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Title :   THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE 1 IN COMPLEX WITH ADP AND 5-IODO-DEOXYURIDINE-MONOPHOSPHATE

Authors :   K. Wild, G. E. Schulz

Date :   01 Apr 97 (Deposition) - 22 Oct 97 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Key Enzyme In Thymidine Salvage Pathway, Additional Thymidylate Kinase Activity, Target For Anti-Herpes Viral Drugs, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Wild, T. Bohner, G. Folkers, G. E. Schulz
The Structures Of Thymidine Kinase From Herpes Simplex Viru Type 1 In Complex With Substrates And A Substrate Analogue.
Protein Sci. V. 6 2097 1997
PubMed-ID: 9336833
(for further references see the PDB file header)

Molecule 1 - THYMIDINE KINASE
	Chains	:	A
	EC Number	:	2.7.1.21
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX2T
	Expression System Strain	:	KY 895
	Expression System Taxid	:	562
	Organism Scientific	:	HERPES SIMPLEX VIRUS (TYPE 1 / STRAIN F)
	Organism Taxid	:	10304
	Strain	:	F

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	5IU	1	Mod. Residue	5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	5IU	2	Mod. Residue	5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:58 , LYS A:62 , GLU A:83 , ILE A:97 , TYR A:101 , GLN A:125 , MET A:128 , ARG A:163 , ALA A:168 , TYR A:172 , GLU A:225 , HOH A:602 , HOH A:605	BINDING SITE FOR RESIDUE 5IU A 500
2	AC2	SOFTWARE	GLY A:59 , MET A:60 , GLY A:61 , LYS A:62 , THR A:63 , THR A:64 , ARG A:216 , ARG A:220 , GLN A:331 , HOH A:605	BINDING SITE FOR RESIDUE ADP A 400

(no "SS Bond" information available for 3VTK)

(no "Cis Peptide Bond" information available for 3VTK)

Asymmetric Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_KITH_HHV11_005 *	C	251	G	KITH_HHV11	---	---	A	C	251	G
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_KITH_HHV11_005 *	C	251	G	KITH_HHV11	---	---	A	C	251	G
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 3VTK)

(no "Exon" information available for 3VTK)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:313
 aligned with KITH_HHV11 | P03176 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:331
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375 
           KITH_HHV11    46 MPTLLRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAGSSHAPPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSGTAVPPQGAEPQSNAGPRPHIGDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGEAN 376
               SCOP domains d3vtka_ A: Thymidine kinase                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 3vtkA00 A:46-376 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                                                                                       CATH domains
               Pfam domains ----------Herpes_TK-3vtkA01 A:56-330                                                                                                                                                                                                                                                         ---------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.......hhhhhh..hhh.....eeee...hhhhh......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......---....eeeeee..hhhhh.hhhhhhhh.....hhhhhhhh..........eeeeee..hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh.---------------....hhh.hhh....hhh........hhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vtk A  46 MPTLLRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAGS---PPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSG---------------PRPHIGDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGEAN 376
                                    55        65        75        85        95       105       115       125       135       145   |   155       165       175       185       195       205       215       225       235       245       255        |-         -    |  285       295       305       315       325       335       345       355       365       375 
                                                                                                                                 149 153                                                                                                            264             280

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Herpes simplex virus (type 1 / strain f). Organism_taxid: 10304. Strain: f. (3)

3vtkA00

A:46-376

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Herpes_TK (18)

Human herpesvirus 1 (strain 17) (HHV-1) (Human herpes simplex virus 1) (13)

Herpes_TK-3vtkA01

A:56-330

Asymmetric Unit(hide GO term definitions)

Chain A (KITH_HHV11 | P03176)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0004797	thymidine kinase activity	Catalysis of the reaction: ATP + thymidine = ADP + thymidine 5'-phosphate.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0071897	DNA biosynthetic process	The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
	GO:0006230	TMP biosynthetic process	The chemical reactions and pathways resulting in the formation of TMP, ribosylthymine monophosphate.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.

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