1KI7 - JenaLib

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Title :   CRYSTAL STRUCTURE OF THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE I COMPLEXED WITH 5-IODODEOXYURIDINE

Authors :   J. N. Champness, M. S. Bennett, F. Wien, R. Visse, W. C. Summers, M. R. Sanderson

Date :   15 May 98 (Deposition) - 02 Dec 98 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Phosphotransferase, Thymidine Kinase, Viridae, Ds-Dna Enveloped Viruses, Herpesviridae, Alphaherpesvirinae, Substrate Analog, 5-Iododeoxyuridine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. N. Champness, M. S. Bennett, F. Wien, R. Visse, W. C. Summers, P. Herdewijn, E. De Clerq, T. Ostrowski, R. L. Jarvest, M. R. Sanderson
Exploring The Active Site Of Herpes Simplex Virus Type-1 Thymidine Kinase By X-Ray Crystallography Of Complexes With Aciclovir And Other Ligands.
Proteins V. 32 350 1998
PubMed-ID: 9715911 | Reference-DOI: 10.1002/(SICI)1097-0134(19980815)32:3<350::AID-PROT 10>3.0.CO;2-8
(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 Gene	:	TK
	Expression System Plasmid	:	PT7:HSVTK
	Expression System Strain	:	SY211
	Expression System Taxid	:	562
	Gene	:	TK
	Organism Scientific	:	HERPES SIMPLEX VIRUS (TYPE 1 / STRAIN 17)
	Organism Taxid	:	10299
	Strain	:	17
	Synonym	:	TK

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	ID2	2	Ligand/Ion	5-IODODEOXYURIDINE
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	ID2	2	Ligand/Ion	5-IODODEOXYURIDINE
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 8)

No.	Name	Count	Type	Full Name
1	ID2	4	Ligand/Ion	5-IODODEOXYURIDINE
2	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:58 , GLY A:59 , MET A:60 , GLY A:61 , LYS A:62 , THR A:63 , ARG A:220 , ARG A:222 , HOH A:523	BINDING SITE FOR RESIDUE SO4 A 3
2	AC2	SOFTWARE	HOH A:645 , HIS B:58 , GLY B:59 , MET B:60 , GLY B:61 , LYS B:62 , THR B:63 , HOH B:611	BINDING SITE FOR RESIDUE SO4 B 4
3	AC3	SOFTWARE	HIS A:58 , GLU A:83 , ILE A:97 , ILE A:100 , TYR A:101 , GLN A:125 , MET A:128 , TYR A:132 , ARG A:163 , ALA A:168 , TYR A:172 , ARG A:222 , GLU A:225 , HOH A:551	BINDING SITE FOR RESIDUE ID2 A 1
4	AC4	SOFTWARE	GLU B:83 , ILE B:97 , ILE B:100 , TYR B:101 , GLN B:125 , MET B:128 , ALA B:168 , TYR B:172 , ARG B:222 , GLU B:225 , HOH B:614	BINDING SITE FOR RESIDUE ID2 B 2

(no "SS Bond" information available for 1KI7)

(no "Cis Peptide Bond" information available for 1KI7)

Asymmetric 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)

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/B	C	251	G
	* ID not provided by source

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

Biological Unit 2 (1, 4)

								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 1KI7)

(no "Exon" information available for 1KI7)

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
	(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:305
 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 d1ki7a_ A: Thymidine kina      se                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1ki7A00 A:46-374 P-loop c      ontaining nucleotide triphosphate hydrolases                                                                                                                                                                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.......hhhh....------.eeee...hhhhh......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........-.....eeeeee...hhhh.hhhhhhh......hhhhhhhhhh.......eeeeeee..hhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhh....hhhh....-----------------....hhh.hhhhh.............hhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G--------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ki7 A  46 MPTLLRVYIDGPHGMGKTTTTQLLV------DIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAGSS-APPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQL-----------------PRPHIGDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGE 374
                                    55        65    |    - |      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         
                                                   70     77                                                                      150 |                                                                                                           262               280                                                                                              
                                                                                                                                    152

Chain B from PDB  Type:PROTEIN  Length:312
 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 d1ki7b_ B: Thymidine kinase                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1ki7B00 B:46-374 P-loop cont   aining nucleotide triphosphate hydrolases                                                                                                                                                                                                                                                                  CATH domains
           Pfam domains (1) ----------Herpes_TK-1ki7B01    B:56-330                                                                                                                                                                                                                                                      -------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----------Herpes_TK-1ki7B02    B:56-330                                                                                                                                                                                                                                                      -------------------------------------------- Pfam domains (2)
         Sec.struct. author ...eeeeeee......hhhhhhhhhh..---.eeee...hhhhh......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........-.....eeeeee..hhhhh.hhhhhhhh.....hhhhhhhhhh........eeeeee..hhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh..-------------.......hhh.hhhhh..hhh........hhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G--------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ki7 B  46 MPTLLRVYIDGPHGMGKTTTTQLLVALG---DIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAGSS-APPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLS-------------NAGPRPHIGDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGE 374
                                    55        65       | - |      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         
                                                      73  77                                                                      150 |                                                                                                            263           277                                                                                                 
                                                                                                                                    152

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 17). Organism_taxid: 10299. Strain: 17. (8)

1a	1ki7A00	A:46-374
1b	1ki7B00	B:46-374

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)

1a	Herpes_TK-1ki7B01	B:56-330
1b	Herpes_TK-1ki7B02	B:56-330

Asymmetric 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 Unit
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Description

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Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

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