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Biological Unit 2 (Jmol Viewer)

Title :   HUMAN THYMIDINE KINASE 1 IN COMPLEX WITH TP4A

Authors :   D. Segura-Pena, S. Lutz, C. Monnerjahn, M. Konrad, A. Lavie

Date :   04 Feb 07 (Deposition) - 27 Mar 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Tk-1 (Thymidine Kinase 1), Tp4A (P1-(5'-Adenosyl)P4-(5'- (2'Deoxythymidil))Tetraphosphate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Segura-Pena, S. Lutz, C. Monnerjahn, M. Konrad, A. Lavie
Binding Of Atp To Tk1-Like Enzymes Is Associated With A Conformational Change In The Quaternary Structure.
J. Mol. Biol. V. 369 129 2007
PubMed-ID: 17407781 | Reference-DOI: 10.1016/J.JMB.2007.02.104

Molecule 1 - THYMIDINE KINASE
	Chains	:	A, B
	EC Number	:	2.7.1.21
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET14B
	Expression System Strain	:	BL21(D3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TK1
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	4TA	2	Ligand/Ion	P1-(5'-ADENOSYL)P4-(5'-(2'-DEOXY-THYMIDYL))TETRAPHOSPHATE
2	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	4TA	4	Ligand/Ion	P1-(5'-ADENOSYL)P4-(5'-(2'-DEOXY-THYMIDYL))TETRAPHOSPHATE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	4TA	2	Ligand/Ion	P1-(5'-ADENOSYL)P4-(5'-(2'-DEOXY-THYMIDYL))TETRAPHOSPHATE
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:153 , CYS A:156 , CYS A:185 , CYS A:188	BINDING SITE FOR RESIDUE ZN A 235
2	AC2	SOFTWARE	CYS B:153 , CYS B:156 , CYS B:185 , CYS B:188	BINDING SITE FOR RESIDUE ZN B 235
3	AC3	SOFTWARE	MET A:28 , PHE A:29 , SER A:30 , GLY A:31 , LYS A:32 , SER A:33 , ASP A:58 , ARG A:60 , ASP A:97 , GLU A:98 , GLN A:100 , PHE A:101 , LEU A:124 , THR A:127 , PHE A:128 , PHE A:133 , VAL A:172 , GLU A:173 , VAL A:174 , ILE A:175 , GLY A:176 , TYR A:181 , HOH A:806 , HOH A:810 , HOH A:823 , HOH A:831 , HOH A:846 , HOH A:863 , HOH A:868 , HOH A:880	BINDING SITE FOR RESIDUE 4TA A 801
4	AC4	SOFTWARE	MET B:28 , PHE B:29 , SER B:30 , GLY B:31 , LYS B:32 , SER B:33 , ASP B:58 , ASP B:97 , GLU B:98 , GLN B:100 , PHE B:101 , LEU B:124 , THR B:127 , PHE B:128 , PHE B:133 , THR B:163 , ARG B:165 , VAL B:172 , GLU B:173 , VAL B:174 , ILE B:175 , GLY B:176 , TYR B:181 , HOH B:808 , HOH B:821 , HOH B:834 , HOH B:872	BINDING SITE FOR RESIDUE 4TA B 802

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

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

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TK_CELLULAR_TYPE	PS00603	Thymidine kinase cellular-type signature.	KITH_HUMAN	176-189	2	A:176-189 B:176-189

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TK_CELLULAR_TYPE	PS00603	Thymidine kinase cellular-type signature.	KITH_HUMAN	176-189	4	A:176-189 B:176-189

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TK_CELLULAR_TYPE	PS00603	Thymidine kinase cellular-type signature.	KITH_HUMAN	176-189	2	A:176-189 B:176-189

Asymmetric Unit (7, 14)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000301634	1a	ENSE00001563417	chr17:76183314-76183010	305	KITH_HUMAN	1-22	22	2	A:18-22 B:18-22	5 5
1.2	ENST00000301634	2	ENSE00001118176	chr17:76182899-76182868	32	KITH_HUMAN	23-33	11	2	A:23-33 B:23-33	11 11
1.3	ENST00000301634	3	ENSE00001194741	chr17:76181246-76181136	111	KITH_HUMAN	33-70	38	2	A:33-61 B:33-58	29 26
1.4	ENST00000301634	4	ENSE00001118177	chr17:76178763-76178670	94	KITH_HUMAN	70-101	32	2	A:73-101 B:73-101	29 29
1.5	ENST00000301634	5	ENSE00001118174	chr17:76171699-76171610	90	KITH_HUMAN	102-131	30	2	A:102-131 B:102-131	30 30
1.6	ENST00000301634	6	ENSE00001118182	chr17:76171250-76171131	120	KITH_HUMAN	132-171	40	2	A:132-171 B:132-171	40 40
1.7b	ENST00000301634	7b	ENSE00001274786	chr17:76171031-76170160	872	KITH_HUMAN	172-234	63	2	A:172-191 B:172-191	20 20

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:163
 aligned with KITH_HUMAN | P04183 from UniProtKB/Swiss-Prot  Length:234

    Alignment length:174
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187    
           KITH_HUMAN    18 RGQIQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKDTRYSSSFCTHDRNTMEALPACLLRDVAQEALGVAVIGIDEGQFFPDIVEFCEAMANAGKTVIVAALDGTFQRKPFGAILNLVPLAESVVKLTAVCMECFREAAYTKRLGTEKEVEVIGGADKYHSVCRLCYFK 191
               SCOP domains d2orva1 A:18-150 Thymidine kinase, TK1, N-te           rminal domain                                                                 d2orva2 A:151-191                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhh....eeeeee......-----------.eeeee.hhhhhhhhhh...eeee.hhhhh.hhhhhhhhhhhh..eeeee............hhhhhhhhh.eeee..ee......ee.eeee...............eeeehhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------TK_CELLULAR_TY-- PROSITE
           Transcript 1 (1) 1.1a Exon 1.2   ------------------------------------Exon 1.4  PDB: A:73-101         Exon 1.5  PDB: A:102-131      Exon 1.6  PDB: A:132-171                Exon 1.7b            Transcript 1 (1)
           Transcript 1 (2) ---------------Exon 1.3  PDB: A:33-61 UniProt: 33-70 ------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2orv A  18 RGQIQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKDTRY-----------MEALPACLLRDVAQEALGVAVIGIDEGQFFPDIVEFCEAMANAGKTVIVAALDGTFQRKPFGAILNLVPLAESVVKLTAVCMECFREAAYTKRLGTEKEVEVIGGADKYHSVCRLCYFK 191
                                    27        37        47        57   |     -     |  77        87        97       107       117       127       137       147       157       167       177       187    
                                                                      61          73

Chain B from PDB  Type:PROTEIN  Length:160
 aligned with KITH_HUMAN | P04183 from UniProtKB/Swiss-Prot  Length:234

    Alignment length:174
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187    
           KITH_HUMAN    18 RGQIQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKDTRYSSSFCTHDRNTMEALPACLLRDVAQEALGVAVIGIDEGQFFPDIVEFCEAMANAGKTVIVAALDGTFQRKPFGAILNLVPLAESVVKLTAVCMECFREAAYTKRLGTEKEVEVIGGADKYHSVCRLCYFK 191
               SCOP domains d2orvb1 B:18-150 Thymidine kinase, TK1, N              -terminal domain                                                              d2orvb2 B:151-191                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhh....eeeeee...--------------.eeeee.hhhhhhhhhh...eeee.hhhhh.hhhhhhhhhhhh..eeeee............hhhhhhhhh.eeee..ee......ee.eeee...............eeeehhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------TK_CELLULAR_TY-- PROSITE
           Transcript 1 (1) 1.1a Exon 1.2   ------------------------------------Exon 1.4  PDB: B:73-101         Exon 1.5  PDB: B:102-131      Exon 1.6  PDB: B:132-171                Exon 1.7b            Transcript 1 (1)
           Transcript 1 (2) ---------------Exon 1.3  PDB: B:33-58 UniProt: 33-70 ------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2orv B  18 RGQIQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKD--------------MEALPACLLRDVAQEALGVAVIGIDEGQFFPDIVEFCEAMANAGKTVIVAALDGTFQRKPFGAILNLVPLAESVVKLTAVCMECFREAAYTKRLGTEKEVEVIGGADKYHSVCRLCYFK 191
                                    27        37        47        57|        -     |  77        87        97       107       117       127       137       147       157       167       177       187    
                                                                   58             73

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 2ORV)

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (KITH_HUMAN | P04183)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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:0019206	nucleoside kinase activity	Catalysis of the reaction: ATP + nucleoside = ADP + nucleoside monophosphate.
	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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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:0048565	digestive tract development	The process whose specific outcome is the progression of the digestive tract over time, from its formation to the mature structure. The digestive tract is the anatomical structure through which food passes and is processed.
	GO:0060138	fetal process involved in parturition	A reproductive process occurring in the embryo that results in birth.
	GO:0001889	liver development	The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes.
	GO:0006139	nucleobase-containing compound metabolic process	Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
	GO:0009165	nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).
	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:0051289	protein homotetramerization	The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
	GO:0043097	pyrimidine nucleoside salvage	Any process that generates a pyrimidine nucleoside, one of a family of organic molecules consisting of a pyrimidine base covalently bonded to a sugar ribose, from derivatives of it, without de novo synthesis.
	GO:0046688	response to copper ion	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a copper ion stimulus.
	GO:0051414	response to cortisol	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cortisol stimulus. Cortisol is the major natural glucocorticoid synthesized in the zona fasciculata of the adrenal cortex; it affects the metabolism of glucose, protein, and fats and has appreciable mineralocorticoid activity. It also regulates the immune system and affects many other functions.
	GO:0031667	response to nutrient levels	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting the presence, absence, or concentration of nutrients.
	GO:0009636	response to toxic substance	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus.
	GO:0014856	skeletal muscle cell proliferation	The multiplication or reproduction of skeletal muscle cells, resulting in the expansion of a cell population.
	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.

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2orw	THERMOTOGA MARITIMA THYMIDINE KINASE 1 LIKE ENZYME IN COMPLEX WITH TP4A

Description

Compounds

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Ligands, Modified Residues, Ions (2, 4)

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