1N5J - JenaLib

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Title :   CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE DIPHOSPHATE (TDP) AND THYMIDINE TRIPHOSPHATE (TTP) AT PH 5.4 (1.85 A RESOLUTION)

Authors :   E. Fioravanti, A. Haouz, T. Ursby, H. Munier-Lehmann, M. Delarue, D. Bourgeois

Date :   06 Nov 02 (Deposition) - 15 Apr 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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

Keywords :   Transferase (Atp:Tmp Phosphotransferase), Kinase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Fioravanti, A. Haouz, T. Ursby, H. Munier-Lehmann, M. Delarue, D. Bourgeois
Mycobacterium Tuberculosis Thymidylate Kinase: Structural Studies Of Intermediates Along The Reaction Pathway
J. Mol. Biol. V. 327 1077 2003
PubMed-ID: 12662932 | Reference-DOI: 10.1016/S0022-2836(03)00202-X
(for further references see the PDB file header)

Molecule 1 - THYMIDYLATE KINASE
	Chains	:	A
	EC Number	:	2.7.4.9
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 5)

No.	Name	Count	Type	Full Name
1	MG	1	Ligand/Ion	MAGNESIUM ION
2	SO4	2	Ligand/Ion	SULFATE ION
3	TTP	1	Ligand/Ion	THYMIDINE-5'-TRIPHOSPHATE
4	TYD	1	Ligand/Ion	THYMIDINE-5'-DIPHOSPHATE

Biological Unit 1 (3, 8)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	SO4	4	Ligand/Ion	SULFATE ION
3	TTP	2	Ligand/Ion	THYMIDINE-5'-TRIPHOSPHATE
4	TYD	2	Ligand/Ion	THYMIDINE-5'-DIPHOSPHATE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:9 , GLU A:166 , TYD A:218 , TTP A:219 , HOH A:1009 , HOH A:1018	BINDING SITE FOR RESIDUE MG A 217
2	AC2	SOFTWARE	GLY A:10 , GLY A:12 , LYS A:13 , ARG A:14 , ARG A:153 , HOH A:1014 , HOH A:1027 , HOH A:1041 , HOH A:1140	BINDING SITE FOR RESIDUE SO4 A 215
3	AC3	SOFTWARE	ALA A:154 , ARG A:162 , ARG A:167 , HOH A:1030	BINDING SITE FOR RESIDUE SO4 A 216
4	AC4	SOFTWARE	ASP A:9 , ARG A:14 , PRO A:37 , TYR A:39 , PHE A:70 , ARG A:74 , ARG A:95 , ASN A:100 , TYR A:103 , TYR A:165 , MG A:217 , HOH A:1002 , HOH A:1009 , HOH A:1014 , HOH A:1018 , HOH A:1046 , HOH A:1119 , HOH A:1128 , HOH A:1140 , HOH A:1151 , HOH A:1234	BINDING SITE FOR RESIDUE TTP A 219
5	AC5	SOFTWARE	ASP A:9 , TYR A:39 , PHE A:70 , ARG A:74 , ARG A:95 , ASN A:100 , TYR A:165 , GLU A:166 , MG A:217 , HOH A:1002 , HOH A:1009 , HOH A:1014 , HOH A:1018 , HOH A:1046 , HOH A:1119 , HOH A:1151 , HOH A:1234	BINDING SITE FOR RESIDUE TYD A 218

(no "SS Bond" information available for 1N5J)

Asymmetric Unit

No.	Residues
1	Phe A:36	-	Pro A:37

(no "SAP(SNP)/Variant" information available for 1N5J)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THYMIDYLATE_KINASE	PS01331	Thymidylate kinase signature.	KTHY_MYCTO	92-104	1	A:92-104
1	THYMIDYLATE_KINASE	PS01331	Thymidylate kinase signature.	KTHY_MYCTU	92-104	1	A:92-104

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THYMIDYLATE_KINASE	PS01331	Thymidylate kinase signature.	KTHY_MYCTO	92-104	2	A:92-104
1	THYMIDYLATE_KINASE	PS01331	Thymidylate kinase signature.	KTHY_MYCTU	92-104	2	A:92-104

(no "Exon" information available for 1N5J)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:208
 aligned with KTHY_MYCTO | P9WKE0 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        
           KTHY_MYCTO     1 MLIAIEGVDGAGKRTLVEKLSGAFRAAGRSVATLAFPRYGQSVAADIAAEALHGEHGDLASSVYAMATLFALDRAGAVHTIQGLCRGYDVVILDRYVASNAAYSAARLHENAAGKAAAWVQRIEFARLGLPKPDWQVLLAVSAELAGERSRGRAQRDPGRARDNYERDAELQQRTGAVYAELAAQGWGGRWLVVGADVDPGRLAATLA 208
               SCOP domains d1n5ja_ A: Thymidylate kinase                                                                                                                                                                                    SCOP domains
               CATH domains 1n5jA00 A:1-208 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                             CATH domains
               Pfam domains ----Thymidylate_kin-1n5jA01 A:5-199                                                                                                                                                                    --------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhh.....hhhhhhhhhhhh.........eeeee..hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------THYMIDYLATE_K-------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n5j A   1 MLIAIEGVDGAGKRTLVEKLSGAFRAAGRSVATLAFPRYGQSVAADIAAEALHGEHGDLASSVYAMATLFALDRAGAVHTIQGLCRGYDVVILDRYVASNAAYSAARLHENAAGKAAAWVQRIEFARLGLPKPDWQVLLAVSAELAGERSRGRAQRDPGRARDNYERDAELQQRTGAVYAELAAQGWGGRWLVVGADVDPGRLAATLA 208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Chain A from PDB  Type:PROTEIN  Length:208
 aligned with KTHY_MYCTU | P9WKE1 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        
           KTHY_MYCTU     1 MLIAIEGVDGAGKRTLVEKLSGAFRAAGRSVATLAFPRYGQSVAADIAAEALHGEHGDLASSVYAMATLFALDRAGAVHTIQGLCRGYDVVILDRYVASNAAYSAARLHENAAGKAAAWVQRIEFARLGLPKPDWQVLLAVSAELAGERSRGRAQRDPGRARDNYERDAELQQRTGAVYAELAAQGWGGRWLVVGADVDPGRLAATLA 208
               SCOP domains d1n5ja_ A: Thymidylate kinase                                                                                                                                                                                    SCOP domains
               CATH domains 1n5jA00 A:1-208 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                             CATH domains
               Pfam domains ----Thymidylate_kin-1n5jA01 A:5-199                                                                                                                                                                    --------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhh.....hhhhhhhhhhhh.........eeeee..hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------------------------------------------------------------------THYMIDYLATE_K-------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n5j A   1 MLIAIEGVDGAGKRTLVEKLSGAFRAAGRSVATLAFPRYGQSVAADIAAEALHGEHGDLASSVYAMATLFALDRAGAVHTIQGLCRGYDVVILDRYVASNAAYSAARLHENAAGKAAAWVQRIEFARLGLPKPDWQVLLAVSAELAGERSRGRAQRDPGRARDNYERDAELQQRTGAVYAELAAQGWGGRWLVVGADVDPGRLAATLA 208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

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(

)

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)

Mycobacterium tuberculosis. Organism_taxid: 1773. (15)

1n5jA00

A:1-208

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Thymidylate_kin (26)

Mycobacterium tuberculosis (7)

Thymidylate_kin-1n5jA01

A:5-199

Asymmetric Unit(hide GO term definitions)

Chain A (KTHY_MYCTO | P9WKE0)

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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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.

Chain A (KTHY_MYCTU | P9WKE1)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	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:0046044	TMP metabolic process	The chemical reactions and pathways involving TMP, ribosylthymine monophosphate.
	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.

Asymmetric Unit
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	Cis Peptide Bonds
		Phe A:36 - Pro A:37	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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1g3u	CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE (TMP) AND MAGNESIUM (1.95 A RESOLUTION)
1gsi	CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE (TMP) AND MAGNESIUM (1.6 A RESOLUTION)
1n5i	CRYSTAL STRUCTURE OF INACTIVE MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE (TMP) AT PH 4.6 (RESOLUTION 1.85 A)
1n5k	CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE CRYSTALLIZED IN SODIUM MALONATE (RESOLUTION 2.1 A)
1n5l	CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE CRYSTALLIZED IN SODIUM MALONATE, AFTER CATALYSIS IN THE CRYSTAL (2.3 A RESOLUTION)

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