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Title :   CRYSTAL STRUCTURE OF THYMIDYLATE KINASE FROM EHRLICHIA CHAFFEENSIS AT 2.15A RESOLUTION

Authors :   Seattle Structural Genomics Center For Infectious Disease (S

Date :   12 Jan 10 (Deposition) - 16 Feb 10 (Release) - 21 Sep 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

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

Keywords :   Ssgcid, Nih, Niaid, Sbri, Uw, Emerald Biostructures, Ehrlichia Chaffeensis, Thymidylate Kinase, Als Collaborative Crystallography, Atp-Binding, Kinase, Nucleotide Biosynthesis, Nucleotide-Binding, Transferase, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. J. Leibly, J. Abendroth, C. M. Bryan, B. Sankaran, A. Kelley, L. K. Barrett, L. Stewart, W. C. Van Voorhis
Structure Of Thymidylate Kinase From Ehrlichia Chaffeensis.
Acta Crystallogr. , Sect. F V. 67 1090 2011
PubMed-ID: 21904055 | Reference-DOI: 10.1107/S174430911101493X

Molecule 1 - THYMIDYLATE KINASE
	Chains	:	A, B, C, D
	EC Number	:	2.7.4.9
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	AVA0421
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	TMK, ECH_0229
	Organism Scientific	:	EHRLICHIA CHAFFEENSIS
	Organism Taxid	:	205920
	Strain	:	ARKANSAS
	Synonym	:	DTMP KINASE

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 6)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:8 , ASP A:9 , GLY A:10 , SER A:11 , GLY A:12 , LYS A:13 , THR A:14 , HOH A:256	BINDING SITE FOR RESIDUE SO4 A 300
2	AC2	SOFTWARE	ILE B:8 , ASP B:9 , GLY B:10 , SER B:11 , GLY B:12 , LYS B:13 , THR B:14 , HOH B:260 , HOH B:275	BINDING SITE FOR RESIDUE SO4 B 300
3	AC3	SOFTWARE	GLU B:38 , ARG B:71 , ARG B:93 , PHE B:94 , THR B:98 , HOH B:204	BINDING SITE FOR RESIDUE EDO B 301
4	AC4	SOFTWARE	ILE C:8 , GLY C:10 , SER C:11 , GLY C:12 , LYS C:13 , THR C:14	BINDING SITE FOR RESIDUE SO4 C 300
5	AC5	SOFTWARE	ASP D:9 , GLY D:10 , SER D:11 , GLY D:12 , LYS D:13 , THR D:14 , HOH D:210 , HOH D:237	BINDING SITE FOR RESIDUE SO4 D 300
6	AC6	SOFTWARE	GLU D:38 , PHE D:67 , ARG D:71 , PHE D:94 , THR D:98 , HOH D:282	BINDING SITE FOR RESIDUE EDO D 301

(no "SS Bond" information available for 3LD9)

Asymmetric/Biological Unit

No.	Residues
1	Glu A:38	-	Pro A:39
2	Glu B:38	-	Pro B:39
3	Glu C:38	-	Pro C:39
4	Glu D:38	-	Pro D:39

(no "SAP(SNP)/Variant" information available for 3LD9)

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THYMIDYLATE_KINASE	PS01331	Thymidylate kinase signature.	KTHY_EHRCR	90-102	4	A:90-102 B:90-102 C:90-102 D:90-102

(no "Exon" information available for 3LD9)

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:187
 aligned with KTHY_EHRCR | Q2GHN3 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:203
                               1                                                                                                                                                                                                       
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197   
           KTHY_EHRCR     - ---MFITFEGIDGSGKTTQSHLLAEYLSEIYGVNNVVLTREPGGTLLNESVRNLLFKAQGLDSLSELLFFIAMRREHFVKIIKPSLMQKKIVICDRFIDSTIAYQGYGQGIDCSLIDQLNDLVIDVYPDITFIIDVDINESLSRSCKNGYEFADMEFYYRVRDGFYDIAKKNPHRCHVITDKSETYDIDDINFVHLEVIKVLQ 200
               SCOP domains d3ld9a_ A: automated matches                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.....hhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhh.....hhhhhhhhhhhhh.....eeeeee..----------------hhhhhhhhhhhhhhhhhhh...eeeee........hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------THYMIDYLATE_K-------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ld9 A  -2 PGSMFITFEGIDGSGKTTQSHLLAEYLSEIYGVNNVVLTREPGGTLLNESVRNLLFKAQGLDSLSELLFFIAMRREHFVKIIKPSLMQKKIVICDRFIDSTIAYQGYGQGIDCSLIDQLNDLVIDVYPDITFIIDVD----------------DMEFYYRVRDGFYDIAKKNPHRCHVITDKSETYDIDDINFVHLEVIKVLQ 200
                                     7        17        27        37        47        57        67        77        87        97       107       117       127      |  -         -   |   157       167       177       187       197   
                                                                                                                                                                  134              151

Chain B from PDB  Type:PROTEIN  Length:178
 aligned with KTHY_EHRCR | Q2GHN3 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:204
                               1                                                                                                                                                                                                        
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197    
           KTHY_EHRCR     - ---MFITFEGIDGSGKTTQSHLLAEYLSEIYGVNNVVLTREPGGTLLNESVRNLLFKAQGLDSLSELLFFIAMRREHFVKIIKPSLMQKKIVICDRFIDSTIAYQGYGQGIDCSLIDQLNDLVIDVYPDITFIIDVDINESLSRSCKNGYEFADMEFYYRVRDGFYDIAKKNPHRCHVITDKSETYDIDDINFVHLEVIKVLQM 201
               SCOP domains d3ld9b_ B: automated matches                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee.....hhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhh.....hhhhhhhhhhhhh.....eeeeee.-----------------hhhhhhhhhhhhhhhhhhh...eeeee.---------hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------THYMIDYLATE_K--------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ld9 B  -2 PGSMFITFEGIDGSGKTTQSHLLAEYLSEIYGVNNVVLTREPGGTLLNESVRNLLFKAQGLDSLSELLFFIAMRREHFVKIIKPSLMQKKIVICDRFIDSTIAYQGYGQGIDCSLIDQLNDLVIDVYPDITFIIDV-----------------DMEFYYRVRDGFYDIAKKNPHRCHVITD---------INFVHLEVIKVLQM 201
                                     7        17        27        37        47        57        67        77        87        97       107       117       127     |   -         -   |   157       167       177|        -|      197    
                                                                                                                                                                 133               151                        178       188

Chain C from PDB  Type:PROTEIN  Length:175
 aligned with KTHY_EHRCR | Q2GHN3 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:203
                               1                                                                                                                                                                                                       
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197   
           KTHY_EHRCR     - ---MFITFEGIDGSGKTTQSHLLAEYLSEIYGVNNVVLTREPGGTLLNESVRNLLFKAQGLDSLSELLFFIAMRREHFVKIIKPSLMQKKIVICDRFIDSTIAYQGYGQGIDCSLIDQLNDLVIDVYPDITFIIDVDINESLSRSCKNGYEFADMEFYYRVRDGFYDIAKKNPHRCHVITDKSETYDIDDINFVHLEVIKVLQ 200
               SCOP domains d3ld9c_ C: automated matches                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.....hhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhh.....hhhhhhhhhhhhh.....eeeee...----------------hhhhhhhhhhhhhhhhhhh...eeee.------------hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------THYMIDYLATE_K-------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ld9 C  -2 PGSMFITFEGIDGSGKTTQSHLLAEYLSEIYGVNNVVLTREPGGTLLNESVRNLLFKAQGLDSLSELLFFIAMRREHFVKIIKPSLMQKKIVICDRFIDSTIAYQGYGQGIDCSLIDQLNDLVIDVYPDITFIIDVD----------------DMEFYYRVRDGFYDIAKKNPHRCHVIT------------FVHLEVIKVLQ 200
                                     7        17        27        37        47        57        67        77        87        97       107       117       127      |  -         -   |   157       167       177         -  |    197   
                                                                                                                                                                  134              151                       177          190

Chain D from PDB  Type:PROTEIN  Length:184
 aligned with KTHY_EHRCR | Q2GHN3 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:204
                               1                                                                                                                                                                                                        
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197    
           KTHY_EHRCR     - ---MFITFEGIDGSGKTTQSHLLAEYLSEIYGVNNVVLTREPGGTLLNESVRNLLFKAQGLDSLSELLFFIAMRREHFVKIIKPSLMQKKIVICDRFIDSTIAYQGYGQGIDCSLIDQLNDLVIDVYPDITFIIDVDINESLSRSCKNGYEFADMEFYYRVRDGFYDIAKKNPHRCHVITDKSETYDIDDINFVHLEVIKVLQM 201
               SCOP domains d3ld9d_ D: automated matches                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -------Thymidylate_kin-3ld9D01 D:5-188                                                                                                                                                         ------------- Pfam domains (1)
           Pfam domains (2) -------Thymidylate_kin-3ld9D02 D:5-188                                                                                                                                                         ------------- Pfam domains (2)
           Pfam domains (3) -------Thymidylate_kin-3ld9D03 D:5-188                                                                                                                                                         ------------- Pfam domains (3)
           Pfam domains (4) -------Thymidylate_kin-3ld9D04 D:5-188                                                                                                                                                         ------------- Pfam domains (4)
         Sec.struct. author ...eeeeee.....hhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhh.....hhhhhhhhhhhhh.....eeeee...----------------hhhhhhhhhhhhhhhhhhh...eeee.----....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------THYMIDYLATE_K--------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ld9 D  -2 PGSMFITFEGIDGSGKTTQSHLLAEYLSEIYGVNNVVLTREPGGTLLNESVRNLLFKAQGLDSLSELLFFIAMRREHFVKIIKPSLMQKKIVICDRFIDSTIAYQGYGQGIDCSLIDQLNDLVIDVYPDITFIIDVD----------------DMEFYYRVRDGFYDIAKKNPHRCHVIT----TYDIDDINFVHLEVIKVLQM 201
                                     7        17        27        37        47        57        67        77        87        97       107       117       127      |  -         -   |   157       167       177    |  187       197    
                                                                                                                                                                  134              151                       177  182

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)

Ehrlichia chaffeensis [TaxId: 205920] (1)

1a	d3ld9a_	A:
1b	d3ld9b_	B:
1c	d3ld9c_	C:
1d	d3ld9d_	D:

(no "CATH Domain" information available for 3LD9)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Thymidylate_kin (26)

Ehrlichia chaffeensis (strain Arkansas) (1)

1a	Thymidylate_kin-3ld9D01	D:5-188
1b	Thymidylate_kin-3ld9D02	D:5-188
1c	Thymidylate_kin-3ld9D03	D:5-188
1d	Thymidylate_kin-3ld9D04	D:5-188

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (KTHY_EHRCR | Q2GHN3)

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:38 - Pro A:39	[ RasMol ]
		Glu B:38 - Pro B:39	[ RasMol ]
		Glu C:38 - Pro C:39	[ RasMol ]
		Glu D:38 - Pro D:39	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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