2VQS - JenaLib

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Title :   STRUCTURAL STUDIES OF NUCLEOSIDE ANALOG AND FEEDBACK INHIBITOR BINDING TO DROSOPHILA MELANOGASTER MULTISUBSTRATE DEOXYRIBONUCLEOSIDE KINASE

Authors :   N. E. Mikkelsen, B. Munch-Petersen, H. Eklund

Date :   18 Mar 08 (Deposition) - 29 Apr 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

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

Keywords :   Atp-Binding, Dna Synthesis, Phosphoprotein, Feedback Inhibition, Deoxyribonucleoside Kinase, Salvage Pathway, Nucleotide-Binding, Dttp, Kinase, Complex, Drosophila, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. E. Mikkelsen, B. Munch-Petersen, H. Eklund
Structural Studies Of Nucleoside Analog And Feedback Inhibitor Binding To Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase.
Febs J. V. 275 2151 2008
PubMed-ID: 18384378 | Reference-DOI: 10.1111/J.1742-4658.2008.06369.X

Molecule 1 - DEOXYNUCLEOSIDE KINASE
	Chains	:	A, B, C, D
	EC Number	:	2.7.1.145
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-2T
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Fragment	:	RESIDUES 1-230
	Organism Common	:	FRUIT FLY
	Organism Scientific	:	DROSOPHILA MELANOGASTER
	Organism Taxid	:	7227
	Synonym	:	DEOXYRIBONUCLEOSIDE KINASE, DM-DNK, MULTISPECIFIC DEOXYNUCLEOSIDE KINASE

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	BVD	4	Ligand/Ion	5-BROMOVINYLDEOXYURIDINE
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	BVD	2	Ligand/Ion	5-BROMOVINYLDEOXYURIDINE
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	BVD	2	Ligand/Ion	5-BROMOVINYLDEOXYURIDINE
2	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:30 , SER A:31 , GLY A:32 , LYS A:33 , THR A:34	BINDING SITE FOR RESIDUE SO4 A1209
2	AC2	SOFTWARE	ASN B:28 , GLY B:30 , SER B:31 , GLY B:32 , LYS B:33 , THR B:34 , ARG B:167	BINDING SITE FOR RESIDUE SO4 B1209
3	AC3	SOFTWARE	ASN C:28 , GLY C:30 , SER C:31 , GLY C:32 , LYS C:33 , THR C:34	BINDING SITE FOR RESIDUE SO4 C1209
4	AC4	SOFTWARE	ASN D:28 , GLY D:30 , SER D:31 , GLY D:32 , LYS D:33 , THR D:34 , HOH D:2006	BINDING SITE FOR RESIDUE SO4 D1209
5	AC5	SOFTWARE	GLU A:52 , MET A:69 , TYR A:70 , PHE A:80 , GLN A:81 , ARG A:105 , SER A:106 , PHE A:114	BINDING SITE FOR RESIDUE BVD A1210
6	AC6	SOFTWARE	GLU B:52 , TRP B:57 , MET B:69 , TYR B:70 , PHE B:80 , GLN B:81 , VAL B:84 , ARG B:105 , SER B:106 , PHE B:114	BINDING SITE FOR RESIDUE BVD B1210
7	AC7	SOFTWARE	ILE C:29 , GLU C:52 , LEU C:66 , MET C:69 , TYR C:70 , PHE C:80 , GLN C:81 , ARG C:105 , PHE C:114	BINDING SITE FOR RESIDUE BVD C1210
8	AC8	SOFTWARE	GLU D:52 , TRP D:57 , LEU D:66 , MET D:69 , TYR D:70 , PHE D:80 , GLN D:81 , ARG D:105 , SER D:106 , PHE D:114 , MET D:118 , HOH D:2006	BINDING SITE FOR RESIDUE BVD D1210

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

(no "Cis Peptide Bond" information available for 2VQS)

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

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

(no "Exon" information available for 2VQS)

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:182
 aligned with DNK_DROME | Q9XZT6 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:197
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       
            DNK_DROME    12 TKYAEGTQPFTVLIEGNIGSGKTTYLNHFEKYKNDICLLTEPVEKWRNVNGVNLLELMYKDPKKWAMPFQSYVTLTMLQSHTAPTNKKLKIMERSIFSARYCFVENMRRNGSLEQGMYNTLEEWYKFIEESIHVQADLIIYLRTSPEVAYERIRQRARSEESCVPLKYLQELHELHEDWLIHQRRPQSCKVLVLDAD 208
               SCOP domains d2vqsa_ A: Deoxyribonucleoside kinase                                                                                                                                                                 SCOP domains
               CATH domains 2vqsA00 A:12-208 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeee....hhhhhhhhhhhhh..eeee..hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhh.------------hhhhhhhhhhhhhhhhh.---.....eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vqs A  12 TKYAEGTQPFTVLIEGNIGSGKTTYLNHFEKYKNDICLLTEPVEKWRNVNGVNLLELMYKDPKKWAMPFQSYVTLTMLQSHTAPTNKKLKIMERSIFSARYCFVENMRRNGSLEQGMYNTLEEWYKFIEESIHVQADLIIYLRTSPEVAYER------------PLKYLQELHELHEDWLIH---PQSCKVLVLDAD 208
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161 |       -    |  181       191 |   | 201       
                                                                                                                                                                                 163          176              193 197

Chain B from PDB  Type:PROTEIN  Length:188
 aligned with DNK_DROME | Q9XZT6 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:197
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       
            DNK_DROME    12 TKYAEGTQPFTVLIEGNIGSGKTTYLNHFEKYKNDICLLTEPVEKWRNVNGVNLLELMYKDPKKWAMPFQSYVTLTMLQSHTAPTNKKLKIMERSIFSARYCFVENMRRNGSLEQGMYNTLEEWYKFIEESIHVQADLIIYLRTSPEVAYERIRQRARSEESCVPLKYLQELHELHEDWLIHQRRPQSCKVLVLDAD 208
               SCOP domains d2vqsb_ B: Deoxyribonucleoside kinase                                                                                                                                                                 SCOP domains
               CATH domains 2vqsB00 B:12-208 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeee....hhhhhhhhhhhhh..eeee..hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhh------..hhhhhhhhhhhhhhhhh.---....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vqs B  12 TKYAEGTQPFTVLIEGNIGSGKTTYLNHFEKYKNDICLLTEPVEKWRNVNGVNLLELMYKDPKKWAMPFQSYVTLTMLQSHTAPTNKKLKIMERSIFSARYCFVENMRRNGSLEQGMYNTLEEWYKFIEESIHVQADLIIYLRTSPEVAYERIRQR------CVPLKYLQELHELHEDWLIH---PQSCKVLVLDAD 208
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161     |   -  |    181       191 |   | 201       
                                                                                                                                                                                     167    174                193 197

Chain C from PDB  Type:PROTEIN  Length:186
 aligned with DNK_DROME | Q9XZT6 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:197
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       
            DNK_DROME    12 TKYAEGTQPFTVLIEGNIGSGKTTYLNHFEKYKNDICLLTEPVEKWRNVNGVNLLELMYKDPKKWAMPFQSYVTLTMLQSHTAPTNKKLKIMERSIFSARYCFVENMRRNGSLEQGMYNTLEEWYKFIEESIHVQADLIIYLRTSPEVAYERIRQRARSEESCVPLKYLQELHELHEDWLIHQRRPQSCKVLVLDAD 208
               SCOP domains d2vqsc_ C: Deoxyribonucleoside kinase                                                                                                                                                                 SCOP domains
               CATH domains 2vqsC00 C:12-208 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeee....hhhhhhhhhhhhh..eeee..hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhh---------hhhhhhhhhhhhhhhhh.--.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vqs C  12 TKYAEGTQPFTVLIEGNIGSGKTTYLNHFEKYKNDICLLTEPVEKWRNVNGVNLLELMYKDPKKWAMPFQSYVTLTMLQSHTAPTNKKLKIMERSIFSARYCFVENMRRNGSLEQGMYNTLEEWYKFIEESIHVQADLIIYLRTSPEVAYERIRQ---------PLKYLQELHELHEDWLIH--RPQSCKVLVLDAD 208
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161    |    -    |  181       191 |  |  201       
                                                                                                                                                                                    166       176              193  |            
                                                                                                                                                                                                                  196

Chain D from PDB  Type:PROTEIN  Length:183
 aligned with DNK_DROME | Q9XZT6 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:197
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       
            DNK_DROME    12 TKYAEGTQPFTVLIEGNIGSGKTTYLNHFEKYKNDICLLTEPVEKWRNVNGVNLLELMYKDPKKWAMPFQSYVTLTMLQSHTAPTNKKLKIMERSIFSARYCFVENMRRNGSLEQGMYNTLEEWYKFIEESIHVQADLIIYLRTSPEVAYERIRQRARSEESCVPLKYLQELHELHEDWLIHQRRPQSCKVLVLDAD 208
               SCOP domains d2vqsd_ D: Deoxyribonucleoside kinase                                                                                                                                                                 SCOP domains
               CATH domains 2vqsD00 D:12-208 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                 CATH domains
           Pfam domains (1) --------------------------------------------------------------------dNK-2vqsD01 D:80-208                                                                                                              Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------dNK-2vqsD02 D:80-208                                                                                                              Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------dNK-2vqsD03 D:80-208                                                                                                              Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------dNK-2vqsD04 D:80-208                                                                                                              Pfam domains (4)
         Sec.struct. author .........eeeeeee....hhhhhhhhhhhhh..eeee..hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhh..---------..hhhhhhhhhhhhhhhhh..-----.eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vqs D  12 TKYAEGTQPFTVLIEGNIGSGKTTYLNHFEKYKNDICLLTEPVEKWRNVNGVNLLELMYKDPKKWAMPFQSYVTLTMLQSHTAPTNKKLKIMERSIFSARYCFVENMRRNGSLEQGMYNTLEEWYKFIEESIHVQADLIIYLRTSPEVAYERI---------CVPLKYLQELHELHEDWLIHQ-----CKVLVLDAD 208
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161  |      -  |    181       191  |    201       
                                                                                                                                                                                  164       174                 194   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)

Fruit fly (Drosophila melanogaster) (15)

1a	2vqsB00	B:12-208
1b	2vqsC00	C:12-208
1c	2vqsD00	D:12-208
1d	2vqsA00	A:12-208

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: dNK (33)

Drosophila melanogaster (Fruit fly) (13)

1a	dNK-2vqsD01	D:80-208
1b	dNK-2vqsD02	D:80-208
1c	dNK-2vqsD03	D:80-208
1d	dNK-2vqsD04	D:80-208

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (DNK_DROME | Q9XZT6)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0019136	deoxynucleoside kinase activity	Catalysis of the reaction: ATP + 2'-deoxynucleoside = ADP + 2'-deoxynucleoside 5'-phosphate.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0019206	nucleoside kinase activity	Catalysis of the reaction: ATP + nucleoside = ADP + nucleoside monophosphate.
	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:0004797	thymidine kinase activity	Catalysis of the reaction: ATP + thymidine = ADP + thymidine 5'-phosphate.
	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:0071897	DNA biosynthetic process	The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
	GO:0006230	TMP biosynthetic process	The chemical reactions and pathways resulting in the formation of TMP, ribosylthymine monophosphate.
	GO:0006139	nucleobase-containing compound metabolic process	Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
	GO:0006165	nucleoside diphosphate phosphorylation	The process of introducing a phosphate group into a nucleoside diphosphate to produce a nucleoside triphosphate.
	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.
	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.

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	2vqs
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	2.7.1.145
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UniProtKB/Swiss-Prot
	DNK_DROME \| Q9XZT6	:	1j90 1oe0 1ot3 1zm7 1zmx 2jcs 2jj8 2vp0 2vp2 2vp4 2vp5 2vp6 2vp9 2vpp

1j90	CRYSTAL STRUCTURE OF DROSOPHILA DEOXYRIBONUCLEOSIDE KINASE
1oe0	CRYSTAL STRUCTURE OF DROSOPHILA DEOXYRIBONUCLEOSIDE KINASE IN COMPLEX WITH DTTP
1ot3	CRYSTAL STRUCTURE OF DROSOPHILA DEOXYRIBONUCLEOTIDE KINASECOMPLEXED WITH THE SUBSTRATE DEOXYTHYMIDINE
1zm7	CRYSTAL STRUCTURE OF D. MELANOGASTER DEOXYRIBONUCLEOSIDEKINASE MUTANT N64D IN COMPLEX WITH DTTP
1zmx	CRYSTAL STRUCTURE OF D. MELANOGASTER DEOXYRIBONUCLEOSIDEKINASE N64D MUTANT IN COMPLEX WITH THYMIDINE
2jcs	ACTIVE SITE MUTANT OF DNK FROM D. MELANOGASTER WITH DTTP BOUND
2vp0	STRUCTURAL STUDIES OF NUCLEOSIDE ANALOG AND FEEDBACK INHIBITOR BINDING TO DROSOPHILA MELANOGASTER MULTISUBSTRATE DEOXYRIBONUCLEOSIDE KINASE
2vp2	STRUCTURAL STUDIES OF NUCLEOSIDE ANALOG AND FEEDBACK INHIBITOR BINDING TO DROSOPHILA MELANOGASTER MULTISUBSTRATE DEOXYRIBONUCLEOSIDE KINASE
2vp4	STRUCTURAL STUDIES OF NUCLEOSIDE ANALOG AND FEEDBACK INHIBITOR BINDING TO DROSOPHILA MELANOGASTER MULTISUBSTRATE DEOXYRIBONUCLEOSIDE KINASE
2vp5	STRUCTURAL STUDIES OF NUCLEOSIDE ANALOG AND FEEDBACK INHIBITOR BINDING TO DROSOPHILA MELANOGASTER MULTISUBSTRATE DEOXYRIBONUCLEOSIDE KINASE
2vp6	STRUCTURAL STUDIES OF NUCLEOSIDE ANALOG AND FEEDBACK INHIBITOR BINDING TO DROSOPHILA MELANOGASTER MULTISUBSTRATE DEOXYRIBONUCLEOSIDE KINASE
2vp9	STRUCTURAL STUDIES OF NUCLEOSIDE ANALOG AND FEEDBACK INHIBITOR BINDING TO DROSOPHILA MELANOGASTER MULTISUBSTRATE DEOXYRIBONUCLEOSIDE KINASE
2vpp	DROSOPHILA MELANOGASTER DEOXYRIBONUCLEOSIDE KINASE SUCCESSFULLY ACTIVATES GEMCITABINE IN TRANSDUCED CANCER CELL LINES

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (1, 4)

Pfam Domains (1, 4)

Gene Ontology (15, 15)

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