2JA1 - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   THYMIDINE KINASE FROM B. CEREUS WITH TTP BOUND AS PHOSPHATE DONOR.

Authors :   U. Kosinska, C. Carnrot, M. P. B. Sandrini, A. R. Clausen, L. Wang, J. Pis S. Eriksson, H. Eklund

Date :   17 Nov 06 (Deposition) - 23 Jan 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)

Keywords :   Tk1, Dnk, Lasso, Kinase, Transferase, Phosphate Donor, Deoxyribonucleoside Kinase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   U. Kosinska, C. Carnrot, M. P. B. Sandrini, A. R. Clausen, L. Wang, J. Piskur, S. Eriksson, H. Eklund
Structural Studies Of Thymidine Kinases From Bacillus Anthracis And Bacillus Cereus Provide Insights Into Quaternary Structure And Conformational Changes Upon Substrate Binding
Febs J. V. 274 727 2007
PubMed-ID: 17288553 | Reference-DOI: 10.1111/J.1742-4658.2006.05617.X

Molecule 1 - THYMIDINE KINASE
	Chains	:	A
	EC Number	:	2.7.1.21
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	KY895
	Expression System Taxid	:	562
	Expression System Vector	:	PGEX-2T
	Organism Scientific	:	BACILLUS CEREUS
	Organism Taxid	:	1396
	Strain	:	DVI
	Variant	:	98-7869

		1
Asymmetric Unit	:	A
Biological Unit 1 (4x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
2	TTP	1	Ligand/Ion	THYMIDINE-5'-TRIPHOSPHATE
3	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	MPD	4	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
2	TTP	4	Ligand/Ion	THYMIDINE-5'-TRIPHOSPHATE
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:145 , CYS A:148 , CYS A:183 , CYS A:186	BINDING SITE FOR RESIDUE ZN A1192
2	AC2	SOFTWARE	SER A:16 , PHE A:18 , SER A:19 , GLY A:20 , LYS A:21 , SER A:22 , GLU A:23 , PHE A:34 , VAL A:56 , SER A:57 , HIS A:58 , ASN A:59 , ASP A:88 , GLU A:89 , VAL A:144 , HOH A:2009 , HOH A:2020	BINDING SITE FOR RESIDUE TTP A1193
3	AC3	SOFTWARE	PHE A:92 , LEU A:116 , ASP A:119 , PHE A:120 , PHE A:125 , ILE A:170 , TYR A:179	BINDING SITE FOR RESIDUE MPD A1194

(no "SS Bond" information available for 2JA1)

(no "Cis Peptide Bond" information available for 2JA1)

(no "SAP(SNP)/Variant" information available for 2JA1)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TK_CELLULAR_TYPE	PS00603	Thymidine kinase cellular-type signature.	KITH_BACCR	174-187	1	A:174-187

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_BACCR	174-187	4	A:174-187

(no "Exon" information available for 2JA1)

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:193
 aligned with KITH_BACCR | Q814U0 from UniProtKB/Swiss-Prot  Length:195

    Alignment length:193
                              1                                                                                                                                                                                              
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188   
           KITH_BACCR     - --MYLINQNGWIEVICGSMFSGKSEELIRRVRRTQFAKQHAIVFKPCIDNRYSEEDVVSHNGLKVKAVPVSASKDIFEHITEELDVIAIDEVQFFDGDIVEVVQVLANRGYRVIVAGLDQDFRGLPFGQVPQLMAIAEHVTKLQAVCSVCGSPASRTQRLIDGEPAAFDDPIILVGASESYEPRCRHCHAVPA 191
               SCOP domains d2ja1a1 A:-1-142 automated matches                                                                                                              d2ja1a2 A:143-191 automated matches               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeee....hhhhhhhhhhhhhhhh...eeeeee.........eee.....eee.eee.hhhhhhhhh.....eeee.hhhhh..hhhhhhhhhhhh..eeeeeee..........hhhhhhhhh.eeee..eee...eeee.eeeeee..ee.............eeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TK_CELLULAR_TY---- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ja1 A  -1 GSMYLINQNGWIEVICGSMFSGKSEELIRRVRRTQFAKQHAIVFKPCIDNRYSEEDVVSHNGLKVKAVPVSASKDIFEHITEELDVIAIDEVQFFDGDIVEVVQVLANRGYRVIVAGLDQDFRGLPFGQVPQLMAIAEHVTKLQAVCSVCGSPASRTQRLIDGEPAAFDDPIILVGASESYEPRCRHCHAVPA 191
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188

Chain A from PDB  Type:PROTEIN  Length:193
 aligned with Q0H0H6_BACCE | Q0H0H6 from UniProtKB/TrEMBL  Length:195

    Alignment length:193
                              1                                                                                                                                                                                              
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188   
         Q0H0H6_BACCE     - --MYLINQNGWIEVICGSMFSGKSEELIRRVRRTQFAKQHAIVFKPCIDNRYSEEDVVSHNGLKVKAVPVSASKDIFEHITEELDVIAIDEVQFFDGDIVEVVQVLANRGYRVIVAGLDQDFRGLPFGQVPQLMAIAEHVTKLQAVCSVCGSPASRTQRLIDGEPAAFDDPIILVGASESYEPRCRHCHAVPA 191
               SCOP domains d2ja1a1 A:-1-142 automated matches                                                                                                              d2ja1a2 A:143-191 automated matches               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeee....hhhhhhhhhhhhhhhh...eeeeee.........eee.....eee.eee.hhhhhhhhh.....eeee.hhhhh..hhhhhhhhhhhh..eeeeeee..........hhhhhhhhh.eeee..eee...eeee.eeeeee..ee.............eeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ja1 A  -1 GSMYLINQNGWIEVICGSMFSGKSEELIRRVRRTQFAKQHAIVFKPCIDNRYSEEDVVSHNGLKVKAVPVSASKDIFEHITEELDVIAIDEVQFFDGDIVEVVQVLANRGYRVIVAGLDQDFRGLPFGQVPQLMAIAEHVTKLQAVCSVCGSPASRTQRLIDGEPAAFDDPIILVGASESYEPRCRHCHAVPA 191
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188

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 2JA1)

(no "Pfam Domain" information available for 2JA1)

Asymmetric Unit(hide GO term definitions)

Chain A (KITH_BACCR | Q814U0)

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.
	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.

Chain A (Q0H0H6_BACCE | Q0H0H6)

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 Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2ja1)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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