1ZM7 - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF D. MELANOGASTER DEOXYRIBONUCLEOSIDE KINASE MUTANT N64D IN COMPLEX WITH DTTP

Authors :   M. Welin, T. Skovgaard, W. Knecht, D. Berenstein, B. Munch-Petersen, J. Piskur, H. Eklund

Date :   10 May 05 (Deposition) - 17 May 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Drosohila Melanogaster, Dnk, N64D, Mutant, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Welin, T. Skovgaard, W. Knecht, C. Zhu, D. Berenstein, B. Munch-Petersen, J. Piskur, H. Eklund
Structural Basis For The Changed Substrate Specificity Of Drosophila Melanogaster Deoxyribonucleoside Kinase Mutant N64D.
Febs J. V. 272 3733 2005
PubMed-ID: 16008571 | Reference-DOI: 10.1111/J.1742-4658.2005.04803.X
(for further references see the PDB file header)

Molecule 1 - DEOXYNUCLEOSIDE KINASE
	Chains	:	A, B, C, D
	EC Number	:	2.7.1.145
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PGEX-2T
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 1-230
	Gene	:	DNK
	Mutation	:	YES
	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, 5)

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

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	TTP	2	Ligand/Ion	THYMIDINE-5'-TRIPHOSPHATE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	TTP	2	Ligand/Ion	THYMIDINE-5'-TRIPHOSPHATE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR D:34 , GLU D:52 , GLU D:104 , ARG D:169 , TTP D:303 , HOH D:446	BINDING SITE FOR RESIDUE MG D 400
2	AC2	SOFTWARE	ILE A:29 , GLY A:30 , SER A:31 , GLY A:32 , LYS A:33 , THR A:34 , GLU A:52 , TRP A:57 , LEU A:66 , MET A:69 , TYR A:70 , PHE A:80 , GLN A:81 , VAL A:84 , GLU A:104 , ARG A:105 , ALA A:110 , PHE A:114 , MET A:118 , ARG A:167 , ARG A:169 , GLU A:172 , HOH A:304 , HOH A:324 , HOH A:326 , HOH A:335	BINDING SITE FOR RESIDUE TTP A 300
3	AC3	SOFTWARE	ASN B:28 , ILE B:29 , GLY B:30 , SER B:31 , GLY B:32 , LYS B:33 , THR B:34 , GLU B:52 , TRP B:57 , MET B:69 , TYR B:70 , PHE B:80 , GLN B:81 , VAL B:84 , GLU B:104 , ARG B:105 , ALA B:110 , PHE B:114 , ARG B:167 , ARG B:169 , GLU B:172 , HOH B:303 , HOH B:320 , HOH B:334 , HOH B:340	BINDING SITE FOR RESIDUE TTP B 301
4	AC4	SOFTWARE	ILE C:29 , GLY C:30 , SER C:31 , GLY C:32 , LYS C:33 , THR C:34 , GLU C:52 , TRP C:57 , MET C:69 , TYR C:70 , PHE C:80 , GLN C:81 , VAL C:84 , GLU C:104 , ARG C:105 , ALA C:110 , PHE C:114 , MET C:118 , ARG C:167 , ARG C:169 , GLU C:172 , HOH C:304 , HOH C:337 , HOH C:342	BINDING SITE FOR RESIDUE TTP C 302
5	AC5	SOFTWARE	ILE D:29 , GLY D:30 , SER D:31 , GLY D:32 , LYS D:33 , THR D:34 , GLU D:52 , TRP D:57 , LEU D:66 , MET D:69 , TYR D:70 , PHE D:80 , GLN D:81 , VAL D:84 , GLU D:104 , ARG D:105 , ALA D:110 , PHE D:114 , MET D:118 , ARG D:167 , ARG D:169 , GLU D:172 , MG D:400 , HOH D:430 , HOH D:433 , HOH D:434 , HOH D:436	BINDING SITE FOR RESIDUE TTP D 303

(no "SS Bond" information available for 1ZM7)

(no "Cis Peptide Bond" information available for 1ZM7)

(no "SAP(SNP)/Variant" information available for 1ZM7)

(no "PROSITE Motif" information available for 1ZM7)

(no "Exon" information available for 1ZM7)

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 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 d1zm7a_ A: automated matches                                                                                                                                                                          SCOP domains
               CATH domains 1zm7A00 A:12-208 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeee....hhhhhhhhhhhhh..eeee..hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh........eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zm7 A  12 TKYAEGTQPFTVLIEGNIGSGKTTYLNHFEKYKNDICLLTEPVEKWRNVNGVDLLELMYKDPKKWAMPFQSYVTLTMLQSHTAPTNKKLKIMERSIFSARYCFVENMRRNGSLEQGMYNTLEEWYKFIEESIHVQADLIIYLRTSPEVAYERIRQRARSEESCVPLKYLQELHELHEDWLIHQRRPQSCKVLVLDAD 208
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201

Chain B from PDB  Type:PROTEIN  Length:198
 aligned with DNK_DROME | Q9XZT6 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:198
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201        
            DNK_DROME    12 TKYAEGTQPFTVLIEGNIGSGKTTYLNHFEKYKNDICLLTEPVEKWRNVNGVNLLELMYKDPKKWAMPFQSYVTLTMLQSHTAPTNKKLKIMERSIFSARYCFVENMRRNGSLEQGMYNTLEEWYKFIEESIHVQADLIIYLRTSPEVAYERIRQRARSEESCVPLKYLQELHELHEDWLIHQRRPQSCKVLVLDADL 209
               SCOP domains d1zm7b_ B: automated matches                                                                                                                                                                           SCOP domains
               CATH domains 1zm7B00 B:12-209 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeeeee....hhhhhhhhhhhhh..eeee..hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh........eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1zm7 B  12 TKYAEGTQPFTVLIEGNIGSGKTTYLNHFEKYKNDICLLTEPVEKWRNVNGVDLLELMYKDPKKWAMPFQSYVTLTMLQSHTAPTNKKLKIMERSIFSARYCFVENMRRNGSLEQGMYNTLEEWYKFIEESIHVQADLIIYLRTSPEVAYERIRQRARSEESCVPLKYLQELHELHEDWLIHQRRPQSCKVLVLDADL 209
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201

Chain C from PDB  Type:PROTEIN  Length:198
 aligned with DNK_DROME | Q9XZT6 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:198
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201        
            DNK_DROME    12 TKYAEGTQPFTVLIEGNIGSGKTTYLNHFEKYKNDICLLTEPVEKWRNVNGVNLLELMYKDPKKWAMPFQSYVTLTMLQSHTAPTNKKLKIMERSIFSARYCFVENMRRNGSLEQGMYNTLEEWYKFIEESIHVQADLIIYLRTSPEVAYERIRQRARSEESCVPLKYLQELHELHEDWLIHQRRPQSCKVLVLDADL 209
               SCOP domains d1zm7c_ C: automated matches                                                                                                                                                                           SCOP domains
               CATH domains 1zm7C00 C:12-209 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeeeee....hhhhhhhhhhhhh..eeee..hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh........eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1zm7 C  12 TKYAEGTQPFTVLIEGNIGSGKTTYLNHFEKYKNDICLLTEPVEKWRNVNGVDLLELMYKDPKKWAMPFQSYVTLTMLQSHTAPTNKKLKIMERSIFSARYCFVENMRRNGSLEQGMYNTLEEWYKFIEESIHVQADLIIYLRTSPEVAYERIRQRARSEESCVPLKYLQELHELHEDWLIHQRRPQSCKVLVLDADL 209
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201

Chain D from PDB  Type:PROTEIN  Length:197
 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 d1zm7d_ D: automated matches                                                                                                                                                                          SCOP domains
               CATH domains 1zm7D00 D:12-208 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                 CATH domains
           Pfam domains (1) --------------------------------------------------------------------dNK-1zm7D01 D:80-208                                                                                                              Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------dNK-1zm7D02 D:80-208                                                                                                              Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------dNK-1zm7D03 D:80-208                                                                                                              Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------dNK-1zm7D04 D:80-208                                                                                                              Pfam domains (4)
         Sec.struct. author .........eeeeeee....hhhhhhhhhhhhh..eeee..hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh........eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zm7 D  12 TKYAEGTQPFTVLIEGNIGSGKTTYLNHFEKYKNDICLLTEPVEKWRNVNGVDLLELMYKDPKKWAMPFQSYVTLTMLQSHTAPTNKKLKIMERSIFSARYCFVENMRRNGSLEQGMYNTLEEWYKFIEESIHVQADLIIYLRTSPEVAYERIRQRARSEESCVPLKYLQELHELHEDWLIHQRRPQSCKVLVLDAD 208
                                    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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

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: Nucleotide and nucleoside kinases (231)

Protein domain: automated matches (25)

Fruit fly (Drosophila melanogaster) [TaxId: 7227] (5)

1a	d1zm7a_	A:
1b	d1zm7b_	B:
1c	d1zm7c_	C:
1d	d1zm7d_	D:

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	1zm7B00	B:12-209
1b	1zm7C00	C:12-209
1c	1zm7A00	A:12-208
1d	1zm7D00	D:12-208

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: dNK (33)

Drosophila melanogaster (Fruit fly) (13)

1a	dNK-1zm7D01	D:80-208
1b	dNK-1zm7D02	D:80-208
1c	dNK-1zm7D03	D:80-208
1d	dNK-1zm7D04	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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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1zm7)

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

Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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