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Title :   CRYSTAL STRUCTURE OF THYMIDYLATE KINASE (AQ_969) FROM AQUIFEX AEOLICUS VF5

Authors :   J. Jeyakanthan, S. P. Kanaujia, C. Vasuki Ranjani, K. Sekar, N. Nakaga A. Ebihara, S. Kuramitsu, A. Shinkai, Y. Shiro, S. Yokoyama, Riken St Genomics/Proteomics Initiative (Rsgi)

Date :   29 Mar 07 (Deposition) - 02 Oct 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.96

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A (1x),B (1x)

Keywords :   Kinase, Transferase, Nucleotide Biosynthesis, Tmp-Binding, Atp- Binding, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Jeyakanthan, S. P. Kanaujia, C. Vasuki Ranjani, K. Sekar, N. Nakagawa, A. Ebihara, S. Kuramitsu, A. Shinkai, Y. Shiro, S. Yokoyama
Crystal Structure Of Thymidylate Kinase (Aq_969) From Aquifex Aeolicus Vf5
To Be Published
PubMed: search

Molecule 1 - THYMIDYLATE KINASE
	Chains	:	A, B
	EC Number	:	2.7.4.9
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21A
	Expression System Strain	:	BL-21 CONDON PLUS (DE3)-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	224324
	Strain	:	VF5
	Synonym	:	DTMP KINASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:	A (1x)	B (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

(no "Site" information available for 2PBR)

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

Asymmetric Unit

No.	Residues
1	Glu A:36	-	Pro A:37
2	Glu B:36	-	Pro B:37

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THYMIDYLATE_KINASE	PS01331	Thymidylate kinase signature.	KTHY_AQUAE	87-99	2	A:87-99 B:87-99

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THYMIDYLATE_KINASE	PS01331	Thymidylate kinase signature.	KTHY_AQUAE	87-99	2	A:87-99 B:87-99

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THYMIDYLATE_KINASE	PS01331	Thymidylate kinase signature.	KTHY_AQUAE	87-99	2	A:87-99 B:87-99

(no "Exon" information available for 2PBR)

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:195
 aligned with KTHY_AQUAE | O67099 from UniProtKB/Swiss-Prot  Length:195

    Alignment length:195
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190     
           KTHY_AQUAE     1 MLIAFEGIDGSGKTTQAKKLYEYLKQKGYFVSLYREPGGTKVGEVLREILLTEELDERTELLLFEASRSKLIEEKIIPDLKRDKVVILDRFVLSTIAYQGYGKGLDVEFIKNLNEFATRGVKPDITLLLDIPVDIALRRLKEKNRFENKEFLEKVRKGFLELAKEEENVVVIDASGEEEEVFKEILRALSGVLRV 195
               SCOP domains d2pbra_ A: automated matches                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhh.....hhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------THYMIDYLATE_K------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pbr A   1 MLIAFEGIDGSGKTTQAKKLYEYLKQKGYFVSLYREPGGTKVGEVLREILLTEELDERTELLLFEASRSKLIEEKIIPDLKRDKVVILDRFVLSTIAYQGYGKGLDVEFIKNLNEFATRGVKPDITLLLDIPVDIALRRLKEKNRFENKEFLEKVRKGFLELAKEEENVVVIDASGEEEEVFKEILRALSGVLRV 195
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

Chain B from PDB  Type:PROTEIN  Length:195
 aligned with KTHY_AQUAE | O67099 from UniProtKB/Swiss-Prot  Length:195

    Alignment length:195
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190     
           KTHY_AQUAE     1 MLIAFEGIDGSGKTTQAKKLYEYLKQKGYFVSLYREPGGTKVGEVLREILLTEELDERTELLLFEASRSKLIEEKIIPDLKRDKVVILDRFVLSTIAYQGYGKGLDVEFIKNLNEFATRGVKPDITLLLDIPVDIALRRLKEKNRFENKEFLEKVRKGFLELAKEEENVVVIDASGEEEEVFKEILRALSGVLRV 195
               SCOP domains d2pbrb_ B: automated matches                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----Thymidylate_kin-2pbrB01 B:5-185                                                                                                                                                      ---------- Pfam domains (1)
           Pfam domains (2) ----Thymidylate_kin-2pbrB02 B:5-185                                                                                                                                                      ---------- Pfam domains (2)
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhh.....hhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------THYMIDYLATE_K------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pbr B   1 MLIAFEGIDGSGKTTQAKKLYEYLKQKGYFVSLYREPGGTKVGEVLREILLTEELDERTELLLFEASRSKLIEEKIIPDLKRDKVVILDRFVLSTIAYQGYGKGLDVEFIKNLNEFATRGVKPDITLLLDIPVDIALRRLKEKNRFENKEFLEKVRKGFLELAKEEENVVVIDASGEEEEVFKEILRALSGVLRV 195
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

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 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)

Aquifex aeolicus [TaxId: 224324] (4)

1a	d2pbra_	A:
1b	d2pbrb_	B:

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Thymidylate_kin (26)

Aquifex aeolicus (1)

1a	Thymidylate_kin-2pbrB01	B:5-185
1b	Thymidylate_kin-2pbrB02	B:5-185

Asymmetric Unit(hide GO term definitions)

Chain A,B (KTHY_AQUAE | O67099)

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.
	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.

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	Sites
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	Cis Peptide Bonds
		Glu A:36 - Pro A:37	[ RasMol ]
		Glu B:36 - Pro B:37	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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