj5a2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Nucleotide and nucleoside kinases	5' polynucleotide kinase-3' phosphatase, C-terminal domain	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d1yj5a1	Alpha and beta proteins (a/b)	HAD-like	HAD-like	phosphatase domain of polynucleotide kinase	5' polynucleotide kinase-3' phosphatase, middle domain	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d1yj5b2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Nucleotide and nucleoside kinases	5' polynucleotide kinase-3' phosphatase, C-terminal domain	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d1yj5b1	Alpha and beta proteins (a/b)	HAD-like	HAD-like	phosphatase domain of polynucleotide kinase	5' polynucleotide kinase-3' phosphatase, middle domain	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d1yj5c1	All beta proteins	SMAD/FHA domain	SMAD/FHA domain	FHA domain	Polynucleotide kinase 3'-phosphatase	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Polynucleotide kinase 3 phosphatase domain-like	8019131	4002989	SCOP2 (2022-06-29)
A	SCOP2 Family	Adenylate kinase-like	8019130	4004025	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	HAD-like	8019133	3001890	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	P-loop nucleotide/nucleoside kinase-like	8019137	3002021	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	HAD-like	8019133	3001890	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8019137	3002021	SCOP2B (2022-06-29)
C	SCOP2 Family	FHA domain	8019132	4002605	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	SMAD/FHA domain-like	8019135	3000137	SCOP2 (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	AAA_33	e1yj5A1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_33	ECOD (1.6)
A	PNK3P	e1yj5A2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: PNK3P	ECOD (1.6)
B	AAA_33	e1yj5B1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_33	ECOD (1.6)
B	PNK3P	e1yj5B2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: PNK3P	ECOD (1.6)
C	FHA_1	e1yj5C1	A: beta sandwiches	X: SMAD/FHA domain (From Topology)	H: SMAD/FHA domain (From Topology)	T: SMAD/FHA domain	F: FHA_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	2.60.200.20	Mainly Beta	Sandwich	Tumour Suppressor Smad4		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF13671	AAA domain (AAA_33)	AAA domain	This family of domains contain only a P-loop motif, that is characteristic of the AAA superfamily. Many of the proteins in this family are just short fragments so there is no Walker B motif.	Domain
A, B	PF08645	Polynucleotide kinase 3 phosphatase (PNK3P)	Polynucleotide kinase 3 phosphatase	-	Family
C	PF17913	FHA domain (FHA_2)	FHA domain	This entry represents a divergent FHA domain which in PNK binds to phosphorylated segment of XRCC1 [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	5' polynucleotide kinase-3' phosphatase catalytic domain	ubiquitin-like ligase-substrate adaptor activity enzyme-substrate adaptor activity protein-macromolecule adaptor activity molecular adaptor activity nucleobase-containing compound kinase activity polynucleotide 5'-hydroxyl-kinase activity kinase activity ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity transferase activity ATP-dependent polynucleotide 5'-hydroxyl-kinase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups binding ubiquitin-like ligase-substrate adaptor activity enzyme-substrate adaptor activity protein-macromolecule adaptor activity molecular adaptor activity nucleobase-containing compound kinase activity polynucleotide 5'-hydroxyl-kinase activity kinase activity ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity transferase activity ATP-dependent polynucleotide 5'-hydroxyl-kinase activity catalytic activity phosphotransferase activity, alcohol group as acceptor 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 organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding double-stranded DNA binding nucleic acid binding phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity polynucleotide 3'-phosphatase activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of cellular process regulation of double-strand break repair regulation of cellular response to stress positive regulation of biological process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of response to stimulus positive regulation of metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of cellular process regulation of double-strand break repair regulation of cellular response to stress positive regulation of biological process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of response to stimulus positive regulation of metabolic process organic substance metabolic process positive regulation of DNA repair regulation of response to stress positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of double-strand break repair via nonhomologous end joining DNA repair double-strand break repair regulation of biological process positive regulation of nucleobase-containing compound metabolic process positive regulation of double-strand break repair via nonhomologous end joining double-strand break repair via nonhomologous end joining biological regulation primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process positive regulation of double-strand break repair regulation of DNA repair organic cyclic compound metabolic process positive regulation of DNA metabolic process regulation of response to stimulus metabolic process macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process DNA ligation involved in DNA repair DNA ligation organonitrogen compound metabolic process protein polyubiquitination protein K63-linked ubiquitination protein ubiquitination macromolecule modification protein metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal positive regulation of organelle organization telomere organization regulation of DNA biosynthetic process positive regulation of macromolecule biosynthetic process RNA-templated DNA biosynthetic process telomere maintenance via telomere lengthening organic substance biosynthetic process positive regulation of telomere maintenance via telomere lengthening positive regulation of telomere maintenance cellular metabolic process regulation of cellular metabolic process regulation of chromosome organization regulation of telomere maintenance via telomere lengthening regulation of organelle organization positive regulation of chromosome organization telomere maintenance biosynthetic process positive regulation of telomere maintenance via telomerase organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic process DNA biosynthetic process regulation of telomere maintenance regulation of cellular component organization positive regulation of cellular component organization cellular biosynthetic process positive regulation of cellular metabolic process cellular component organization nucleic acid biosynthetic process positive regulation of biosynthetic process cellular component organization or biogenesis regulation of biosynthetic process telomere maintenance via telomerase chromosome organization positive regulation of DNA biosynthetic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process regulation of telomere maintenance via telomerase regulation of cellular biosynthetic process organelle organization positive regulation of cellular biosynthetic process phosphorylation phosphate-containing compound metabolic process phosphorus metabolic process response to oxidative stress positive regulation of telomere capping telomere capping regulation of telomere capping	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle nucleoplasm cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex SCF ubiquitin ligase complex transferase complex intracellular protein-containing complex site of double-strand break site of DNA damage chromosome
C	5' polynucleotide kinase-3' phosphatase FHA domain	ubiquitin-like ligase-substrate adaptor activity enzyme-substrate adaptor activity protein-macromolecule adaptor activity molecular adaptor activity nucleobase-containing compound kinase activity polynucleotide 5'-hydroxyl-kinase activity kinase activity ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity transferase activity ATP-dependent polynucleotide 5'-hydroxyl-kinase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups binding ubiquitin-like ligase-substrate adaptor activity enzyme-substrate adaptor activity protein-macromolecule adaptor activity molecular adaptor activity nucleobase-containing compound kinase activity polynucleotide 5'-hydroxyl-kinase activity kinase activity ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity transferase activity ATP-dependent polynucleotide 5'-hydroxyl-kinase activity catalytic activity phosphotransferase activity, alcohol group as acceptor 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 organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding double-stranded DNA binding nucleic acid binding phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity polynucleotide 3'-phosphatase activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of cellular process regulation of double-strand break repair regulation of cellular response to stress positive regulation of biological process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of response to stimulus positive regulation of metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of cellular process regulation of double-strand break repair regulation of cellular response to stress positive regulation of biological process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of response to stimulus positive regulation of metabolic process organic substance metabolic process positive regulation of DNA repair regulation of response to stress positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of double-strand break repair via nonhomologous end joining DNA repair double-strand break repair regulation of biological process positive regulation of nucleobase-containing compound metabolic process positive regulation of double-strand break repair via nonhomologous end joining double-strand break repair via nonhomologous end joining biological regulation primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process positive regulation of double-strand break repair regulation of DNA repair organic cyclic compound metabolic process positive regulation of DNA metabolic process regulation of response to stimulus metabolic process macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process DNA ligation involved in DNA repair DNA ligation organonitrogen compound metabolic process protein polyubiquitination protein K63-linked ubiquitination protein ubiquitination macromolecule modification protein metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal positive regulation of organelle organization telomere organization regulation of DNA biosynthetic process positive regulation of macromolecule biosynthetic process RNA-templated DNA biosynthetic process telomere maintenance via telomere lengthening organic substance biosynthetic process positive regulation of telomere maintenance via telomere lengthening positive regulation of telomere maintenance cellular metabolic process regulation of cellular metabolic process regulation of chromosome organization regulation of telomere maintenance via telomere lengthening regulation of organelle organization positive regulation of chromosome organization telomere maintenance biosynthetic process positive regulation of telomere maintenance via telomerase organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic process DNA biosynthetic process regulation of telomere maintenance regulation of cellular component organization positive regulation of cellular component organization cellular biosynthetic process positive regulation of cellular metabolic process cellular component organization nucleic acid biosynthetic process positive regulation of biosynthetic process cellular component organization or biogenesis regulation of biosynthetic process telomere maintenance via telomerase chromosome organization positive regulation of DNA biosynthetic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process regulation of telomere maintenance via telomerase regulation of cellular biosynthetic process organelle organization positive regulation of cellular biosynthetic process phosphorylation phosphate-containing compound metabolic process phosphorus metabolic process response to oxidative stress positive regulation of telomere capping telomere capping regulation of telomere capping	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle nucleoplasm cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex SCF ubiquitin ligase complex transferase complex intracellular protein-containing complex site of double-strand break site of DNA damage chromosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR006551	Polynucleotide 3'-phosphatase	Domain
A, B	IPR041388	PNK, FHA domain	Domain
A, B	IPR006550	Bifunctional polynucleotide phosphatase/kinase PNKP	Family
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B	IPR006549	HAD-superfamily hydrolase,subfamily IIIA	Domain
A, B	IPR023214	HAD superfamily	Homologous Superfamily
A, B	IPR008984	SMAD/FHA domain superfamily	Homologous Superfamily
A, B	IPR013954	Polynucleotide kinase 3 phosphatase	Family
A, B	IPR036412	HAD-like superfamily	Homologous Superfamily
C	IPR006551	Polynucleotide 3'-phosphatase	Domain
C	IPR041388	PNK, FHA domain	Domain
C	IPR006550	Bifunctional polynucleotide phosphatase/kinase PNKP	Family
C	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
C	IPR006549	HAD-superfamily hydrolase,subfamily IIIA	Domain
C	IPR023214	HAD superfamily	Homologous Superfamily
C	IPR008984	SMAD/FHA domain superfamily	Homologous Superfamily
C	IPR013954	Polynucleotide kinase 3 phosphatase	Family
C	IPR036412	HAD-like superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.