2QPO - JenaLib

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Title :   THERMOTOGA MARITIMA THYMIDINE KINASE IN THE APO FORM

Authors :   D. Segura-Pena, J. Lichter, M. Trani, M. Konrad, A. Lavie, S. Lutz

Date :   24 Jul 07 (Deposition) - 16 Oct 07 (Release) - 30 Dec 08 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

Keywords :   Apo-Form, Atp-Binding, Cytoplasm, Dna Synthesis, Kinase, Nucleotide-Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Segura-Pena, J. Lichter, M. Trani, M. Konrad, A. Lavie, S. Lutz
Quaternary Structure Change As A Mechanism For The Regulation Of Thymidine Kinase 1-Like Enzymes.
Structure V. 15 1555 2007
PubMed-ID: 18073106 | Reference-DOI: 10.1016/J.STR.2007.09.025
(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 BL21
	Expression System Plasmid	:	PET-14B
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Gene	:	TDK
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 8)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION
2	ZN	4	Ligand/Ion	ZINC ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:140 , CYS A:143 , CYS A:173 , CYS A:176	BINDING SITE FOR RESIDUE ZN A 201
2	AC2	SOFTWARE	TYR A:13 , SER A:14 , GLY A:15 , LYS A:16 , THR A:17	BINDING SITE FOR RESIDUE SO4 A 301
3	AC3	SOFTWARE	CYS B:140 , CYS B:143 , CYS B:173 , CYS B:176	BINDING SITE FOR RESIDUE ZN B 202
4	AC4	SOFTWARE	TYR B:13 , SER B:14 , GLY B:15 , LYS B:16 , THR B:17 , HOH B:314 , HOH B:315	BINDING SITE FOR RESIDUE SO4 B 302
5	AC5	SOFTWARE	CYS C:140 , CYS C:143 , CYS C:173 , CYS C:176	BINDING SITE FOR RESIDUE ZN C 204
6	AC6	SOFTWARE	TYR C:13 , SER C:14 , GLY C:15 , LYS C:16 , THR C:17	BINDING SITE FOR RESIDUE SO4 C 303
7	AC7	SOFTWARE	CYS D:140 , CYS D:143 , CYS D:173 , CYS D:176	BINDING SITE FOR RESIDUE ZN D 203
8	AC8	SOFTWARE	TYR D:13 , SER D:14 , GLY D:15 , LYS D:16 , THR D:17 , HOH D:307	BINDING SITE FOR RESIDUE SO4 D 304

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

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

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

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_THEMA	164-177	4	A:167-177 B:167-177 C:168-177 D:168-177

(no "Exon" information available for 2QPO)

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:153
 aligned with KITH_THEMA | Q9WYN2 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:180
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181
           KITH_THEMA     2 SGKLTVITGPMYSGKTTELLSFVEIYKLGKKKVAVFKPKIDSRYHSTMIVSHSGNGVEAHVIERPEEMRKYIEEDTRGVFIDEVQFFNPSLFEVVKDLLDRGIDVFCAGLDLTHKQNPFETTALLLSLADTVIKKKAVCHRCGEYNATLTLKVAGGEEEIDVGGQEKYIAVCRDCYNTLK 181
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee....hhhhhhhhhhhhhhhh..eeeeee.--------------------.ee..hhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhh..eeeeeee........hhhhhhhhhhh.eeee..ee......eee.eeeee.....-------.eeeeehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------TK_CELLULAR_TY---- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2qpo A   2 SGKLTVITGPMYSGKTTELLSFVEIYKLGKKKVAVFKP--------------------AHVIERPEEMRKYIEEDTRGVFIDEVQFFNPSLFEVVKDLLDRGIDVFCAGLDLTHKQNPFETTALLLSLADTVIKKKAVCHRCGEYNATLTLKVAGGEE-------EKYIAVCRDCYNTLK 181
                                    11        21        31       | -         -        61        71        81        91       101       111       121       131       141       151       | -     | 171       181
                                                                39                   60                                                                                                159     167

Chain B from PDB  Type:PROTEIN  Length:150
 aligned with KITH_THEMA | Q9WYN2 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:180
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181
           KITH_THEMA     2 SGKLTVITGPMYSGKTTELLSFVEIYKLGKKKVAVFKPKIDSRYHSTMIVSHSGNGVEAHVIERPEEMRKYIEEDTRGVFIDEVQFFNPSLFEVVKDLLDRGIDVFCAGLDLTHKQNPFETTALLLSLADTVIKKKAVCHRCGEYNATLTLKVAGGEEEIDVGGQEKYIAVCRDCYNTLK 181
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee.....hhhhhhhhhhhhhhhh..eeeeee.------------------.eeee..hhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhh..eeeeee.........hhhhhhhhhhh.eeee..ee......eee.eeee.------------..eeeehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------TK_CELLULAR_TY---- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2qpo B   2 SGKLTVITGPMYSGKTTELLSFVEIYKLGKKKVAVFKP------------------VEAHVIERPEEMRKYIEEDTRGVFIDEVQFFNPSLFEVVKDLLDRGIDVFCAGLDLTHKQNPFETTALLLSLADTVIKKKAVCHRCGEYNATLTLKV------------EKYIAVCRDCYNTLK 181
                                    11        21        31       | -         -      | 61        71        81        91       101       111       121       131       141       151  |      -     | 171       181
                                                                39                 58                                                                                             154          167

Chain C from PDB  Type:PROTEIN  Length:148
 aligned with KITH_THEMA | Q9WYN2 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:180
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181
           KITH_THEMA     2 SGKLTVITGPMYSGKTTELLSFVEIYKLGKKKVAVFKPKIDSRYHSTMIVSHSGNGVEAHVIERPEEMRKYIEEDTRGVFIDEVQFFNPSLFEVVKDLLDRGIDVFCAGLDLTHKQNPFETTALLLSLADTVIKKKAVCHRCGEYNATLTLKVAGGEEEIDVGGQEKYIAVCRDCYNTLK 181
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee....hhhhhhhhhhhhhhhh...eeeee.-------------------..ee..hhhhhhhhh.....eeee.hhhhhhhhhhhhhhhhhhh..eeeeeee........hhhhhhhhhhh.eeee..ee......eee.eee..-------------..eeehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------TK_CELLULAR_TY---- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2qpo C   2 SGKLTVITGPMYSGKTTELLSFVEIYKLGKKKVAVFKP-------------------EAHVIERPEEMRKYIEEDTRGVFIDEVQFFNPSLFEVVKDLLDRGIDVFCAGLDLTHKQNPFETTALLLSLADTVIKKKAVCHRCGEYNATLTLKV-------------KYIAVCRDCYNTLK 181
                                    11        21        31       | -         -       |61        71        81        91       101       111       121       131       141       151  |      -      |171       181
                                                                39                  59                                                                                            154           168

Chain D from PDB  Type:PROTEIN  Length:151
 aligned with KITH_THEMA | Q9WYN2 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:180
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181
           KITH_THEMA     2 SGKLTVITGPMYSGKTTELLSFVEIYKLGKKKVAVFKPKIDSRYHSTMIVSHSGNGVEAHVIERPEEMRKYIEEDTRGVFIDEVQFFNPSLFEVVKDLLDRGIDVFCAGLDLTHKQNPFETTALLLSLADTVIKKKAVCHRCGEYNATLTLKVAGGEEEIDVGGQEKYIAVCRDCYNTLK 181
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -TK-2qpoD01 D:3-177                                                                                                                                                             ---- Pfam domains (1)
           Pfam domains (2) -TK-2qpoD02 D:3-177                                                                                                                                                             ---- Pfam domains (2)
           Pfam domains (3) -TK-2qpoD03 D:3-177                                                                                                                                                             ---- Pfam domains (3)
           Pfam domains (4) -TK-2qpoD04 D:3-177                                                                                                                                                             ---- Pfam domains (4)
         Sec.struct. author ...eeeeee....hhhhhhhhhhhhhhhh...eeeeee..---------------....eee.hhhhhhhhh.....eeee.hhhhhhhhhhhhhhhhhhh..eeeeeee........hhhhhhhhhhh.eeee..............eee.--------------..eeehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------TK_CELLULAR_TY---- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2qpo D   2 SGKLTVITGPMYSGKTTELLSFVEIYKLGKKKVAVFKPKI---------------GVEAHVIERPEEMRKYIEEDTRGVFIDEVQFFNPSLFEVVKDLLDRGIDVFCAGLDLTHKQNPFETTALLLSLADTVIKKKAVCHRCGEYNATLTLK--------------KYIAVCRDCYNTLK 181
                                    11        21        31        41         -     |  61        71        81        91       101       111       121       131       141       151 |       -      |171       181
                                                                  41              57                                                                                             153            168

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 "SCOP Domain" information available for 2QPO)

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: TK (9)

Thermotoga maritima (4)

1a	TK-2qpoD01	D:3-177
1b	TK-2qpoD02	D:3-177
1c	TK-2qpoD03	D:3-177
1d	TK-2qpoD04	D:3-177

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (KITH_THEMA | Q9WYN2)

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.
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.
	GO:0046104	thymidine metabolic process	The chemical reactions and pathways involving thymidine, deoxyribosylthymine thymine 2-deoxyriboside, a deoxynucleoside very widely distributed but occurring almost entirely as phosphoric esters in deoxynucleotides and deoxyribonucleic acid, DNA.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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

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	2qpo
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	KITH_THEMA \| Q9WYN2	:	2orw 2qq0 2qqe

(no "Related Entries Specified in the PDB File" available for 2QPO)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

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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