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Title :   2.25 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF A THYMIDYLATE KINASE (TMK) FROM VIBRIO CHOLERAE O1 BIOVAR ELTOR STR. N16961 IN COMPLEX WITH THYMIDINE

Authors :   A. S. Halavaty, G. Minasov, L. Shuvalova, J. Winsor, I. Dubrovska, S. Pe W. F. Anderson, Center For Structural Genomics Of Infectious D (Csgid)

Date :   18 May 10 (Deposition) - 02 Jun 10 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

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

Keywords :   Thymidylate Kinase, Vibrio Cholerae, Structural Genomics, Infectious Diseases, Center For Structural Genomics Of Infectious Diseases, Atp-Binding, Kinase, Nucleotide Biosynthesis, Nucleotide-Binding, Transferase, Csgid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. S. Halavaty, G. Minasov, L. Shuvalova, J. Winsor, I. Dubrovska, S. Peterson, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
2. 25 Angstrom Resolution Crystal Structure Of A Thymidylate Kinase (Tmk) From Vibrio Cholerae O1 Biovar Eltor Str. N16961 In Complex With Thymidine
To Be Published
PubMed: search

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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:206
 aligned with KTHY_VIBCH | Q9KQI2 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        
           KTHY_VIBCH     1 MNAKFIVIEGLEGAGKSTAIQVVVETLQQNGIDHITRTREPGGTLLAEKLRALVKEEHPGEELQDITELLLVYAARVQLVENVIKPALARGEWVVGDRHDMSSQAYQGGGRQIAPSTMQSLKQTALGDFKPDLTLYLDIDPKLGLERARGRGELDRIEKMDISFFERARERYLELANSDDSVVMIDAAQSIEQVTADIRRALQDWLSQ 208
               SCOP domains d3n2ia_ A: automated matches                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee....hhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhh......hhhhhhhhhhhhhh.....eeeeee.hhhhhhhhh..--...hhhhhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------THYMIDYLATE_K----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n2i A   1 MNAKFIVIEGLEGAGKSTAIQVVVETLQQNGIDHITRTREPGGTLLAEKLRALVKEEHPGEELQDITELLLVYAARVQLVENVIKPALARGEWVVGDRHDMSSQAYQGGGRQIAPSTMQSLKQTALGDFKPDLTLYLDIDPKLGLERARG--ELDRIEKMDISFFERARERYLELANSDDSVVMIDAAQSIEQVTADIRRALQDWLSQ 208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150  |    160       170       180       190       200        
                                                                                                                                                                               150  |                                                       
                                                                                                                                                                                  153

Chain B from PDB  Type:PROTEIN  Length:209
 aligned with KTHY_VIBCH | Q9KQI2 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:209
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201         
           KTHY_VIBCH     2 NAKFIVIEGLEGAGKSTAIQVVVETLQQNGIDHITRTREPGGTLLAEKLRALVKEEHPGEELQDITELLLVYAARVQLVENVIKPALARGEWVVGDRHDMSSQAYQGGGRQIAPSTMQSLKQTALGDFKPDLTLYLDIDPKLGLERARGRGELDRIEKMDISFFERARERYLELANSDDSVVMIDAAQSIEQVTADIRRALQDWLSQVN 210
               SCOP domains d3n2ib_ B: automated matches                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------Thymidylate_kin-3n2iB01 B:8-198                                                                                                                                                                ------------ Pfam domains (1)
           Pfam domains (2) ------Thymidylate_kin-3n2iB02 B:8-198                                                                                                                                                                ------------ Pfam domains (2)
         Sec.struct. author ...eeeee.....hhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhh......hhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------THYMIDYLATE_K------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n2i B   2 NAKFIVIEGLEGAGKSTAIQVVVETLQQNGIDHITRTREPGGTLLAEKLRALVKEEHPGEELQDITELLLVYAARVQLVENVIKPALARGEWVVGDRHDMSSQAYQGGGRQIAPSTMQSLKQTALGDFKPDLTLYLDIDPKLGLERARGRGELDRIEKMDISFFERARERYLELANSDDSVVMIDAAQSIEQVTADIRRALQDWLSQVN 210
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201

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 '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (KTHY_VIBCH | Q9KQI2)

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:0015949	nucleobase-containing small molecule interconversion	The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide small molecule is synthesized from another nucleobase, nucleoside or nucleotide small molecule.
	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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