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Title :   CRYSTAL STRUCTURE OF THYMIDINE KINASE WITH DTTP FROM U. UREALYTICUM

Authors :   M. Welin, U. Kosinska, N. E. Mikkelsen, C. Carnrot, C. Zhu, L. Wang, S. Eriksson, B. Munch-Petersen, H. Eklund

Date :   24 Apr 07 (Deposition) - 29 May 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Deoxyribonucleoside Kinase, Zinc-Binding Domain, Feed-Back Inhibitor, Tk1, Dttp, Uu-Tk, Kinase, Transferase, Atp- Binding, Lasso-Domain, Dna Synthesis, Nucleotide-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Welin, U. Kosinska, N. E. Mikkelsen, C. Carnrot, C. Zhu, L. Wang, S. Eriksson, B. Munch-Petersen, H. Eklund
Structures Of Thymidine Kinase 1 Of Human And Mycoplasmic Origin
Proc. Natl. Acad. Sci. Usa V. 101 17970 2004
PubMed-ID: 15611477 | Reference-DOI: 10.1073/PNAS.0406332102

Molecule 1 - THYMIDINE KINASE
	Chains	:	A, B, C, D
	EC Number	:	2.7.1.21
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-14B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	PLYSS
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	UREAPLASMA UREALYTICUM
	Organism Taxid	:	2130

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 10)

No.	Name	Count	Type	Full Name
1	MG	2	Ligand/Ion	MAGNESIUM ION
2	TTP	4	Ligand/Ion	THYMIDINE-5'-TRIPHOSPHATE
3	ZN	4	Ligand/Ion	ZINC ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:153 , CYS A:156 , CYS A:191 , HIS A:194	BINDING SITE FOR RESIDUE ZN A1218
02	AC2	SOFTWARE	CYS B:153 , CYS B:156 , CYS B:191 , HIS B:194	BINDING SITE FOR RESIDUE ZN B2218
03	AC3	SOFTWARE	THR B:26 , TTP B:2220	BINDING SITE FOR RESIDUE MG B2219
04	AC4	SOFTWARE	CYS C:153 , CYS C:156 , CYS C:191 , HIS C:194	BINDING SITE FOR RESIDUE ZN C3218
05	AC5	SOFTWARE	CYS D:153 , CYS D:156 , CYS D:191 , HIS D:194	BINDING SITE FOR RESIDUE ZN D4218
06	AC6	SOFTWARE	THR D:26 , TTP D:4220	BINDING SITE FOR RESIDUE MG D4219
07	AC7	SOFTWARE	MET A:21 , PHE A:22 , ALA A:23 , GLY A:24 , LYS A:25 , THR A:26 , GLN A:99 , PHE A:100 , ASN A:127 , PHE A:128 , PHE A:133 , SER A:163 , ILE A:178 , VAL A:179 , LYS A:180 , ILE A:181 , GLY A:182 , TYR A:187 , HOH A:2018	BINDING SITE FOR RESIDUE TTP A1220
08	AC8	SOFTWARE	MET B:21 , PHE B:22 , ALA B:23 , GLY B:24 , LYS B:25 , THR B:26 , ASP B:51 , ARG B:53 , ARG B:61 , GLU B:97 , PHE B:100 , LEU B:124 , ASN B:127 , PHE B:128 , PHE B:133 , SER B:163 , ARG B:165 , ILE B:178 , VAL B:179 , LYS B:180 , ILE B:181 , GLY B:182 , TYR B:187 , HOH B:2003 , HOH B:2052 , MG B:2219	BINDING SITE FOR RESIDUE TTP B2220
09	AC9	SOFTWARE	MET C:21 , PHE C:22 , ALA C:23 , GLY C:24 , LYS C:25 , THR C:26 , PHE C:100 , LEU C:124 , ASN C:127 , PHE C:128 , PHE C:133 , SER C:163 , ARG C:165 , ILE C:178 , VAL C:179 , LYS C:180 , GLY C:182 , TYR C:187 , HOH C:2029 , HOH C:2030	BINDING SITE FOR RESIDUE TTP C3220
10	BC1	SOFTWARE	MET D:21 , PHE D:22 , ALA D:23 , GLY D:24 , LYS D:25 , THR D:26 , PHE D:100 , LEU D:124 , ASN D:127 , PHE D:128 , PHE D:133 , SER D:163 , ILE D:178 , VAL D:179 , LYS D:180 , ILE D:181 , GLY D:182 , TYR D:187 , HOH D:2004 , HOH D:2043 , MG D:4219	BINDING SITE FOR RESIDUE TTP D4220

(no "SS Bond" information available for 2UZ3)

(no "Cis Peptide Bond" information available for 2UZ3)

(no "SAP(SNP)/Variant" information available for 2UZ3)

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TK_CELLULAR_TYPE	PS00603	Thymidine kinase cellular-type signature.	KITH_UREPA	182-195	4	A:182-195 B:182-195 C:182-195 D:182-195

(no "Exon" information available for 2UZ3)

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:190
 aligned with KITH_UREPA | Q9PPP5 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:207
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       
           KITH_UREPA    11 IGWIELITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKIDTRSIRNIQSRTGTSLPSVEVESAPEILNYIMSNSFNDETKVIGIDEVQFFDDRICEVANILAENGFVVIISGLDKNFKGEPFGPIAKLFTYADKITKLTAICNECGAEATHSLRKIDGKHADYNDDIVKIGCQEFYSAVCRHHHKVPNRPYLNSNSEEFIKFFKNK 217
               SCOP domains d2uz3a1 A:11-149 Thymidine kinase, TK1,                  N-terminal domain                                                                 d2uz3a2 A:150-217 Thymidine kinase, TK1, C-terminal domain           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....hhhhhhhhhhhhhhh....eeeeee..-----------------.eee..hhhhhhhhhh........eeee.hhhhh.hhhhhhhhhhhhh..eeeeeee..........hhhhhhhhh.eeee..ee......ee.eeeeee..ee...............eeee...............hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------TK_CELLULAR_TY---------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uz3 A  11 IGWIEFITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKI-----------------SVEVESAPEILNYIMSNSFNDETKVIGIDEVQFFDDRICEVANILAENGFVVIISGLDKNFKGEPFGPIAKLFTYADKITKLTAICNECGAEATHSLRKIDGKHADYNDDIVKIGCQEFYSAVCRHHHKVPNRPYLNSNSEEFIKFFKNK 217
                                    20        30        40        50         -       |70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       
                                                                  50                68

Chain B from PDB  Type:PROTEIN  Length:207
 aligned with KITH_UREPA | Q9PPP5 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:207
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       
           KITH_UREPA    11 IGWIELITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKIDTRSIRNIQSRTGTSLPSVEVESAPEILNYIMSNSFNDETKVIGIDEVQFFDDRICEVANILAENGFVVIISGLDKNFKGEPFGPIAKLFTYADKITKLTAICNECGAEATHSLRKIDGKHADYNDDIVKIGCQEFYSAVCRHHHKVPNRPYLNSNSEEFIKFFKNK 217
               SCOP domains d2uz3b1 B:11-149 Thymidine kinase, TK1, N-terminal domain                                                                                  d2uz3b2 B:150-217 Thymidine kinase, TK1, C-terminal domain           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhh....eeeeee........eee.....eee.eee..hhhhhhhhhh........eeee.hhhhh.hhhhhhhhhhhhh..eeeee............hhhhhhhhh.eeee..ee......ee.eeeeee..ee...............eeee...............hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------TK_CELLULAR_TY---------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uz3 B  11 IGWIEFITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKIDTRSIRNIQSRTGTSLPSVEVESAPEILNYIMSNSFNDETKVIGIDEVQFFDDRICEVANILAENGFVVIISGLDKNFKGEPFGPIAKLFTYADKITKLTAICNECGAEATHSLRKIDGKHADYNDDIVKIGCQEFYSAVCRHHHKVPNRPYLNSNSEEFIKFFKNK 217
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain C from PDB  Type:PROTEIN  Length:192
 aligned with KITH_UREPA | Q9PPP5 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:207
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       
           KITH_UREPA    11 IGWIELITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKIDTRSIRNIQSRTGTSLPSVEVESAPEILNYIMSNSFNDETKVIGIDEVQFFDDRICEVANILAENGFVVIISGLDKNFKGEPFGPIAKLFTYADKITKLTAICNECGAEATHSLRKIDGKHADYNDDIVKIGCQEFYSAVCRHHHKVPNRPYLNSNSEEFIKFFKNK 217
               SCOP domains d2uz3c1 C:11-149 Thymidine kinase, TK1,                N-terminal domain                                                                   d2uz3c2 C:150-217 Thymidine kinase, TK1, C-terminal domain           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....hhhhhhhhhhhhhhh....eeeeee.---------------....eee..hhhhhhhhhh........eeee.hhhhh.hhhhhhhhhhhhh..eeeeeee..........hhhhhhhhh.eeee..ee......ee.eeeeee..ee...............eeee...............hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------TK_CELLULAR_TY---------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uz3 C  11 IGWIEFITGPMFAGKTAELIRRLHRLEYADVKYLVFKPK---------------SLPSVEVESAPEILNYIMSNSFNDETKVIGIDEVQFFDDRICEVANILAENGFVVIISGLDKNFKGEPFGPIAKLFTYADKITKLTAICNECGAEATHSLRKIDGKHADYNDDIVKIGCQEFYSAVCRHHHKVPNRPYLNSNSEEFIKFFKNK 217
                                    20        30        40        |-         -    |   70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       
                                                                 49              65

Chain D from PDB  Type:PROTEIN  Length:207
 aligned with KITH_UREPA | Q9PPP5 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:207
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       
           KITH_UREPA    11 IGWIELITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKIDTRSIRNIQSRTGTSLPSVEVESAPEILNYIMSNSFNDETKVIGIDEVQFFDDRICEVANILAENGFVVIISGLDKNFKGEPFGPIAKLFTYADKITKLTAICNECGAEATHSLRKIDGKHADYNDDIVKIGCQEFYSAVCRHHHKVPNRPYLNSNSEEFIKFFKNK 217
               SCOP domains d2uz3d1 D:11-149 Thymidine kinase, TK1, N-terminal domain                                                                                  d2uz3d2 D:150-217 Thymidine kinase, TK1, C-terminal domain           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -TK-2uz3D01 D:12-195                                                                                                                                                                     ---------------------- Pfam domains (1)
           Pfam domains (2) -TK-2uz3D02 D:12-195                                                                                                                                                                     ---------------------- Pfam domains (2)
           Pfam domains (3) -TK-2uz3D03 D:12-195                                                                                                                                                                     ---------------------- Pfam domains (3)
           Pfam domains (4) -TK-2uz3D04 D:12-195                                                                                                                                                                     ---------------------- Pfam domains (4)
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhh....eeeeee........eee.....eee.eee..hhhhhhhhhh........eeee.hhhhh.hhhhhhhhhhhhh..eeeee............hhhhhhhhh.eeee..ee......ee.eeeeee..ee...............eeee...............hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------TK_CELLULAR_TY---------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uz3 D  11 IGWIEFITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKIDTRSIRNIQSRTGTSLPSVEVESAPEILNYIMSNSFNDETKVIGIDEVQFFDDRICEVANILAENGFVVIISGLDKNFKGEPFGPIAKLFTYADKITKLTAICNECGAEATHSLRKIDGKHADYNDDIVKIGCQEFYSAVCRHHHKVPNRPYLNSNSEEFIKFFKNK 217
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

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 '\|'

(no "CATH Domain" information available for 2UZ3)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: TK (9)

Ureaplasma parvum (Ureaplasma urealyticum biotype 1) (1)

1a	TK-2uz3D01	D:12-195
1b	TK-2uz3D02	D:12-195
1c	TK-2uz3D03	D:12-195
1d	TK-2uz3D04	D:12-195

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (KITH_UREPA | Q9PPP5)

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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
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:0006259	DNA metabolic process	Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
	GO:0009157	deoxyribonucleoside monophosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of a deoxyribonucleoside monophosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with phosphate on the sugar.
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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(no "Cis Peptide Bonds" information available for 2uz3)

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	2uz3
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	2.7.1.21
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	KITH_UREPA \| Q9PPP5	:	2b8t

1xmr	CRYSTAL STRUCTURE OF THYMIDINE KINASE WITH DTTP FROM U.UREALYTICUM
2b8t	CRYSTAL STRUCTURE OF THYMIDINE KINASE FROM U .UREALYTICUM INCOMPLEX WITH THYMIDINE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

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SCOP Domains (2, 8)

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