2OCP

Crystal Structure of Human Deoxyguanosine Kinase

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
Pharos: Disease Associations
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2ocpa_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Nucleotide and nucleoside kinases	Deoxyguanosine kinase	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d2ocpc_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Nucleotide and nucleoside kinases	Deoxyguanosine kinase	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2ocpb_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Nucleotide and nucleoside kinases	Deoxyguanosine kinase	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d2ocpd_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Nucleotide and nucleoside kinases	Deoxyguanosine kinase	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d2ocpe_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Nucleotide and nucleoside kinases	Deoxyguanosine kinase	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d2ocpf_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Nucleotide and nucleoside kinases	Deoxyguanosine kinase	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d2ocpg_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Nucleotide and nucleoside kinases	Deoxyguanosine kinase	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d2ocph_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Nucleotide and nucleoside kinases	Deoxyguanosine kinase	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Deoxynucleoside kinase-like	8058409	4004030	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	P-loop nucleotide/nucleoside kinase-like	8058410	3002021	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8058410	3002021	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8058410	3002021	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8058410	3002021	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8058410	3002021	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8058410	3002021	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8058410	3002021	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8058410	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)
A	dNK	e2ocpA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: dNK	ECOD (1.6)
C	dNK	e2ocpC1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: dNK	ECOD (1.6)
B	dNK	e2ocpB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: dNK	ECOD (1.6)
D	dNK	e2ocpD1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: dNK	ECOD (1.6)
E	dNK	e2ocpE1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: dNK	ECOD (1.6)
F	dNK	e2ocpF1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: dNK	ECOD (1.6)
G	dNK	e2ocpG1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: dNK	ECOD (1.6)
H	dNK	e2ocpH1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: dNK	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
E	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
F	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
G	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
H	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, C, D, E A, B, C, D, E, F, G, H	PF01712	Deoxynucleoside kinase (dNK)	Deoxynucleoside kinase	This family consists of various deoxynucleoside kinases cytidine EC:2.7.1.74, guanosine EC:2.7.1.113, adenosine EC:2.7.1.76 and thymidine kinase EC:2.7.1.21 (which also phosphorylates deoxyuridine and deoxycytosine.) These enzymes catalyse the prod ...	This family consists of various deoxynucleoside kinases cytidine EC:2.7.1.74, guanosine EC:2.7.1.113, adenosine EC:2.7.1.76 and thymidine kinase EC:2.7.1.21 (which also phosphorylates deoxyuridine and deoxycytosine.) These enzymes catalyse the production of deoxynucleotide 5'-monophosphate from a deoxynucleoside. Using ATP and yielding ADP in the process.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H	Deoxyguanosine kinase	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 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 nucleobase-containing compound kinase activity deoxynucleoside kinase activity kinase activity deoxyadenosine kinase activity nucleoside kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups deoxyguanosine kinase activity	dAMP biosynthetic process deoxyribose phosphate biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process dAMP metabolic process nucleobase-containing compound metabolic process nucleotide salvage purine nucleoside monophosphate biosynthetic process purine deoxyribonucleoside monophosphate biosynthetic process purine nucleotide metabolic process deoxyribonucleotide biosynthetic process deoxyribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process purine nucleoside monophosphate metabolic process dAMP biosynthetic process deoxyribose phosphate biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process dAMP metabolic process nucleobase-containing compound metabolic process nucleotide salvage purine nucleoside monophosphate biosynthetic process purine deoxyribonucleoside monophosphate biosynthetic process purine nucleotide metabolic process deoxyribonucleotide biosynthetic process deoxyribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process purine nucleoside monophosphate metabolic process phosphate-containing compound metabolic process deoxyribonucleoside monophosphate biosynthetic process purine nucleotide salvage small molecule metabolic process phosphorus metabolic process nucleoside monophosphate metabolic process cellular metabolic compound salvage purine deoxyribonucleotide salvage nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process purine-containing compound salvage 2'-deoxyribonucleotide metabolic process purine deoxyribonucleoside monophosphate metabolic process 2'-deoxyribonucleotide biosynthetic process primary metabolic process nucleotide metabolic process deoxyribose phosphate metabolic process nucleobase-containing compound biosynthetic process deoxyribonucleoside monophosphate metabolic process nucleoside monophosphate biosynthetic process purine-containing compound metabolic process dAMP salvage biosynthetic process organophosphate metabolic process organophosphate biosynthetic process purine deoxyribonucleotide metabolic process nucleoside phosphate biosynthetic process metabolic process cellular process purine deoxyribonucleotide biosynthetic process purine nucleotide biosynthetic process glycosyl compound metabolic process deoxyribonucleoside metabolic process nucleoside metabolic process purine deoxyribonucleoside metabolic process purine nucleoside metabolic process aerobic respiration cellular respiration oxidative phosphorylation energy derivation by oxidation of organic compounds ATP synthesis coupled electron transport electron transport chain generation of precursor metabolites and energy respiratory electron transport chain mitochondrial ATP synthesis coupled electron transport guanosine metabolic process guanosine-containing compound metabolic process ribonucleoside metabolic process purine ribonucleoside metabolic process purine deoxyribonucleoside triphosphate metabolic process dGTP metabolic process deoxyribonucleoside triphosphate metabolic process purine nucleoside triphosphate metabolic process nucleoside triphosphate metabolic process regulation of neuron projection development multicellular organismal process regulation of cellular component organization regulation of cellular process cellular developmental process cell projection organization negative regulation of biological process cell development neuron projection development cellular component organization neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development negative regulation of cellular process cellular component organization or biogenesis negative regulation of cell projection organization system development developmental process regulation of biological process plasma membrane bounded cell projection organization negative regulation of cellular component organization regulation of cell projection organization biological regulation nervous system development negative regulation of neuron projection development generation of neurons neuron development regulation of plasma membrane bounded cell projection organization	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR002624	Deoxynucleoside kinase	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR050566	Deoxyribonucleoside Kinase	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR031314	Deoxynucleoside kinase domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F, G, H	Pharos: Q16854	mitochondrial DNA depletion syndrome 3 adult-onset multiple mitochondrial DNA deletion syndrome due to DGUOK deficiency progressive external ophthalmoplegia portal hypertension portal hypertension, noncirrhotic mitochondrial DNA depletion syndrome, hepatocerebral form peripheral neuropathy Cruveilhier-Baumgarten Syndrome lung cancer mitochondrial DNA depletion syndrome muscle tissue disease ovarian cancer systemic lupus erythematosus cholestasis malignant mesothelioma mitochondrial DNA depletion syndrome 3 adult-onset multiple mitochondrial DNA deletion syndrome due to DGUOK deficiency progressive external ophthalmoplegia portal hypertension portal hypertension, noncirrhotic mitochondrial DNA depletion syndrome, hepatocerebral form peripheral neuropathy Cruveilhier-Baumgarten Syndrome lung cancer mitochondrial DNA depletion syndrome muscle tissue disease ovarian cancer systemic lupus erythematosus cholestasis malignant mesothelioma muscular disease peripheral nervous system disease tuberculosis leukodystrophy myopathy

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	deoxyguanosine kinase M-CSA #615	Deoxyribonucleoside kinases such as deoxyguanoside kinase (dGK) phosphorylate deoxyribonucleosides. The human form is highly specific for purine substrates. Deoxynucleoside kinases are key targets in chemotherapy of cancer as they are recquired to activate nucleoside analogues by phosphorylation. dGK is involved in the regulation of dGTP and dATP pools, and may have a role in apoptosis.	Defined by 2 residues: GLU:A-34 [auth A-70]ARG:A-106 [auth A-142] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 2.7.1.113 (PDB Primary Data) Search M-CSA Motif + EC 2.7.1.113 EC: 2.7.1.76 (UniProt) Search M-CSA Motif + EC 2.7.1.76

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.