General Information

Database accession: MF6110001

Name: Nucleoside diphosphate kinase (Dictyostelium discoideum)

PDB ID: 1npk PDB

Experimental method: X-ray (1.80 Å)

Assembly: homohexamer

Source organism: Dictyostelium discoideum

Primer publication of the structure:

Moréra S, LeBras G, Lascu I, Lacombe ML, Véron M, Janin J
Refined X-ray structure of Dictyostelium discoideum nucleoside diphosphate kinase at 1.8 A resolution.
(1994) J. Mol. Biol. 243: 873-90

PMID: 7966307 PubMed

Abstract:

The X-ray structure of the nucleoside diphosphate kinase (NDP kinase) from Dictyostelium discoideum has been refined at 1.8 A resolution from a hexagonal crystal form with a 17 kDa monomer in its asymmetric unit. The atomic model was derived from the previously determined structure of a point mutant of the protein. It contains 150 amino acid residues out of 155, and 95 solvent molecules. The R-factor is 0.196 and the estimated accuracy of the average atomic position, 0.25 A. The Dictyostelium structure is described in detail and compared to those of Drosophila and Myxococcus xanthus NDP kinases. The protein is a hexamer with D3 symmetry. Residues 8 to 138 of each subunit form a globular alpha/beta domain. The four-stranded beta-sheet is antiparallel; its topology is different from other phosphate transfer enzymes, and also from the HPr protein which, like NDP kinase, carries a phosphorylated histidine. The same topology is nevertheless found in several other proteins that bind mononucleotides, RNA or DNA. Strand connections in NDP kinase involve alpha-helices and a 20-residue segment called the Kpn loop. The beta-sheet is regular except for a beta-bulge in edge strand beta 2 and a gamma-turn at residue Ile120 just preceding strand beta 4. The latter may induce strain in the main chain near the active site His122. The alpha 1 beta 2 motif participates in forming dimers within the hexamer, helices alpha 1 and alpha 3, the Kpn loop and C terminus, in forming trimers. The subunit fold and dimer interactions found in Dictyostelium are conserved in other NDP kinases. Trimer interactions probably occur in all eukaryotic enzymes. They are absent in the bacterial Myxococcus xanthus enzyme which is a tetramer, even though the subunit structure is very similar. In Dictyostelium, contacts between Kpn loops near the 3-fold axis block access to a central cavity lined with polar residues and filled with well-defined solvent molecules. Biochemical data on point mutants highlight the contribution of the Kpn loop to protein stability. In Myxococcus, the Kpn loops are on the tetramer surface and their sequence is poorly conserved. Yet, their conformation is maintained and they make a similar contribution to the substrate binding site.


Function and Biology Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown.

Molecular function:

ATP binding Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GeneOntology

nucleoside diphosphate kinase activity Catalysis of the reaction: ATP + nucleoside diphosphate = ADP + nucleoside triphosphate. GeneOntology

metal ion binding Interacting selectively and non-covalently with any metal ion. GeneOntology

Biological process:

dGDP phosphorylation The process of introducing a phosphate group into dGDP, deoxyguanosine diphosphate, to produce dGTP. GeneOntology

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. GeneOntology

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. GeneOntology

translational elongation The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis. GeneOntology

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). GeneOntology

negative regulation of exocytosis Any process that stops, prevents, or reduces the frequency, rate or extent of exocytosis. GeneOntology

CTP biosynthetic process The chemical reactions and pathways resulting in the formation of CTP, cytidine 5'-triphosphate. GeneOntology

negative regulation of phagocytosis Any process that stops, prevents, or reduces the frequency, rate or extent of phagocytosis. GeneOntology

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. GeneOntology

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. GeneOntology

GTP biosynthetic process The chemical reactions and pathways resulting in the formation of GTP, guanosine triphosphate. GeneOntology

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. GeneOntology

UTP biosynthetic process The chemical reactions and pathways resulting in the formation of UTP, uridine (5'-)triphosphate. GeneOntology

Cellular component:

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. GeneOntology

phagocytic vesicle A membrane-bounded intracellular vesicle that arises from the ingestion of particulate material by phagocytosis. GeneOntology

plasma membrane The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GeneOntology

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. GeneOntology

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. GeneOntology

Structure Summary Structural annotations of the participating protein chains.

Entry contents: 6 distinct polypeptide molecules

Chains: A, B, C, D, E, F

Notes: Chains B, C, D, E and F were generated from chain A using the biomatrices described in the original PDB file.

Number of unique protein segments: 1


Chain A

Name: Nucleoside diphosphate kinase, cytosolic

Source organism: Dictyostelium discoideum

Length: 154 residues

Sequence:Sequence according to PDB SEQRESSTNKVNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIHGSDSVESANREIALWFKPEELLTEVKPNPNLYE

UniProtKB AC: P22887 (positions: 2-155) UniProt Coverage: 99.4%

UniRef90 AC: UniRef90_P22887 (positions: 2-155) UniRef90

Chain B

Name: Nucleoside diphosphate kinase, cytosolic

Source organism: Dictyostelium discoideum

Length: 154 residues

Sequence:Sequence according to PDB SEQRESSTNKVNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIHGSDSVESANREIALWFKPEELLTEVKPNPNLYE

UniProtKB AC: P22887 (positions: 2-155) UniProt Coverage: 99.4%

UniRef90 AC: UniRef90_P22887 (positions: 2-155) UniRef90

Chain C

Name: Nucleoside diphosphate kinase, cytosolic

Source organism: Dictyostelium discoideum

Length: 154 residues

Sequence:Sequence according to PDB SEQRESSTNKVNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIHGSDSVESANREIALWFKPEELLTEVKPNPNLYE

UniProtKB AC: P22887 (positions: 2-155) UniProt Coverage: 99.4%

UniRef90 AC: UniRef90_P22887 (positions: 2-155) UniRef90

Chain D

Name: Nucleoside diphosphate kinase, cytosolic

Source organism: Dictyostelium discoideum

Length: 154 residues

Sequence:Sequence according to PDB SEQRESSTNKVNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIHGSDSVESANREIALWFKPEELLTEVKPNPNLYE

UniProtKB AC: P22887 (positions: 2-155) UniProt Coverage: 99.4%

UniRef90 AC: UniRef90_P22887 (positions: 2-155) UniRef90

Chain E

Name: Nucleoside diphosphate kinase, cytosolic

Source organism: Dictyostelium discoideum

Length: 154 residues

Sequence:Sequence according to PDB SEQRESSTNKVNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIHGSDSVESANREIALWFKPEELLTEVKPNPNLYE

UniProtKB AC: P22887 (positions: 2-155) UniProt Coverage: 99.4%

UniRef90 AC: UniRef90_P22887 (positions: 2-155) UniRef90

Chain F

Name: Nucleoside diphosphate kinase, cytosolic

Source organism: Dictyostelium discoideum

Length: 154 residues

Sequence:Sequence according to PDB SEQRESSTNKVNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIHGSDSVESANREIALWFKPEELLTEVKPNPNLYE

UniProtKB AC: P22887 (positions: 2-155) UniProt Coverage: 99.4%

UniRef90 AC: UniRef90_P22887 (positions: 2-155) UniRef90

Evidence Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding.

Complex evidence:

The hexameric NDP kinase from Dictyostelium discoideum displays one single, irreversible differential scanning calorimetry peak (Tm=62°C) over a broad protein concentration, indicating a single step denaturation. However, the P105G substitution, which affects a loop implicated in subunit contacts, yields a protein that reversibly dissociates to folded monomers at 38°C before the irreversible denaturation occurs (Tm=47°C). These data indicate a “coupling” of the quaternary structure with the tertiary structure in the wild-type, but not in the mutated protein (PMID: 8663370).

Related Structure(s) Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap).

There are 24 related structures in the Protein Data Bank:











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