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	Adenylate kinase-like	8019130	4004025	SCOP2 (2022-06-29)
A	SCOP2 Family	Polynucleotide kinase 3 phosphatase domain-like	8019131	4002989	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	P-loop nucleotide/nucleoside kinase-like	8019137	3002021	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	HAD-like	8019133	3001890	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	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 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 phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity catalytic activity polynucleotide 3'-phosphatase activity 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 phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process protein polyubiquitination primary metabolic process protein K63-linked ubiquitination protein ubiquitination macromolecule modification metabolic process protein metabolic process macromolecule metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process protein polyubiquitination primary metabolic process protein K63-linked ubiquitination protein ubiquitination macromolecule modification metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal double-strand break repair double-strand break repair via nonhomologous end joining DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA repair	intracellular organelle site of double-strand break cellular anatomical structure intracellular anatomical structure organelle membraneless organelle site of DNA damage intracellular membraneless organelle chromosome cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex SCF ubiquitin ligase complex intracellular organelle site of double-strand break cellular anatomical structure intracellular anatomical structure organelle membraneless organelle site of DNA damage intracellular membraneless organelle chromosome cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex SCF ubiquitin ligase complex transferase complex intracellular protein-containing complex membrane-bounded organelle nucleus intracellular membrane-bounded organelle
C	5' polynucleotide kinase-3' phosphatase FHA domain	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 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 phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity catalytic activity polynucleotide 3'-phosphatase activity 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 phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process protein polyubiquitination primary metabolic process protein K63-linked ubiquitination protein ubiquitination macromolecule modification metabolic process protein metabolic process macromolecule metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process protein polyubiquitination primary metabolic process protein K63-linked ubiquitination protein ubiquitination macromolecule modification metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal double-strand break repair double-strand break repair via nonhomologous end joining DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA repair	intracellular organelle site of double-strand break cellular anatomical structure intracellular anatomical structure organelle membraneless organelle site of DNA damage intracellular membraneless organelle chromosome cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex SCF ubiquitin ligase complex intracellular organelle site of double-strand break cellular anatomical structure intracellular anatomical structure organelle membraneless organelle site of DNA damage intracellular membraneless organelle chromosome cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex SCF ubiquitin ligase complex transferase complex intracellular protein-containing complex membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

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

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.