2YOG - JenaLib

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Title :   PLASMODIUM FALCIPARUM THYMIDYLATE KINASE IN COMPLEX WITH A (THIO)UREA-ALPHA-DEOXYTHYMIDINE INHIBITOR

Authors :   C. Huaqing, J. Carrero-Lerida, A. P. G. Silva, J. L. Whittingham, J. A. B L. M. Ruiz-Perez, K. D. Read, K. S. Wilson, D. Gonzalez-Pacanowska, I. H. Gilbert

Date :   24 Oct 12 (Deposition) - 24 Jul 13 (Release) - 24 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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

Keywords :   Transferase, Malaria, Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Cui, J. Carrero-Lerida, A. P. G. Silva, J. L. Whittingham, J. A. Brannigan, L. M. Ruiz-Perez, K. D. Read, K. S. Wilson, D. Gonzalez-Pacanowska, I. H. Gilbert
Synthesis And Evaluation Of Alpha-Thymidine Analogues As Novel Antimalarials.
J. Med. Chem. V. 55 10948 2012
PubMed-ID: 23240776 | Reference-DOI: 10.1021/JM301328H

Molecule 1 - THYMIDYLATE KINASE
	Chains	:	A, B
	EC Number	:	2.7.4.9
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET28
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	PLASMODIUM FALCIPARUM
	Organism Taxid	:	36329
	Strain	:	3D7

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	74X	2	Ligand/Ion	1-[4-CHLORANYL-3-(TRIFLUOROMETHYL)PHENYL]-3-[[(2R,3S)-5-[5-METHYL-2,4-BIS(OXIDANYLIDENE)PYRIMIDIN-1-YL]-3-OXIDANYL-OXOLAN-2-YL]METHYL]THIOUREA

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	74X	1	Ligand/Ion	1-[4-CHLORANYL-3-(TRIFLUOROMETHYL)PHENYL]-3-[[(2R,3S)-5-[5-METHYL-2,4-BIS(OXIDANYLIDENE)PYRIMIDIN-1-YL]-3-OXIDANYL-OXOLAN-2-YL]METHYL]THIOUREA

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	74X	1	Ligand/Ion	1-[4-CHLORANYL-3-(TRIFLUOROMETHYL)PHENYL]-3-[[(2R,3S)-5-[5-METHYL-2,4-BIS(OXIDANYLIDENE)PYRIMIDIN-1-YL]-3-OXIDANYL-OXOLAN-2-YL]METHYL]THIOUREA

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:17 , PHE A:44 , PRO A:45 , LEU A:59 , LYS A:60 , PHE A:74 , ARG A:78 , ARG A:99 , SER A:103 , GLY A:104 , TYR A:107 , HOH A:2011 , HOH A:2102 , HOH A:2167 , HOH A:2220	BINDING SITE FOR RESIDUE 74X A 211
2	AC2	SOFTWARE	PHE B:44 , PRO B:45 , ARG B:47 , LEU B:59 , LYS B:60 , PHE B:74 , ARG B:78 , ARG B:99 , SER B:103 , GLY B:104 , TYR B:107 , HOH B:2085 , HOH B:2112 , HOH B:2157 , HOH B:2213 , HOH B:2214	BINDING SITE FOR RESIDUE 74X B 211

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

Asymmetric Unit

No.	Residues
1	Phe A:44	-	Pro A:45
2	Leu A:208	-	Trp A:209
3	Phe B:44	-	Pro B:45
4	Leu B:208	-	Trp B:209

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

(no "PROSITE Motif" information available for 2YOG)

(no "Exon" information available for 2YOG)

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:197
 aligned with Q8I4S1_PLAF7 | Q8I4S1 from UniProtKB/TrEMBL  Length:210

    Alignment length:207
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       
         Q8I4S1_PLAF7     4 DKKKGKFIVFEGLDRSGKSTQSKLLVEYLKNNNVEVKHLYFPNRETGIGQIISKYLKMENSMSNETIHLLFSANRWEHMNEIKSLLLKGIWVVCDRYAYSGVAYSSGALNLNKTWCMNPDQGLIKPDVVFYLNVPPNYAQNRSDYGEEIYEKVETQKKIYETYKHFAHEDYWINIDATRKIEDIHNDIVKEVTKIKVEPEEFNFLWS 210
               SCOP domains d2yoga_ A: automated matches                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee....hhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhh..hhhhhhhhhh......eeeeee.....----------...hhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yog A   4 DKKKGKFIVFEGLDRSGKSTQSKLLVEYLKNNNVEVKHLYFPNRETGIGQIISKYLKMENSMSNETIHLLFSANRWEHMNEIKSLLLKGIWVVCDRYAYSGVAYSSGALNLNKTWCMNPDQGLIKPDVVFYLNVPPNY----------IYEKVETQKKIYETYKHFAHEDYWINIDATRKIEDIHNDIVKEVTKIKVEPEEFNFLWS 210
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       | -       153       163       173       183       193       203       
                                                                                                                                                                   141        152

Chain B from PDB  Type:PROTEIN  Length:196
 aligned with Q8I4S1_PLAF7 | Q8I4S1 from UniProtKB/TrEMBL  Length:210

    Alignment length:208
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202        
         Q8I4S1_PLAF7     3 DDKKKGKFIVFEGLDRSGKSTQSKLLVEYLKNNNVEVKHLYFPNRETGIGQIISKYLKMENSMSNETIHLLFSANRWEHMNEIKSLLLKGIWVVCDRYAYSGVAYSSGALNLNKTWCMNPDQGLIKPDVVFYLNVPPNYAQNRSDYGEEIYEKVETQKKIYETYKHFAHEDYWINIDATRKIEDIHNDIVKEVTKIKVEPEEFNFLWS 210
               SCOP domains d2yogb_ B: auto   mated matches                                                                                                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee..---hhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh.hhhhhhhhhh......eeeeee......---------...hhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yog B   3 DDKKKGKFIVFEGLD---KSTQSKLLVEYLKNNNVEVKHLYFPNRETGIGQIISKYLKMENSMSNETIHLLFSANRWEHMNEIKSLLLKGIWVVCDRYAYSGVAYSSGALNLNKTWCMNPDQGLIKPDVVFYLNVPPNYA---------IYEKVETQKKIYETYKHFAHEDYWINIDATRKIEDIHNDIVKEVTKIKVEPEEFNFLWS 210
                                    12    |   22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202        
                                         17  21                                                                                                                      142       152

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(

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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)

Plasmodium falciparum [TaxId: 36329] (8)

1a	d2yoga_	A:
1b	d2yogb_	B:

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

(no "Pfam Domain" information available for 2YOG)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q8I4S1_PLAF7 | Q8I4S1)

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: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: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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		74X	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Leu A:208 - Trp A:209	[ RasMol ]
		Leu B:208 - Trp B:209	[ RasMol ]
		Phe A:44 - Pro A:45	[ RasMol ]
		Phe B:44 - Pro B:45	[ RasMol ]

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	2yog
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	2.7.4.9
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UniProtKB/TrEMBL
	Q8I4S1_PLAF7 \| Q8I4S1	:	2wwf 2wwg 2wwh 2wwi 2yof 2yoh

2wwf	PLASMODIUM FALCIPARUM THYMIDYLATE KINASE IN COMPLEX WITH TMP AND ADP
2wwg	PLASMODIUM FALCIPARUM THYMIDYLATE KINASE IN COMPLEX WITH DGMP AND ADP
2wwh	PLASMODIUM FALCIPARUM THYMIDYLATE KINASE IN COMPLEX WITH AP5DT
2wwi	PLASMODIUM FALCIPARUM THYMIDYLATE KINASE IN COMPLEX WITH AZTMP AND ADP
2yof	PLASMODIUM FALCIPARUM THYMIDYLATE KINASE IN COMPLEX WITH A (THIO)UREA-BETA-DEOXYTHYMIDINE INHIBITOR
2yoh	PLASMODIUM FALCIPARUM THYMIDYLATE KINASE IN COMPLEX WITH A UREA-ALPHA-DEOXYTHYMIDINE INHIBITOR

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (13, 13)

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