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Title :   YEAST THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE (DTMP)

Authors :   A. Lavie, I. Schlichting

Date :   12 Jun 97 (Deposition) - 17 Jun 98 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Transferase (Phosphotransferase), Kinase, Thymidine Activation Pathway, Enzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Lavie, I. R. Vetter, M. Konrad, R. S. Goody, J. Reinstein, I. Schlichting
Structure Of Thymidylate Kinase Reveals The Cause Behind The Limiting Step In Azt Activation.
Nat. Struct. Biol. V. 4 601 1997
PubMed-ID: 9253404 | Reference-DOI: 10.1038/NSB0897-601
(for further references see the PDB file header)

Molecule 1 - THYMIDYLATE KINASE
	Chains	:	A, B
	EC Number	:	2.7.4.9
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	CDC8
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION
2	TMP	2	Ligand/Ion	THYMIDINE-5'-PHOSPHATE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:14 , ARG B:15 , THR B:16 , GLY B:17 , LYS B:18 , THR B:19 , HOH B:1035 , HOH B:1036 , HOH B:1203 , HOH B:1352	BINDING SITE FOR RESIDUE SO4 B 218
2	AC2	SOFTWARE	ASP A:14 , LYS A:37 , PHE A:38 , ARG A:41 , LEU A:53 , PHE A:69 , ARG A:73 , ARG A:94 , SER A:98 , GLY A:99 , TYR A:102 , TYR A:151 , HOH A:1235 , HOH A:1236 , HOH A:1241 , HOH A:1301 , HOH A:1302 , HOH A:1303 , HOH A:1304	BINDING SITE FOR RESIDUE TMP A 217
3	AC3	SOFTWARE	ASP B:14 , LYS B:37 , PHE B:38 , PRO B:39 , ARG B:41 , LEU B:53 , PHE B:69 , ARG B:73 , ARG B:94 , GLY B:99 , TYR B:102 , GLU B:149 , TYR B:151 , HOH B:1029 , HOH B:1030 , HOH B:1036 , HOH B:1037 , HOH B:1038	BINDING SITE FOR RESIDUE TMP B 217

(no "SS Bond" information available for 1TMK)

Asymmetric/Biological Unit

No.	Residues
1	Gln A:30	-	Pro A:31
2	Phe A:38	-	Pro A:39
3	Gln B:30	-	Pro B:31
4	Phe B:38	-	Pro B:39

(no "SAP(SNP)/Variant" information available for 1TMK)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THYMIDYLATE_KINASE	PS01331	Thymidylate kinase signature.	KTHY_YEAST	91-103	2	A:91-103 B:91-103

Asymmetric/Biological Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YJR057W	1	YJR057W.1	X:544054-544704	651	KTHY_YEAST	1-216	216	2	A:3-216 (gaps) B:3-216 (gaps)	214 214

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
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Chain A from PDB  Type:PROTEIN  Length:204
 aligned with KTHY_YEAST | P00572 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:214
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212    
           KTHY_YEAST     3 GRGKLILIEGLDRTGKTTQCNILYKKLQPNCKLLKFPERSTRIGGLINEYLTDDSFQLSDQAIHLLFSANRWEIVDKIKKDLLEGKNIVMDRYVYSGVAYSAAKGTNGMDLDWCLQPDVGLLKPDLTLFLSTQDVDNNAEKSGFGDERYETVKFQEKVKQTFMKLLDKEIRKGDESITIVDVTNKGIQEVEALIWQIVEPVLSTHIDHDKFSFF 216
               SCOP domains d1tmka_ A: Thymidylate kinase                                                                                                                                                                                          SCOP domains
               CATH domains 1tmkA00 A:3-216 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.....hhhhhhhhhhh....eeeee......hhhhhhhhhhh.......hhhhhhhhhhhhh..hhhhhhhhh...eeeee..hhhhhhhhhhh......hhhhhhhh.......eeeeee..----------........hhhhhhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------THYMIDYLATE_K----------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:3-216 (gaps) UniProt: 1-216 [INCOMPLETE]                                                                                                                                                              Transcript 1
                 1tmk A   3 GRGKLILIEGLDRTGKTTQCNILYKKLQPNCKLLKFPERSTRIGGLINEYLTDDSFQLSDQAIHLLFSANRWEIVDKIKKDLLEGKNIVMDRYVYSGVAYSAAKGTNGMDLDWCLQPDVGLLKPDLTLFLSTQ----------FGDERYETVKFQEKVKQTFMKLLDKEIRKGDESITIVDVTNKGIQEVEALIWQIVEPVLSTHIDHDKFSFF 216
                                    12        22        32        42        52        62        72        82        92       102       112       122       132  |      -   |   152       162       172       182       192       202       212    
                                                                                                                                                              135        146

Chain B from PDB  Type:PROTEIN  Length:204
 aligned with KTHY_YEAST | P00572 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:214
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212    
           KTHY_YEAST     3 GRGKLILIEGLDRTGKTTQCNILYKKLQPNCKLLKFPERSTRIGGLINEYLTDDSFQLSDQAIHLLFSANRWEIVDKIKKDLLEGKNIVMDRYVYSGVAYSAAKGTNGMDLDWCLQPDVGLLKPDLTLFLSTQDVDNNAEKSGFGDERYETVKFQEKVKQTFMKLLDKEIRKGDESITIVDVTNKGIQEVEALIWQIVEPVLSTHIDHDKFSFF 216
               SCOP domains d1tmkb_ B: Thymidylate kinase                                                                                                                                                                                          SCOP domains
               CATH domains 1tmkB00 B:3-216 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                   CATH domains
           Pfam domains (1) -------Thymidylate_kin-1tmkB01 B:10-196                                                                                                                                                           -------------------- Pfam domains (1)
           Pfam domains (2) -------Thymidylate_kin-1tmkB02 B:10-196                                                                                                                                                           -------------------- Pfam domains (2)
         Sec.struct. author ....eeeeee.....hhhhhhhhhhh....eeeee......hhhhhhhhhhh.......hhhhhhhhhhhhh..hhhhhhhhh...eeeee..hhhhhhhhhhh......hhhhhhhh.......eeeeee..----------........hhhhhhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------THYMIDYLATE_K----------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:3-216 (gaps) UniProt: 1-216 [INCOMPLETE]                                                                                                                                                              Transcript 1
                 1tmk B   3 GRGKLILIEGLDRTGKTTQCNILYKKLQPNCKLLKFPERSTRIGGLINEYLTDDSFQLSDQAIHLLFSANRWEIVDKIKKDLLEGKNIVMDRYVYSGVAYSAAKGTNGMDLDWCLQPDVGLLKPDLTLFLSTQ----------FGDERYETVKFQEKVKQTFMKLLDKEIRKGDESITIVDVTNKGIQEVEALIWQIVEPVLSTHIDHDKFSFF 216
                                    12        22        32        42        52        62        72        82        92       102       112       122       132  |      -   |   152       162       172       182       192       202       212    
                                                                                                                                                              135        146

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: Nucleotide and nucleoside kinases (231)

Protein domain: Thymidylate kinase (34)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (3)

1a	d1tmka_	A:
1b	d1tmkb_	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)

Baker's yeast (Saccharomyces cerevisiae) (61)

1a	1tmkA00	A:3-216
1b	1tmkB00	B:3-216

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Thymidylate_kin (26)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (3)

1a	Thymidylate_kin-1tmkB01	B:10-196
1b	Thymidylate_kin-1tmkB02	B:10-196

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (KTHY_YEAST | P00572)

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: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: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.
	GO:0009041	uridylate kinase activity	Catalysis of the reaction: ATP + (d)UMP = ADP + (d)UDP.
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:0006227	dUDP biosynthetic process	The chemical reactions and pathways resulting in the formation of dUDP, deoxyuridine diphosphate (2'-deoxy-5'-uridylyl phosphate).
	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.
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.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Asymmetric/Biological Unit
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Description

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