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Title :   CRYSTAL STRUCTURE OF THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE 1 IN COMPLEX WITH N-METHYL-FHBT

Authors :   L. Pernot, R. Perozzo, Y. Westermaier, M. Martic, S. Ametamey, L. Scapo

Date :   01 Apr 11 (Deposition) - 03 Aug 11 (Release) - 02 Oct 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym./Biol. Unit : A,B

Keywords :   Transferase, Thymidine Kinase, Dna-Synthesis, Pet Tracer, Atp- Binding, Dna Synthesis, Early Protein, Nucleotide-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Martic, L. Pernot, Y. Westermaier, R. Perozzo, T. G. Kraljevic, S. Kristafor, S. Raic-Malic, L. Scapozza, S. Ametamey
Synthesis, Crystal Structure, And In Vitro Biological Evaluation Of C-6 Pyrimidine Derivatives: New Lead Structures For Monitoring Gene Expression In Vivo.
Nucleosides Nucleotides V. 30 293 2011 Nucleic Acids
PubMed-ID: 21623543 | Reference-DOI: 10.1080/15257770.2011.581258
(for further references see the PDB file header)

Molecule 1 - THYMIDINE KINASE
	Chains	:	A, B
	EC Number	:	2.7.1.21
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P2
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 46-376
	Gene	:	TK, UL23
	Organism Common	:	HHV-1
	Organism Scientific	:	HUMAN HERPESVIRUS 1
	Organism Taxid	:	10299
	Strain	:	STRAIN 17

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 5)

No.	Name	Count	Type	Full Name
1	NMF	2	Ligand/Ion	6-[(2R)-2-(FLUOROMETHYL)-3-HYDROXY-PROPYL]-1,5-DIMETHYL-PYRIMIDINE-2,4-DIONE
2	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:59 , MET A:60 , GLY A:61 , ARG A:222	BINDING SITE FOR RESIDUE SO4 A 1
2	AC2	SOFTWARE	HIS A:58 , GLU A:83 , TRP A:88 , ILE A:100 , GLN A:125 , MET A:128 , ARG A:163 , ALA A:168 , TYR A:172 , ARG A:222 , HOH A:402 , HOH A:403	BINDING SITE FOR RESIDUE NMF A 601
3	AC3	SOFTWARE	HIS B:58 , GLY B:59 , MET B:60 , GLY B:61 , LYS B:62 , THR B:63 , ARG B:222	BINDING SITE FOR RESIDUE SO4 B 2
4	AC4	SOFTWARE	LYS B:317 , ARG B:320 , SER B:321	BINDING SITE FOR RESIDUE SO4 B 3
5	AC5	SOFTWARE	GLU B:83 , TRP B:88 , ILE B:100 , TYR B:101 , GLN B:125 , MET B:128 , ARG B:163 , TYR B:172 , ARG B:222 , HOH B:386 , HOH B:387	BINDING SITE FOR RESIDUE NMF B 601

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

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

Asymmetric/Biological Unit (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/B	C	251	G
	* ID not provided by source

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

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

(no "Exon" information available for 3RDP)

Asymmetric/Biological 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
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:314
 aligned with KITH_HHV11 | P03176 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:329
                                    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         
           KITH_HHV11    46 MPTLLRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAGSSHAPPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSGTAVPPQGAEPQSNAGPRPHIGDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGE 374
               SCOP domains d3rdpa_ A: Thymidine kinase                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.......hhhhhhhhhhhh....eeee..hhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..........eeeee...hhhhhhhhhhhhhhh...hhhhhhhhhhh.......eeeeeee.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.---------------...hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh.eeeeee...hhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G--------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rdp A  46 MPTLLRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAGSSHAPPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSG---------------PRPHIGDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGE 374
                                    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         
                                                                                                                                                                                                                                                    264             280

Chain B from PDB  Type:PROTEIN  Length:320
 aligned with KITH_HHV11 | P03176 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:329
                                    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         
           KITH_HHV11    46 MPTLLRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAGSSHAPPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSGTAVPPQGAEPQSNAGPRPHIGDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGE 374
               SCOP domains d3rdpb_ B: Thymidine kinase                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee......hhhhhhhhhhh......eeee..hhhhhhh....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..........eeeeee..hhhhhhhhhhhhhh....hhhhhhhhhh.........eeeeee.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh..---------.........hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G--------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rdp B  46 MPTLLRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAGSSHAPPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSG---------PQSNAGPRPHIGDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGE 374
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255        |-       275       285       295       305       315       325       335       345       355       365         
                                                                                                                                                                                                                                                    264       274

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: P-loop containing nucleoside triphosphate hydrolases (2083)

Superfamily: P-loop containing nucleoside triphosphate hydrolases (2083)

Family: Nucleotide and nucleoside kinases (231)

Protein domain: Thymidine kinase (34)

Herpes simplex virus type 1, different strains [TaxId: 10298] (29)

1a	d3rdpa_	A:
1b	d3rdpb_	B:

(no "CATH Domain" information available for 3RDP)

(no "Pfam Domain" information available for 3RDP)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3rdp)

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	3rdp
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	2.7.1.21
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1e2h	THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE 1 IN THE APO FORM
1e2p	THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE 1 COMPLEXED WITH DHBT
3f0t	CRYSTAL STRUCTURE OF THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE 1 IN COMPLEX WITH N-METHYL-DHBT

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

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Exons (0, 0)

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