2B8T - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

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

Authors :   U. Kosinska, C. Carnrot, S. Eriksson, L. Wang, H. Eklund

Date :   10 Oct 05 (Deposition) - 20 Dec 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Deoxyribonucleoside Kinase, Zinc-Binding Domain, Tk1, Uu-Tk, Thymidine, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   U. Kosinska, C. Carnrot, S. Eriksson, L. Wang, H. Eklund
Structure Of The Substrate Complex Of Thymidine Kinase From Ureaplasma Urealyticum And Investigations Of Possible Drug Targets For The Enzyme
Febs Lett. V. 272 6365 2005
PubMed-ID: 16336273 | Reference-DOI: 10.1111/J.1742-4658.2005.05030.X
(for further references see the PDB file header)

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)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TDK
	Organism Scientific	:	UREAPLASMA PARVUM
	Organism Taxid	:	134821

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 9)

No.	Name	Count	Type	Full Name
1	THM	4	Ligand/Ion	THYMIDINE
2	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3	ZN	4	Ligand/Ion	ZINC ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:153 , CYS A:156 , CYS A:191 , HIS A:194	BINDING SITE FOR RESIDUE ZN A 1218
2	AC2	SOFTWARE	CYS B:153 , CYS B:156 , CYS B:191 , HIS B:194	BINDING SITE FOR RESIDUE ZN B 2218
3	AC3	SOFTWARE	CYS C:153 , CYS C:156 , CYS C:191 , HIS C:194	BINDING SITE FOR RESIDUE ZN C 3218
4	AC4	SOFTWARE	CYS D:153 , CYS D:156 , CYS D:191 , HIS D:194	BINDING SITE FOR RESIDUE ZN D 4218
5	AC5	SOFTWARE	GLU A:97 , PHE A:100 , LEU A:124 , ASN A:127 , PHE A:128 , PHE A:133 , SER A:163 , ARG A:165 , ILE A:178 , VAL A:179 , LYS A:180 , ILE A:181 , GLY A:182 , TYR A:187	BINDING SITE FOR RESIDUE THM A 4970
6	AC6	SOFTWARE	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	BINDING SITE FOR RESIDUE THM B 5970
7	AC7	SOFTWARE	GLU C:97 , 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 , ILE C:181 , GLY C:182 , TYR C:187	BINDING SITE FOR RESIDUE THM C 6970
8	AC8	SOFTWARE	GLU D:97 , PHE D:100 , LEU D:124 , ASN D:127 , PHE D:128 , PHE D:133 , SER D:163 , ARG D:165 , ILE D:178 , VAL D:179 , LYS D:180 , GLY D:182 , TYR D:187 , HOH D:8015	BINDING SITE FOR RESIDUE THM D 7970
9	AC9	SOFTWARE	PRO D:20 , MET D:21 , PHE D:22 , ALA D:23 , GLY D:24 , LYS D:25 , THR D:26 , ARG D:61 , HOH D:7980 , HOH D:8015 , HOH D:8023	BINDING SITE FOR RESIDUE TRS D 5006

(no "SS Bond" information available for 2B8T)

(no "Cis Peptide Bond" information available for 2B8T)

(no "SAP(SNP)/Variant" information available for 2B8T)

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 2B8T)

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:206
 aligned with KITH_UREPA | Q9PPP5 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:206
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      
           KITH_UREPA    11 IGWIELITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKIDTRSIRNIQSRTGTSLPSVEVESAPEILNYIMSNSFNDETKVIGIDEVQFFDDRICEVANILAENGFVVIISGLDKNFKGEPFGPIAKLFTYADKITKLTAICNECGAEATHSLRKIDGKHADYNDDIVKIGCQEFYSAVCRHHHKVPNRPYLNSNSEEFIKFFKN 216
               SCOP domains d2b8ta1 A:11-149 Thymidine kinase, TK1, N-terminal domain                                                                                  d2b8ta2 A:150-216 Thymidine kinase, TK1, C-terminal domain          SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhhh...eeeeee..hhhhh.............eee..hhhhhhhhhh........eeee.hhhhhhhhhhhhhhhhhhh..eeeee............hhhhhhhhh.eeee..ee......ee.eeeeee..ee...............eeeehhhhh..........hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------TK_CELLULAR_TY--------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b8t A  11 IGWIEFITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKIDTRSIRNIQSRTGTSLPSVEVESAPEILNYIMSNSFNDETKVIGIDEVQFFDDRICEVANILAENGFVVIISGLDKNFKGEPFGPIAKLFTYADKITKLTAICNECGAEATHSLRKIDGKHADYNDDIVKIGCQEFYSAVCRHHHKVPNRPYLNSNSEEFIKFFKN 216
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain B from PDB  Type:PROTEIN  Length:189
 aligned with KITH_UREPA | Q9PPP5 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:204
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    
           KITH_UREPA    11 IGWIELITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKIDTRSIRNIQSRTGTSLPSVEVESAPEILNYIMSNSFNDETKVIGIDEVQFFDDRICEVANILAENGFVVIISGLDKNFKGEPFGPIAKLFTYADKITKLTAICNECGAEATHSLRKIDGKHADYNDDIVKIGCQEFYSAVCRHHHKVPNRPYLNSNSEEFIKFF 214
               SCOP domains d2b8tb1 B:11-149 Thymidine kinase, TK1,                N-terminal domain                                                                   d2b8tb2 B:150-214 Thymidine kinase, TK1, C-terminal domain        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhhh...eeeeee..---------------...eee..hhhhhhhhhh........eeee.hhhhhhhhhhhhhhhhhhh..eeeee............hhhhhhhhh.eeee..ee......ee.eeee.....................eeeehhhhh..........hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------TK_CELLULAR_TY------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2b8t B  11 IGWIEFITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKI---------------LPSVEVESAPEILNYIMSNSFNDETKVIGIDEVQFFDDRICEVANILAENGFVVIISGLDKNFKGEPFGPIAKLFTYADKITKLTAICNECGAEATHSLRKIDGKHADYNDDIVKIGCQEFYSAVCRHHHKVPNRPYLNSNSEEFIKFF 214
                                    20        30        40        50         -     |  70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    
                                                                  50              66

Chain C from PDB  Type:PROTEIN  Length:199
 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 d2b8tc1 C:11-149 Thymidine kinase, TK1, N        -terminal domain                                                                          d2b8tc2 C:150-217 Thymidine kinase, TK1, C-terminal domain           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhhhh..eeeeee...--------........eeee..hhhhhhhhh.........eeee.hhhhhhhhhhhhhhhhhhh..eeeee............hhhhhhhhh.eeee..ee......ee.eeeeee..ee...............eeeehhhhh..........hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------TK_CELLULAR_TY---------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b8t C  11 IGWIEFITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKID--------SRTGTSLPSVEVESAPEILNYIMSNSFNDETKVIGIDEVQFFDDRICEVANILAENGFVVIISGLDKNFKGEPFGPIAKLFTYADKITKLTAICNECGAEATHSLRKIDGKHADYNDDIVKIGCQEFYSAVCRHHHKVPNRPYLNSNSEEFIKFFKNK 217
                                    20        30        40        50|       60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       
                                                                   51       60

Chain D from PDB  Type:PROTEIN  Length:204
 aligned with KITH_UREPA | Q9PPP5 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:208
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211        
           KITH_UREPA    12 GWIELITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKIDTRSIRNIQSRTGTSLPSVEVESAPEILNYIMSNSFNDETKVIGIDEVQFFDDRICEVANILAENGFVVIISGLDKNFKGEPFGPIAKLFTYADKITKLTAICNECGAEATHSLRKIDGKHADYNDDIVKIGCQEFYSAVCRHHHKVPNRPYLNSNSEEFIKFFKNKKR 219
               SCOP domains d2b8td1 D:12-149 Thymidine kinase, TK1    , N-terminal domain                                                                             d2b8td2 D:150-219 Thymidine kinase, TK1, C-terminal domain             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhhhhh...eeeeee.----...eee.....eee.eee..hhhhhhhhh.........eeee.hhhhhhhhhhhhhhhhhhh..eeeee............hhhhhhhhh.eeee..ee......ee.eeeeee..ee...............eeee...............hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------TK_CELLULAR_TY------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b8t D  12 GWIEFITGPMFAGKTAELIRRLHRLEYADVKYLVFKPK----SIRNIQSRTGTSLPSVEVESAPEILNYIMSNSFNDETKVIGIDEVQFFDDRICEVANILAENGFVVIISGLDKNFKGEPFGPIAKLFTYADKITKLTAICNECGAEATHSLRKIDGKHADYNDDIVKIGCQEFYSAVCRHHHKVPNRPYLNSNSEEFIKFFKNKKR 219
                                    21        31        41       | -  |     61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211        
                                                                49   54

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 2B8T)

(no "Pfam Domain" information available for 2B8T)

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 8)

CATH Domains (0, 0)

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Gene Ontology (12, 12)

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