3LV8 - JenaLib

Title :   1.8 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF A THYMIDYLATE KINASE (TMK) FROM VIBRIO CHOLERAE O1 BIOVAR ELTOR STR. N16961 IN COMPLEX WITH TMP, THYMIDINE-5'-DIPHOSPHATE AND ADP

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

Date :   19 Feb 10 (Deposition) - 02 Mar 10 (Release) - 18 May 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

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, I. Dubrovska, J. Winsor, L. Shuvalova, K. Kwon, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
1. 8 Angstrom Resolution Crystal Structure Of A Thymidylate Kinase (Tmk) From Vibrio Cholerae O1 Biovar Eltor Str. N16961 In Complex With Tmp, Thymidine-5'-Diphosphate And Ad
To Be Published
PubMed: search

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 10)

Sites (10, 10)

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:13 , ALA A:14 , GLY A:15 , LYS A:16 , SER A:17 , ARG A:147 , GLN A:189 , SER A:190 , ILE A:191 , VAL A:194 , CA A:217 , HOH A:251 , HOH A:265 , HOH A:284 , HOH A:285 , HOH A:286 , HOH A:381 , HOH A:478 , HOH A:483	BINDING SITE FOR RESIDUE ADP A 213
02	AC2	SOFTWARE	GLU A:12 , GLU A:40 , PRO A:41 , ARG A:51 , LYS A:55 , ARG A:76 , ARG A:98 , SER A:102 , SER A:103 , TYR A:106 , GLN A:107 , ILE A:157 , CA A:218 , HOH A:327 , HOH A:353 , HOH A:381 , HOH A:477	BINDING SITE FOR RESIDUE TMP A 214
03	AC3	SOFTWARE	GLU A:12 , GLU A:40 , ARG A:51 , LYS A:55 , VAL A:72 , ARG A:76 , ARG A:98 , SER A:102 , SER A:103 , TYR A:106 , GLN A:107 , GLU A:158 , CA A:217 , CA A:218 , HOH A:230 , HOH A:265 , HOH A:327 , HOH A:353 , HOH A:381 , HOH A:434 , HOH A:476 , HOH A:477 , HOH A:490	BINDING SITE FOR RESIDUE TYD A 215
04	AC4	SOFTWARE	GLU A:92 , HOH A:314 , HOH A:441 , HOH A:479 , HOH A:480 , HOH A:481 , HOH A:482	BINDING SITE FOR RESIDUE CA A 216
05	AC5	SOFTWARE	ADP A:213 , TYD A:215 , HOH A:265 , HOH A:475 , HOH A:476 , HOH A:477 , HOH A:478	BINDING SITE FOR RESIDUE CA A 217
06	AC6	SOFTWARE	GLU A:12 , GLU A:158 , TMP A:214 , TYD A:215 , HOH A:327 , HOH A:434	BINDING SITE FOR RESIDUE CA A 218
07	AC7	SOFTWARE	ALA A:176 , ASP A:179 , VAL A:182 , HOH A:231 , HOH A:232 , HOH A:392	BINDING SITE FOR RESIDUE CA A 219
08	AC8	SOFTWARE	ASN A:177 , HOH A:267 , HOH A:268 , HOH A:291 , HOH A:292 , HOH A:293	BINDING SITE FOR RESIDUE CA A 220
09	AC9	SOFTWARE	LYS A:130 , HOH A:225 , HOH A:266 , HOH A:328 , HOH A:379	BINDING SITE FOR RESIDUE CA A 221
10	BC1	SOFTWARE	ARG A:111 , HOH A:362 , HOH A:411	BINDING SITE FOR RESIDUE CL A 222

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

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
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Chain A from PDB  Type:PROTEIN  Length:204
 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 d3lv8a_ A: automated matches                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------Thymidylate_kin-3lv8A01 A:8-198                                                                                                                                                                ------------ Pfam domains
         Sec.struct. author ...eeeeee....hhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhh......hhhhhhhhhhhhhh.....eeeeee.hhhhhhhh-----........hhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------THYMIDYLATE_K------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lv8 A   2 NAKFIVIEGLEGAGKSTAIQVVVETLQQNGIDHITRTREPGGTLLAEKLRALVKEEHPGEELQDITELLLVYAARVQLVENVIKPALARGEWVVGDRHDMSSQAYQGGGRQIAPSTMQSLKQTALGDFKPDLTLYLDIDPKLGLER-----ELDRIEKMDISFFERARERYLELANSDDSVVMIDAAQSIEQVTADIRRALQDWLSQVN 210
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141     |   - |     161       171       181       191       201         
                                                                                                                                                                           147   153

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, 1)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (14, 14)

Asymmetric Unit(hide GO term definitions)

Chain A (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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