3ZVM | pdb_00003zvm

The structural basis for substrate recognition by mammalian polynucleotide kinase 3' phosphatase

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8019137	3002021	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	HAD-like	8019133	3001890	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	HAD-like	8019133	3001890	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8019137	3002021	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	Reo_sigma1	e3zvmB1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Reo_sigma1	ECOD (develop294)
A	Reo_sigma1	e3zvmA1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Reo_sigma1	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)

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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth E], D [auth F]	5'-D(GPTPCPAP*CP)-3'	-	-	-
A, B	BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE	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 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 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 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 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 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 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 regulation of telomere maintenance regulation of cellular component organization positive regulation of cellular component organization telomere organization cellular component organization cellular component organization or biogenesis positive regulation of telomere maintenance chromosome organization regulation of chromosome organization regulation of organelle organization positive regulation of chromosome organization telomere maintenance organelle organization response to oxidative stress	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen 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

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.