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Title :   STRUCTURE OF THE H122G NUCLEOSIDE DIPHOSPHATE KINASE / D4T-TRIPHOSPHATE.MG COMPLEX

Authors :   P. Meyer, B. Schneider, S. Sarfati, D. Deville-Bonne, C. Guerreiro, J. J. Janin, M. Veron, B. Canard

Date :   02 Jun 00 (Deposition) - 13 Sep 00 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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

Keywords :   Nucleoside Diphosphate Kinase, Anti-Hiv Nucleoside Analogue, Phosphorylation, Ch. . . O Bond, , Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Meyer, B. Schneider, S. Sarfati, D. Deville-Bonne, C. Guerreiro, J. Boretto, J. Janin, M. Veron, B. Canard
Structural Basis For Activation Of Alpha-Boranophosphate Nucleotide Analogues Targeting Drug-Resistant Reverse Transcriptase.
Embo J. V. 19 3520 2000
PubMed-ID: 10899107 | Reference-DOI: 10.1093/EMBOJ/19.14.3520

Molecule 1 - PROTEIN (NUCLEOSIDE DIPHOSPHATE KINASE)
	Chains	:	A, B, C
	EC Number	:	2.7.4.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTZ18R
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	DICTYOSTELIUM DISCOIDEUM
	Organism Taxid	:	44689
	Synonym	:	NDP KINASE, NDK

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 8)

No.	Name	Count	Type	Full Name
1	D4D	1	Ligand/Ion	2',3'-DEHYDRO-2',3'-DEOXY-THYMIDINE 5'-DIPHOSPHATE
2	D4T	3	Ligand/Ion	2',3'-DEHYDRO-2',3'-DEOXY-THYMIDINE 5'-TRIPHOSPHATE
3	MG	3	Ligand/Ion	MAGNESIUM ION
4	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (3, 10)

No.	Name	Count	Type	Full Name
1	D4D	2	Ligand/Ion	2',3'-DEHYDRO-2',3'-DEOXY-THYMIDINE 5'-DIPHOSPHATE
2	D4T	6	Ligand/Ion	2',3'-DEHYDRO-2',3'-DEOXY-THYMIDINE 5'-TRIPHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS B:16 , HIS B:55 , TYR B:56 , ARG B:92 , GLY B:122 , GLY B:123 , D4D B:163 , MG B:166 , HOH B:728 , HOH B:730 , HOH B:843	BINDING SITE FOR RESIDUE PO4 B 162
2	AC2	SOFTWARE	D4T A:160 , HOH A:725 , HOH A:726 , HOH A:727	BINDING SITE FOR RESIDUE MG A 165
3	AC3	SOFTWARE	D4T B:161 , PO4 B:162 , D4D B:163 , HOH B:728 , HOH B:729 , HOH B:730	BINDING SITE FOR RESIDUE MG B 166
4	AC4	SOFTWARE	D4T C:164 , HOH C:731 , HOH C:732	BINDING SITE FOR RESIDUE MG C 167
5	AC5	SOFTWARE	LYS A:16 , TYR A:56 , HIS A:59 , PHE A:64 , LEU A:68 , ARG A:92 , THR A:98 , ARG A:109 , VAL A:116 , GLY A:117 , ASN A:119 , GLY A:122 , GLY A:123 , MG A:165 , HOH A:664 , HOH A:725 , HOH A:726 , HOH A:727 , HOH A:809 , HOH A:810	BINDING SITE FOR RESIDUE D4T A 160
6	AC6	SOFTWARE	LYS B:16 , TYR B:56 , HIS B:59 , PHE B:64 , LEU B:68 , ARG B:92 , THR B:98 , ARG B:109 , VAL B:116 , GLY B:117 , ASN B:119 , GLY B:122 , GLY B:123 , MG B:166 , HOH B:728 , HOH B:729 , HOH B:730 , HOH B:784 , HOH B:811 , HOH B:828 , HOH B:843	BINDING SITE FOR RESIDUE D4T B 161
7	AC7	SOFTWARE	LYS B:16 , HIS B:59 , PHE B:64 , LEU B:68 , ARG B:92 , THR B:98 , ARG B:109 , VAL B:116 , GLY B:117 , ASN B:119 , PO4 B:162 , MG B:166 , HOH B:705 , HOH B:723 , HOH B:729 , HOH B:784 , HOH B:811 , HOH B:828	BINDING SITE FOR RESIDUE D4D B 163
8	AC8	SOFTWARE	LYS C:16 , TYR C:56 , HIS C:59 , PHE C:64 , LEU C:68 , ARG C:92 , THR C:98 , ARG C:109 , VAL C:116 , GLY C:117 , ASN C:119 , GLY C:122 , GLY C:123 , MG C:167 , HOH C:731 , HOH C:732	BINDING SITE FOR RESIDUE D4T C 164

(no "SS Bond" information available for 1F3F)

(no "Cis Peptide Bond" information available for 1F3F)

(no "SAP(SNP)/Variant" information available for 1F3F)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NDP_KINASES	PS00469	Nucleoside diphosphate kinases active site.	NDKC_DICDI	119-127	3	A:119-127 B:119-127 C:119-127

Biological Unit 1 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NDP_KINASES	PS00469	Nucleoside diphosphate kinases active site.	NDKC_DICDI	119-127	6	A:119-127 B:119-127 C:119-127

(no "Exon" information available for 1F3F)

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:150
 aligned with NDKC_DICDI | P22887 from UniProtKB/Swiss-Prot  Length:155

    Alignment length:150
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155
           NDKC_DICDI     6 VNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIHGSDSVESANREIALWFKPEELLTEVKPNPNLYE 155
               SCOP domains d1f3fa_ A: Nucleoside diphosphate kinase, NDK                                                                                                          SCOP domains
               CATH domains 1f3fA00 A:6-155  [code=3.30.70.141, no name defined]                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.......eee..hhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------NDP_KINAS---------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1f3f A   6 VNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIGGSDSVESANREIALWFKPEELLTEVKPNPNLYE 155
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155

Chain B from PDB  Type:PROTEIN  Length:150
 aligned with NDKC_DICDI | P22887 from UniProtKB/Swiss-Prot  Length:155

    Alignment length:150
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155
           NDKC_DICDI     6 VNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIHGSDSVESANREIALWFKPEELLTEVKPNPNLYE 155
               SCOP domains d1f3fb_ B: Nucleoside diphosphate kinase, NDK                                                                                                          SCOP domains
               CATH domains 1f3fB00 B:6-155  [code=3.30.70.141, no name defined]                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.......eee..hhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------NDP_KINAS---------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1f3f B   6 VNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIGGSDSVESANREIALWFKPEELLTEVKPNPNLYE 155
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155

Chain C from PDB  Type:PROTEIN  Length:150
 aligned with NDKC_DICDI | P22887 from UniProtKB/Swiss-Prot  Length:155

    Alignment length:150
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155
           NDKC_DICDI     6 VNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIHGSDSVESANREIALWFKPEELLTEVKPNPNLYE 155
               SCOP domains d1f3fc_ C: Nucleoside diphosphate kinase, NDK                                                                                                          SCOP domains
               CATH domains 1f3fC00 C:6-155  [code=3.30.70.141, no name defined]                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.......eee..hhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------NDP_KINAS---------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1f3f C   6 VNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIGGSDSVESANREIALWFKPEELLTEVKPNPNLYE 155
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155

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	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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a+b) (23004)

Fold: Ferredoxin-like (1795)

Superfamily: Nucleoside diphosphate kinase, NDK (129)

Family: Nucleoside diphosphate kinase, NDK (112)

Protein domain: Nucleoside diphosphate kinase, NDK (66)

Slime mold (Dictyostelium discoideum) [TaxId: 44689] (21)

1a	d1f3fa_	A:
1b	d1f3fb_	B:
1c	d1f3fc_	C:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: [code=3.30.70.141, no name defined] (46)

Dictyostelium discoideum. Organism_taxid: 44689. (15)

1a	1f3fA00	A:6-155
1b	1f3fB00	B:6-155
1c	1f3fC00	C:6-155

(no "Pfam Domain" information available for 1F3F)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (NDKC_DICDI | P22887)

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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004550	nucleoside diphosphate kinase activity	Catalysis of the reaction: ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.
	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: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:0006241	CTP biosynthetic process	The chemical reactions and pathways resulting in the formation of CTP, cytidine 5'-triphosphate.
	GO:0007186	G-protein coupled receptor signaling pathway	A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
	GO:0006183	GTP biosynthetic process	The chemical reactions and pathways resulting in the formation of GTP, guanosine triphosphate.
	GO:0006228	UTP biosynthetic process	The chemical reactions and pathways resulting in the formation of UTP, uridine (5'-)triphosphate.
	GO:0030036	actin cytoskeleton organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
	GO:0016049	cell growth	The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.
	GO:0006186	dGDP phosphorylation	The process of introducing a phosphate group into dGDP, deoxyguanosine diphosphate, to produce dGTP.
	GO:0006187	dGTP biosynthetic process from dGDP	The chemical reactions and pathways resulting in the formation of dGTP, deoxyguanosine triphosphate (2'-deoxyguanosine 5'-triphosphate) from other compounds, including gGDP, deoxyguanosine diphosphate.
	GO:0044351	macropinocytosis	An endocytosis process that results in the uptake of liquid material by cells from their external environment by the 'ruffling' of the cell membrane to form heterogeneously sized intracellular vesicles called macropinosomes, which can be up to 5 micrometers in size.
	GO:0045920	negative regulation of exocytosis	Any process that stops, prevents, or reduces the frequency, rate or extent of exocytosis.
	GO:0050765	negative regulation of phagocytosis	Any process that stops, prevents, or reduces the frequency, rate or extent of phagocytosis.
	GO:0048550	negative regulation of pinocytosis	Any process that stops, prevents, or reduces the frequency, rate or extent of pinocytosis. Pinocytosis is the process in which cells take in liquid material from their external environment; literally 'cell drinking'. Liquid is enclosed in vesicles, formed by invagination of the plasma membrane. These vesicles then move into the cell and pass their contents to endosomes.
	GO:0006165	nucleoside diphosphate phosphorylation	The process of introducing a phosphate group into a nucleoside diphosphate to produce a nucleoside triphosphate.
	GO:0009142	nucleoside triphosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar.
	GO:0009117	nucleotide metabolic process	The chemical reactions and pathways involving a nucleotide, a 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: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.
	GO:0006220	pyrimidine nucleotide metabolic process	The chemical reactions and pathways involving a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
	GO:0009617	response to bacterium	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a bacterium.
	GO:0006414	translational elongation	The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.
cellular component
	GO:0015629	actin cytoskeleton	The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	GO:0045335	phagocytic vesicle	A membrane-bounded intracellular vesicle that arises from the ingestion of particulate material by phagocytosis.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0005840	ribosome	An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.
	GO:0030141	secretory granule	A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules.

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	1f3f
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