1KIM

CRYSTAL STRUCTURE OF THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE I COMPLEXED WITH DEOXYTHYMIDINE

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
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)
B	d1kimb_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Nucleotide and nucleoside kinases	Thymidine kinase	(Human alphaherpesvirus 1 strain 17 ) [TaxId: 10299 ],	SCOPe (2.08)
A	d1kima_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Nucleotide and nucleoside kinases	Thymidine kinase	(Human alphaherpesvirus 1 strain 17 ) [TaxId: 10299 ],	SCOPe (2.08)

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	8019153	3002021	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8019153	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	Herpes_TK	e1kimB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Herpes_TK	ECOD (1.6)
A	Herpes_TK	e1kimA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Herpes_TK	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	3.40.50.300	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	PF00693	Thymidine kinase from herpesvirus (Herpes_TK)	Thymidine kinase from herpesvirus	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	THYMIDINE 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 thymidine kinase activity nucleobase-containing compound kinase activity deoxynucleoside kinase activity kinase activity nucleoside kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process DNA biosynthetic process ribose phosphate metabolic process TMP 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 nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process DNA biosynthetic process ribose phosphate metabolic process TMP metabolic process nucleotide biosynthetic process carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process ribonucleotide biosynthetic process ribonucleotide metabolic process ribonucleoside monophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process small molecule metabolic process pyrimidine-containing compound biosynthetic process phosphorus metabolic process nucleoside monophosphate metabolic process ribose phosphate biosynthetic process pyrimidine ribonucleotide metabolic process TMP biosynthetic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process pyrimidine nucleoside monophosphate metabolic process pyrimidine ribonucleoside monophosphate metabolic process pyrimidine-containing compound metabolic process nucleotide metabolic process nucleoside monophosphate biosynthetic process pyrimidine ribonucleoside monophosphate biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process pyrimidine nucleoside monophosphate biosynthetic process ribonucleoside monophosphate biosynthetic process pyrimidine nucleotide biosynthetic process pyrimidine ribonucleotide biosynthetic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001889	Herpesvirus thymidine kinase	Family
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

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

Chains	Enzyme Name	Description	Catalytic Residues
A	thymidine kinase M-CSA #588	Thymidine kinases (TK) are key enzymes in the pyrimidine salvage pathway catalyzing the phosphate transfer from ATP to thymidine (dT) in the presence of Mg2+ and thus, yielding thymidine monophosphate (dTMP) and ADP. Herpesviridae, such as Herpes simplex virus type 1, encode for their own, multifunctional TK. Unlike the very specific human cytosolic TK (TK1), it is able to phosphorylate pyrimidine as well as purine analogs and demands less stereochemical restrictions concerning the sugar moiety also accepting acyclic side chains as phosphate acceptors (e.g., aciclovir). Therefore, the difference in substrate specificity of human TK 1 and TKHSV1 is a crucial point in establishing a molecular basis for selective antiviral therapy, featuring TKHSV1 as the center of activation of antiviral drugs such as aciclovir (ACV), penciclovir, and ganciclovir (GCV). First being activated by phosphorylation by viral encoded TK, these nucleoside analogs in their triphosphate form block the viral replication by subsequently terminating DNA elongation at the viral DNA polymerase. In combination with GCV TKHSV1 is an established tool used as a prodrug-activating enzyme, so-called suicide enzyme, in gene therapy of cancer, AIDS, and in controlling graft-versus-host disease by allogenic bone marrow transplant (allo BMT).	Defined by 7 residues: LYS:A-52 [auth A-62]GLU:A-73 [auth A-83]ASP:A-152 [auth A-162]ARG:A-153 [auth A-163]ARG:A-210 [auth A-220]ARG:A-212 [auth A-222]GLU:A-215 [auth A-225] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 2.7.1.21 (PDB Primary Data) Search M-CSA Motif + EC 2.7.1.21

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.