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Transferase PDB id
1ndk
Jmol
Contents
Protein chain
148 a.a. *
Waters ×28
* Residue conservation analysis
PDB id:
1ndk
Name: Transferase
Title: X-ray structure of nucleoside diphosphate kinase
Structure: Nucleoside diphosphate kinase. Chain: a. Engineered: yes
Source: Dictyostelium discoideum. Organism_taxid: 44689
Biol. unit: Hexamer (from PQS)
Resolution:
2.20Å     R-factor:   0.203    
Authors: J.Janin,C.Dumas,S.Morera,I.Lascu,M.Veron
Key ref: C.Dumas et al. (1992). X-ray structure of nucleoside diphosphate kinase. Embo J, 11, 3203-3208. PubMed id: 1324167 Ref: Full text
Date:
15-Jul-93     Release date:   31-Oct-93    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P22887  (NDKC_DICDI) -  Nucleoside diphosphate kinase, cytosolic
Seq:
Struc: 		155 a.a.
148 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.2.7.4.6  - Nucleoside-diphosphate kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
ATP
 + nucleoside diphosphate
 = ADP
 + nucleoside triphosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     plasma membrane   6 terms 
  Biological process     cytoskeleton organization   13 terms 
  Biochemical function     nucleotide binding     6 terms  

 

 
    reference    
 
 
Full text Embo J 11:3203-3208 (1992)
PubMed id: 1324167  
 
 
X-ray structure of nucleoside diphosphate kinase.
C.Dumas, I.Lascu, S.Moréra, P.Glaser, R.Fourme, V.Wallet, M.L.Lacombe, M.Véron, J.Janin.
 
  ABSTRACT  
 
The X-ray structure of a point mutant of nucleoside diphosphate kinase (NDP kinase) from Dictyostelium discoideum has been determined to 2.2 A resolution. The enzyme is a hexamer made of identical subunits with a novel mononucleotide binding fold. Each subunit contains an alpha/beta domain with a four stranded, antiparallel beta-sheet. The topology is different from adenylate kinase, but identical to the allosteric domain of Escherichia coli ATCase regulatory subunits, which bind mononucleotides at an equivalent position. Dimer contacts between NDP kinase subunits within the hexamer are similar to those in ATCase. Trimer contacts involve a large loop of polypeptide chain that bears the site of the Pro----Ser substitution in Killer of prune (K-pn) mutants of the highly homologous Drosophila enzyme. Properties of Drosophila NDP kinase, the product of the awd developmental gene, and of the human enzyme, the product of the nm23 genes in tumorigenesis, are discussed in view of the three-dimensional structure and of possible interactions of NDP kinase with other nucleotide binding proteins.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19235734 E.H.Postel, I.Wohlman, X.Zou, T.Juan, N.Sun, D.D'Agostin, M.Cuellar, T.Choi, D.A.Notterman, and K.M.La Perle (2009).
Targeted deletion of Nm23/nucleoside diphosphate kinase A and B reveals their requirement for definitive erythropoiesis in the mouse embryo.
  Dev Dyn, 238, 775-787.  
19381783 E.H.Postel, X.Zou, D.A.Notterman, and K.M.La Perle (2009).
Double knockout Nme1/Nme2 mouse model suggests a critical role for NDP kinases in erythroid development.
  Mol Cell Biochem, 329, 45-50.  
19387798 S.J.Annesley, and P.R.Fisher (2009).
Dictyostelium discoideum--a model for many reasons.
  Mol Cell Biochem, 329, 73-91.  
17314099 H.A.Seong, H.Jung, and H.Ha (2007).
NM23-H1 tumor suppressor physically interacts with serine-threonine kinase receptor-associated protein, a transforming growth factor-beta (TGF-beta) receptor-interacting protein, and negatively regulates TGF-beta signaling.
  J Biol Chem, 282, 12075-12096.  
17330300 L.Moynié, M.F.Giraud, F.Georgescauld, I.Lascu, and A.Dautant (2007).
The structure of the Escherichia coli nucleoside diphosphate kinase reveals a new quaternary architecture for this enzyme family.
  Proteins, 67, 755-765.
PDB code: 2hur
17715145 S.Balaji, and L.Aravind (2007).
The RAGNYA fold: a novel fold with multiple topological variants found in functionally diverse nucleic acid, nucleotide and peptide-binding proteins.
  Nucleic Acids Res, 35, 5658-5671.  
16195547 J.D.Pédelacq, G.S.Waldo, S.Cabantous, E.C.Liong, and T.C.Terwilliger (2005).
Structural and functional features of an NDP kinase from the hyperthermophile crenarchaeon Pyrobaculum aerophilum.
  Protein Sci, 14, 2562-2573.
PDB code: 1xqi
15561724 Y.Shen, J.I.Kim, and P.S.Song (2005).
NDPK2 as a signal transducer in the phytochrome-mediated light signaling.
  J Biol Chem, 280, 5740-5749.  
15377659 A.K.Saini, K.Maithal, P.Chand, S.Chowdhury, R.Vohra, A.Goyal, G.P.Dubey, P.Chopra, R.Chandra, A.K.Tyagi, Y.Singh, and V.Tandon (2004).
Nuclear localization and in situ DNA damage by Mycobacterium tuberculosis nucleoside-diphosphate kinase.
  J Biol Chem, 279, 50142-50149.  
15146492 C.DeWeese-Scott, and J.Moult (2004).
Molecular modeling of protein function regions.
  Proteins, 55, 942-961.  
14665452 X.Lin, C.Momany, and M.Momany (2003).
SwoHp, a nucleoside diphosphate kinase, is essential in Aspergillus nidulans.
  Eukaryot Cell, 2, 1169-1177.  
12070317 B.Schneider, A.Norda, A.Karlsson, M.Veron, and D.Deville-Bonne (2002).
Nucleotide affinity for a stable phosphorylated intermediate of nucleoside diphosphate kinase.
  Protein Sci, 11, 1648-1656.  
11919189 H.N.Fournier, S.Dupé-Manet, D.Bouvard, M.L.Lacombe, C.Marie, M.R.Block, and C.Albiges-Rizo (2002).
Integrin cytoplasmic domain-associated protein 1alpha (ICAP-1alpha ) interacts directly with the metastasis suppressor nm23-H2, and both proteins are targeted to newly formed cell adhesion sites upon integrin engagement.
  J Biol Chem, 277, 20895-20902.  
11294625 L.Cervoni, I.Lascu, Y.Xu, P.Gonin, M.Morr, M.Merouani, J.Janin, and A.Giartosio (2001).
Binding of nucleotides to nucleoside diphosphate kinase: a calorimetric study.
  Biochemistry, 40, 4583-4589.
PDB code: 1hiy
11352723 S.Raveh, J.Vinh, J.Rossier, F.Agou, and M.Véron (2001).
Peptidic determinants and structural model of human NDP kinase B (Nm23-H2) bound to single-stranded DNA.
  Biochemistry, 40, 5882-5893.  
11053861 K.Min, H.K.Song, C.Chang, J.Y.Lee, S.H.Eom, K.K.Kim, Y.G.Yu, and S.W.Suh (2000).
Nucleoside diphosphate kinase from the hyperthermophilic archaeon Methanococcus jannaschii: overexpression, crystallization and preliminary X-ray crystallographic analysis.
  Acta Crystallogr D Biol Crystallogr, 56, 1485-1487.  
10799505 L.Milon, P.Meyer, M.Chiadmi, A.Munier, M.Johansson, A.Karlsson, I.Lascu, J.Capeau, J.Janin, and M.L.Lacombe (2000).
The human nm23-H4 gene product is a mitochondrial nucleoside diphosphate kinase.
  J Biol Chem, 275, 14264-14272.
PDB code: 1ehw
10899107 P.Meyer, B.Schneider, S.Sarfati, D.Deville-Bonne, C.Guerreiro, J.Boretto, J.Janin, M.Véron, and B.Canard (2000).
Structural basis for activation of alpha-boranophosphate nucleotide analogues targeting drug-resistant reverse transcriptase.
  EMBO J, 19, 3520-3529.
PDB codes: 1f3f 1f6t
10391900 F.Agou, S.Raveh, S.Mesnildrey, and M.Véron (1999).
Single strand DNA specificity analysis of human nucleoside diphosphate kinase B.
  J Biol Chem, 274, 19630-19638.  
10585400 H.Prinz, A.Lavie, A.J.Scheidig, O.Spangenberg, and M.Konrad (1999).
Binding of nucleotides to guanylate kinase, p21(ras), and nucleoside-diphosphate kinase studied by nano-electrospray mass spectrometry.
  J Biol Chem, 274, 35337-35342.  
10329774 J.E.Ladner, N.G.Abdulaev, D.L.Kakuev, M.Tordová, K.D.Ridge, and G.L.Gilliland (1999).
The three-dimensional structures of two isoforms of nucleoside diphosphate kinase from bovine retina.
  Acta Crystallogr D Biol Crystallogr, 55, 1127-1135.
PDB code: 1bhn
10353838 P.Gonin, Y.Xu, L.Milon, S.Dabernat, M.Morr, R.Kumar, M.L.Lacombe, J.Janin, and I.Lascu (1999).
Catalytic mechanism of nucleoside diphosphate kinase investigated using nucleotide analogues, viscosity effects, and X-ray crystallography.
  Biochemistry, 38, 7265-7272.
PDB code: 1b99
10583364 Y.Ogura, Y.Yoshida, K.Ichimura, C.Aoyagi, N.Yabe, and K.Hasunuma (1999).
Isolation and characterization of Neurospora crassa nucleoside diphosphate kinase NDK-1.
  Eur J Biochem, 266, 709-714.  
9786875 B.Schneider, Y.W.Xu, J.Janin, M.Véron, and D.Deville-Bonne (1998).
3'-Phosphorylated nucleotides are tight binding inhibitors of nucleoside diphosphate kinase activity.
  J Biol Chem, 273, 28773-28778.
PDB code: 1bux
9565562 B.Schneider, Y.W.Xu, O.Sellam, R.Sarfati, J.Janin, M.Veron, and D.Deville-Bonne (1998).
Pre-steady state of reaction of nucleoside diphosphate kinase with anti-HIV nucleotides.
  J Biol Chem, 273, 11491-11497.  
  9881672 F.Gervasi, F.Capozza, T.Bruno, M.Fanciulli, and D.Lombardi (1998).
Identification of novel mRNA transcripts of the nm23-M1 gene that are modulated during mouse embryo development and are differently expressed in adult murine tissues.
  DNA Cell Biol, 17, 1047-1055.  
9685345 M.Engel, M.Seifert, B.Theisinger, U.Seyfert, and C.Welter (1998).
Glyceraldehyde-3-phosphate dehydrogenase and Nm23-H1/nucleoside diphosphate kinase A. Two old enzymes combine for the novel Nm23 protein phosphotransferase function.
  J Biol Chem, 273, 20058-20065.  
9760230 N.G.Abdulaev, G.N.Karaschuk, J.E.Ladner, D.L.Kakuev, A.V.Yakhyaev, M.Tordova, I.O.Gaidarov, V.I.Popov, J.H.Fujiwara, D.Chinchilla, E.Eisenstein, G.L.Gilliland, and K.D.Ridge (1998).
Nucleoside diphosphate kinase from bovine retina: purification, subcellular localization, molecular cloning, and three-dimensional structure.
  Biochemistry, 37, 13958-13967.
PDB code: 1be4
9468495 S.Mesnildrey, F.Agou, A.Karlsson, D.D.Bonne, and M.Véron (1998).
Coupling between catalysis and oligomeric structure in nucleoside diphosphate kinase.
  J Biol Chem, 273, 4436-4442.  
9488696 S.Schaertl, M.Konrad, and M.A.Geeves (1998).
Substrate specificity of human nucleoside-diphosphate kinase revealed by transient kinetic analysis.
  J Biol Chem, 273, 5662-5669.  
9188741 A.V.Efimov (1997).
Structural trees for protein superfamilies.
  Proteins, 28, 241-260.  
  9309225 J.L.Hansen, A.M.Long, and S.C.Schultz (1997).
Structure of the RNA-dependent RNA polymerase of poliovirus.
  Structure, 5, 1109-1122.
PDB code: 1rdr
9108019 Y.W.Xu, S.Moréra, J.Janin, and J.Cherfils (1997).
AlF3 mimics the transition state of protein phosphorylation in the crystal structure of nucleoside diphosphate kinase and MgADP.
  Proc Natl Acad Sci U S A, 94, 3579-3583.
PDB codes: 1kdn 2bef
8702707 A.Karlsson, S.Mesnildrey, Y.Xu, S.Moréra, J.Janin, and M.Véron (1996).
Nucleoside diphosphate kinase. Investigation of the intersubunit contacts by site-directed mutagenesis and crystallography.
  J Biol Chem, 271, 19928-19934.
PDB code: 1leo
8931563 D.Deville-Bonne, O.Sellam, F.Merola, I.Lascu, M.Desmadril, and M.Véron (1996).
Phosphorylation of nucleoside diphosphate kinase at the active site studied by steady-state and time-resolved fluorescence.
  Biochemistry, 35, 14643-14650.  
8692914 E.H.Postel, V.H.Weiss, J.Beneken, and A.Kirtane (1996).
Mutational analysis of NM23-H2/NDP kinase identifies the structural domains critical to recognition of a c-myc regulatory element.
  Proc Natl Acad Sci U S A, 93, 6892-6897.  
  8955392 G.W.Sundin, S.Shankar, and A.M.Chakrabarty (1996).
Mutational analysis of nucleoside diphosphate kinase from Pseudomonas aeruginosa: characterization of critical amino acid residues involved in exopolysaccharide alginate synthesis.
  J Bacteriol, 178, 7120-7128.  
8809750 G.W.Sundin, S.Shankar, S.A.Chugani, B.A.Chopade, A.Kavanaugh-Black, and A.M.Chakrabarty (1996).
Nucleoside diphosphate kinase from Pseudomonas aeruginosa: characterization of the gene and its role in cellular growth and exopolysaccharide alginate synthesis.
  Mol Microbiol, 20, 965-979.  
8626464 J.Bourdais, R.Biondi, S.Sarfati, C.Guerreiro, I.Lascu, J.Janin, and M.Véron (1996).
Cellular phosphorylation of anti-HIV nucleosides. Role of nucleoside diphosphate kinase.
  J Biol Chem, 271, 7887-7890.  
8822806 K.S.Ann, and D.L.Nelson (1996).
A nucleoside diphosphate kinase from Paramecium tetraurelia with protein kinase activity.
  J Eukaryot Microbiol, 43, 365-372.  
8810265 N.J.MacDonald, J.M.Freije, M.L.Stracke, R.E.Manrow, and P.S.Steeg (1996).
Site-directed mutagenesis of nm23-H1. Mutation of proline 96 or serine 120 abrogates its motility inhibitory activity upon transfection into human breast carcinoma cells.
  J Biol Chem, 271, 25107-25116.  
7702594 A.de la Rosa, R.L.Williams, and P.S.Steeg (1995).
Nm23/nucleoside diphosphate kinase: toward a structural and biochemical understanding of its biological functions.
  Bioessays, 17, 53-62.  
7719856 D.J.Schuller, G.A.Grant, and L.J.Banaszak (1995).
The allosteric ligand site in the Vmax-type cooperative enzyme phosphoglycerate dehydrogenase.
  Nat Struct Biol, 2, 69-76.
PDB code: 1psd
7494863 E.S.Arnér, and S.Eriksson (1995).
Mammalian deoxyribonucleoside kinases.
  Pharmacol Ther, 67, 155-186.  
7559441 L.Timmons, J.Xu, G.Hersperger, X.F.Deng, and A.Shearn (1995).
Point mutations in awdKpn which revert the prune/Killer of prune lethal interaction affect conserved residues that are involved in nucleoside diphosphate kinase substrate binding and catalysis.
  J Biol Chem, 270, 23021-23030.  
8529641 M.Engel, M.Véron, B.Theisinger, M.L.Lacombe, T.Seib, S.Dooley, and C.Welter (1995).
A novel serine/threonine-specific protein phosphotransferase activity of Nm23/nucleoside-diphosphate kinase.
  Eur J Biochem, 234, 200-207.  
7479028 M.Hildebrandt, M.L.Lacombe, S.Mesnildrey, and M.Véron (1995).
A human NDP-kinase B specifically binds single-stranded poly-pyrimidine sequences.
  Nucleic Acids Res, 23, 3858-3864.  
  7730286 N.Almaula, Q.Lu, J.Delgado, S.Belkin, and M.Inouye (1995).
Nucleoside diphosphate kinase from Escherichia coli.
  J Bacteriol, 177, 2524-2529.  
7651139 O.Sellam, M.Véron, and M.Hildebrandt (1995).
Overexpression of wild-type and mutant NDP kinase in Dictyostelium discoideum.
  Mol Microbiol, 16, 79-85.  
7665595 P.D.Wagner, and N.D.Vu (1995).
Phosphorylation of ATP-citrate lyase by nucleoside diphosphate kinase.
  J Biol Chem, 270, 21758-21764.  
8749843 R.W.Harrison, D.Chatterjee, and I.T.Weber (1995).
Analysis of six protein structures predicted by comparative modeling techniques.
  Proteins, 23, 463-471.  
  8747457 S.Moréra, M.L.Lacombe, Y.Xu, G.LeBras, and J.Janin (1995).
X-ray structure of human nucleoside diphosphate kinase B complexed with GDP at 2 A resolution.
  Structure, 3, 1307-1314.
PDB code: 1nue
  7704530 D.I.Liao, and O.Herzberg (1994).
Refined structures of the active Ser83-->Cys and impaired Ser46-->Asp histidine-containing phosphocarrier proteins.
  Structure, 2, 1203-1216.
PDB codes: 1sph 2hpr
  7866749 E.Cheah, P.D.Carr, P.M.Suffolk, S.G.Vasudevan, N.E.Dixon, and D.L.Ollis (1994).
Structure of the Escherichia coli signal transducing protein PII.
  Structure, 2, 981-990.
PDB code: 1pil
7931840 J.A.Royds, R.C.Rees, and T.J.Stephenson (1994).
nm23--a metastasis suppressor gene?
  J Pathol, 173, 211-212.  
8195929 J.A.Royds, S.S.Cross, P.B.Silcocks, J.H.Scholefield, R.C.Rees, and T.J.Stephenson (1994).
Nm23 'anti-metastatic' gene product expression in colorectal carcinoma.
  J Pathol, 172, 261-266.  
7925396 J.Veselý, L.Havlicek, M.Strnad, J.J.Blow, A.Donella-Deana, L.Pinna, D.S.Letham, J.Kato, L.Detivaud, and S.Leclerc (1994).
Inhibition of cyclin-dependent kinases by purine analogues.
  Eur J Biochem, 224, 771-786.  
  8045252 M.Delarue, A.Poterszman, S.Nikonov, M.Garber, D.Moras, and J.C.Thierry (1994).
Crystal structure of a prokaryotic aspartyl tRNA-synthetase.
  EMBO J, 13, 3219-3229.  
  8137808 M.Lindahl, L.A.Svensson, A.Liljas, S.E.Sedelnikova, I.A.Eliseikina, N.P.Fomenkova, N.Nevskaya, S.V.Nikonov, M.B.Garber, and T.A.Muranova (1994).
Crystal structure of the ribosomal protein S6 from Thermus thermophilus.
  EMBO J, 13, 1249-1254.
PDB code: 1ris
  8389692 A.A.Bominaar, A.C.Molijn, M.Pestel, M.Veron, and P.J.Van Haastert (1993).
Activation of G-proteins by receptor-stimulated nucleoside diphosphate kinase in Dictyostelium.
  EMBO J, 12, 2275-2279.  
  8081741 M.Chiadmi, S.Moréra, I.Lascu, C.Dumas, G.Le Bras, M.Véron, and J.Janin (1993).
Crystal structure of the Awd nucleotide diphosphate kinase from Drosophila.
  Structure, 1, 283-293.
PDB code: 1ndl
8274143 M.Delarue, and D.Moras (1993).
The aminoacyl-tRNA synthetase family: modules at work.
  Bioessays, 15, 675-687.  
8347849 P.S.Steeg, A.de la Rosa, U.Flatow, N.J.MacDonald, M.Benedict, and A.Leone (1993).
Nm23 and breast cancer metastasis.
  Breast Cancer Res Treat, 25, 175-187.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.