2V54 - JenaLib

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Title :   CRYSTAL STRUCTURE OF VACCINIA VIRUS THYMIDYLATE KINASE BOUND TO TDP

Authors :   C. Caillat, D. Topalis, L. A. Agrofoglio, S. Pochet, J. Balzarini, D. Deville-Bonne, P. Meyer

Date :   01 Oct 08 (Deposition) - 21 Oct 08 (Release) - 16 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Nucleotide Biosynthesis, Atp-Binding, Nucleotide-Binding, Kinase, Poxvirus, Tmp Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Caillat, D. Topalis, L. A. Agrofoglio, S. Pochet, J. Balzarini, D. Deville-Bonne, P. Meyer
Crystal Structure Of Poxvirus Thymidylate Kinase: An Unexpected Dimerization Has Implications For Antiviral Therapy
Proc. Nat. Acad. Sci. Usa V. 105 16900 2008
PubMed-ID: 18971333 | Reference-DOI: 10.1073/PNAS.0804525105

Molecule 1 - THYMIDYLATE KINASE
	Chains	:	A, B
	EC Number	:	2.7.4.9
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3) ROSETTA PLYSS
	Expression System Taxid	:	469008
	Organism Scientific	:	VACCINIA VIRUS COPENHAGEN
	Organism Taxid	:	10249
	Synonym	:	DTMP KINASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 4)

No.	Name	Count	Type	Full Name
1	MG	1	Ligand/Ion	MAGNESIUM ION
2	POP	1	Ligand/Ion	PYROPHOSPHATE 2-
3	TYD	2	Ligand/Ion	THYMIDINE-5'-DIPHOSPHATE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:13 , GLU B:145 , POP B:1206 , TYD B:1207 , HOH B:2046	BINDING SITE FOR RESIDUE MG B1205
2	AC2	SOFTWARE	ASP A:13 , LYS A:17 , THR A:18 , ASN A:37 , PHE A:38 , PRO A:39 , ARG A:41 , LEU A:53 , PHE A:68 , ARG A:72 , ASP A:92 , ARG A:93 , GLY A:98 , TYR A:101 , TYR A:144 , HOH A:2009 , HOH A:2024 , HOH A:2046	BINDING SITE FOR RESIDUE TYD A1205
3	AC3	SOFTWARE	LYS B:14 , SER B:15 , GLY B:16 , LYS B:17 , THR B:18 , GLU B:145 , MG B:1205 , TYD B:1207 , HOH B:2005	BINDING SITE FOR RESIDUE POP B1206
4	AC4	SOFTWARE	ASP B:13 , LYS B:17 , PHE B:38 , PRO B:39 , ARG B:41 , LEU B:53 , PHE B:68 , ARG B:72 , ARG B:93 , SER B:97 , GLY B:98 , TYR B:101 , TYR B:144 , MG B:1205 , POP B:1206 , HOH B:2009 , HOH B:2028 , HOH B:2046	BINDING SITE FOR RESIDUE TYD B1207

(no "SS Bond" information available for 2V54)

Asymmetric/Biological Unit

No.	Residues
1	Phe A:38	-	Pro A:39
2	Phe B:38	-	Pro B:39

(no "SAP(SNP)/Variant" information available for 2V54)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THYMIDYLATE_KINASE	PS01331	Thymidylate kinase signature.	KTHY_VACCC	90-102	2	A:90-102 B:90-102

(no "Exon" information available for 2V54)

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:204
 aligned with KTHY_VACCC | P68693 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:204
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200    
           KTHY_VACCC     1 MSRGALIVFEGLDKSGKTTQCMNIMESIPANTIKYLNFPQRSTVTGKMIDDYLTRKKTYNDHIVNLLFCANRWEFASFIQEQLEQGITLIVDRYAFSGVAYAAAKGASMTLSKSYESGLPKPDLVIFLESGSKEINRNVGEEIYEDVTFQQKVLQEYKKMIEEGDIHWQIISSEFEEDVKKELIKNIVIEAIHTVTGPVGQLWM 204
               SCOP domains d2v54a_ A: automated matches                                                                                                                                                                                 SCOP domains
               CATH domains 2v54A00 A:1-204 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeee.....hhhhhhhhhhhh.hhh.eeeee.....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhh..hhhhhhhhhh......eeeee..hhhhhh..........hhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------THYMIDYLATE_K------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2v54 A   1 MSRGALIVFEGLDKSGKTTQCMNIMESIPANTIKYLNFPQRSTVTGKMIDDYLTRKKTYNDHIVNLLFCANRWEFASFIQEQLEQGITLIVDRYAFSGVAYAAAKGASMTLSKSYESGLPKPDLVIFLESGSKEINRNVGEEIYEDVTFQQKVLQEYKKMIEEGDIHWQIISSEFEEDVKKELIKNIVIEAIHTVTGPVGQLWM 204
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Chain B from PDB  Type:PROTEIN  Length:203
 aligned with KTHY_VACCC | P68693 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:203
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201   
           KTHY_VACCC     2 SRGALIVFEGLDKSGKTTQCMNIMESIPANTIKYLNFPQRSTVTGKMIDDYLTRKKTYNDHIVNLLFCANRWEFASFIQEQLEQGITLIVDRYAFSGVAYAAAKGASMTLSKSYESGLPKPDLVIFLESGSKEINRNVGEEIYEDVTFQQKVLQEYKKMIEEGDIHWQIISSEFEEDVKKELIKNIVIEAIHTVTGPVGQLWM 204
               SCOP domains d2v54b_ B: automated matches                                                                                                                                                                                SCOP domains
               CATH domains 2v54B00 B:2-204 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                        CATH domains
           Pfam domains (1) -------Thymidylate_kin-2v54B01 B:9-184                                                                                                                                                 -------------------- Pfam domains (1)
           Pfam domains (2) -------Thymidylate_kin-2v54B02 B:9-184                                                                                                                                                 -------------------- Pfam domains (2)
         Sec.struct. author ....eeeeee....hhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhh..hhhhhhhhhh......eeeee..hhhhhhh........hhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------THYMIDYLATE_K------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v54 B   2 SRGALIVFEGLDKSGKTTQCMNIMESIPANTIKYLNFPQRSTVTGKMIDDYLTRKKTYNDHIVNLLFCANRWEFASFIQEQLEQGITLIVDRYAFSGVAYAAAKGASMTLSKSYESGLPKPDLVIFLESGSKEINRNVGEEIYEDVTFQQKVLQEYKKMIEEGDIHWQIISSEFEEDVKKELIKNIVIEAIHTVTGPVGQLWM 204
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: P-loop containing nucleoside triphosphate hydrolases (2083)

Superfamily: P-loop containing nucleoside triphosphate hydrolases (2083)

Family: automated matches (303)

Protein domain: automated matches (303)

Vaccinia virus copenhagen [TaxId: 10249] (2)

1a	d2v54a_	A:
1b	d2v54b_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Vaccinia virus copenhagen. Organism_taxid: 10249. (2)

1a	2v54A00	A:1-204
1b	2v54B00	B:2-204

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Thymidylate_kin (26)

Vaccinia virus (strain Copenhagen) (VACV) (2)

1a	Thymidylate_kin-2v54B01	B:9-184
1b	Thymidylate_kin-2v54B02	B:9-184

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (KTHY_VACCC | P68693)

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: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:0004798	thymidylate kinase activity	Catalysis of the reaction: ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate.
	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:0006233	dTDP biosynthetic process	The chemical reactions and pathways resulting in the formation of dTDP, deoxyribosylthymine diphosphate (2'-deoxyribosylthymine5'-diphosphate).
	GO:0006235	dTTP biosynthetic process	The chemical reactions and pathways resulting in the formation of dTTP, deoxyribosylthymine triphosphate.
	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:0046939	nucleotide phosphorylation	The process of introducing one or more phosphate groups into a nucleotide to produce a phosphorylated nucleoside.
	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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Phe A:38 - Pro A:39	[ RasMol ]
		Phe B:38 - Pro B:39	[ RasMol ]

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	KTHY_VACCC \| P68693	:	2w0s

2w0s	CRYSTAL STRUCTURE OF VACCINIA VIRUS THYMIDYLATE KINASE BOUND TO BRIVUDIN-5'- MONOPHOSPHATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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