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Title :   CRYSTAL STRUCTURE OF UNLIGANDED S. AUREUS THYMIDYLATE KINASE

Authors :   M. Kotaka, B. Dhaliwal, J. Ren, C. E. Nichols, R. Angell, M. Lockyer, A. R. Hawkins, D. K. Stammers

Date :   16 Jan 06 (Deposition) - 08 Mar 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.21

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

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

Reference :   M. Kotaka, B. Dhaliwal, J. Ren, C. E. Nichols, R. Angell, M. Lockyer, A. R. Hawkins, D. K. Stammers
Structures Of S. Aureus Thymidylate Kinase Reveal An Atypical Active Site Configuration And An Intermediate Conformational State Upon Substrate Binding
Protein Sci. V. 15 774 2006
PubMed-ID: 16522804 | Reference-DOI: 10.1110/PS.052002406

Molecule 1 - THYMIDYLATE KINASE
	Chains	:	A, B
	EC Number	:	2.7.4.9
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET3A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	1280
	Synonym	:	DTMP KINASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 6)

No.	Name	Count	Type	Full Name
1	CL	5	Ligand/Ion	CHLORIDE ION
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:132 , SER A:180 , ASN A:182	BINDING SITE FOR RESIDUE CL A1206
2	AC2	SOFTWARE	LEU A:187 , HOH B:2065	BINDING SITE FOR RESIDUE CL A1207
3	AC3	SOFTWARE	THR A:35 , ARG A:36 , GLY A:39 , LYS A:77 , HOH A:2029 , HOH A:2030	BINDING SITE FOR RESIDUE CL A1208
4	AC4	SOFTWARE	LYS A:83	BINDING SITE FOR RESIDUE CL A1209
5	AC5	SOFTWARE	LEU B:187 , HOH B:2079	BINDING SITE FOR RESIDUE CL B1206
6	AC6	SOFTWARE	ARG A:71 , ILE A:79 , ILE A:120 , ASN A:121	BINDING SITE FOR RESIDUE EDO A1210

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

Asymmetric/Biological Unit

No.	Residues
1	Glu A:37	-	Pro A:38
2	Glu B:37	-	Pro B:38

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THYMIDYLATE_KINASE	PS01331	Thymidylate kinase signature.	KTHY_STAAM	89-101	2	A:89-101 B:89-101

(no "Exon" information available for 2CCK)

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:193
 aligned with KTHY_STAAM | P65248 from UniProtKB/Swiss-Prot  Length:205

    Alignment length:204
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201    
           KTHY_STAAM     2 SAFITFEGPEGSGKTTVINEVYHRLVKDYDVIMTREPGGVPTGEEIRKIVLEGNDMDIRTEAMLFAASRREHLVLKVIPALKEGKVVLCDRYIDSSLAYQGYARGIGVEEVRALNEFAINGLYPDLTIYLNVSAEVGRERIIKNSRDQNRLDQEDLKFHEKVIEGYQEIIHNESQRFKSVNADQPLENVVEDTYQTIIKYLEKI 205
               SCOP domains d2ccka_ A: automated matches                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhh--..hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhh......hhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhh.----..hhhhhhhhhhhhhhhhhhh-----.eeeee...hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------THYMIDYLATE_K-------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2cck A   2 SAFITFEGPEGSGKTTVINEVYHRLVKDYDVIMTREPGGVPTGEEIRKIVLE--DMDIRTEAMLFAASRREHLVLKVIPALKEGKVVLCDRYIDSSLAYQGYARGIGVEEVRALNEFAINGLYPDLTIYLNVSAEVGRERIIKNS----RLDQEDLKFHEKVIEGYQEII-----RFKSVNADQPLENVVEDTYQTIIKYLEKI 205
                                    11        21        31        41        51 |  |   61        71        81        91       101       111       121       131       141    |  151       161       171     | 181       191       201    
                                                                              53 56                                                                                       146  151                 171   177

Chain B from PDB  Type:PROTEIN  Length:193
 aligned with KTHY_STAAM | P65248 from UniProtKB/Swiss-Prot  Length:205

    Alignment length:204
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201    
           KTHY_STAAM     2 SAFITFEGPEGSGKTTVINEVYHRLVKDYDVIMTREPGGVPTGEEIRKIVLEGNDMDIRTEAMLFAASRREHLVLKVIPALKEGKVVLCDRYIDSSLAYQGYARGIGVEEVRALNEFAINGLYPDLTIYLNVSAEVGRERIIKNSRDQNRLDQEDLKFHEKVIEGYQEIIHNESQRFKSVNADQPLENVVEDTYQTIIKYLEKI 205
               SCOP domains d2cckb_ B: automated matches                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhh.-..hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhh......hhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhh-----..hhhhhhhhhhhhhhhhhhh-----.eeeee...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------THYMIDYLATE_K-------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2cck B   2 SAFITFEGPEGSGKTTVINEVYHRLVKDYDVIMTREPGGVPTGEEIRKIVLEG-DMDIRTEAMLFAASRREHLVLKVIPALKEGKVVLCDRYIDSSLAYQGYARGIGVEEVRALNEFAINGLYPDLTIYLNVSAEVGRERIIKN-----RLDQEDLKFHEKVIEGYQEII-----RFKSVNADQPLENVVEDTYQTIIKYLEKI 205
                                    11        21        31        41        51  | |   61        71        81        91       101       111       121       131       141   |   151       161       171     | 181       191       201    
                                                                               54 |                                                                                      145   151                 171   177                            
                                                                                 56

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)

Staphylococcus aureus [TaxId: 1280] (4)

1a	d2ccka_	A:
1b	d2cckb_	B:

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (KTHY_STAAM | P65248)

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
		Glu A:37 - Pro A:38	[ RasMol ]
		Glu B:37 - Pro B:38	[ RasMol ]

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	2.7.4.9
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UniProtKB/Swiss-Prot
	KTHY_STAAM \| P65248	:	2ccg 2ccj 4dwj 4eaq 4f4i 4gfd 4mqb

2ccg	CRYSTAL STRUCTURE OF HIS-TAGGED S. AUREUS THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE (TMP)
2ccj	CRYSTAL STRUCTURE OF S. AUREUS THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE (TMP)

Description

Compounds

Structural Features

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Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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SAPs(SNPs)/Variants (0, 0)

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