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Phosphotransferase PDB id
1ndl
Jmol
Contents
Protein chains
152 a.a. *
Waters ×315
* Residue conservation analysis
PDB id:
1ndl
Name: Phosphotransferase
Title: The awd nucleotide diphosphate kinase from drosophila
Structure: Nucleoside diphosphate kinase. Chain: a, b, c. Engineered: yes
Source: Drosophila melanogaster. Fruit fly. Organism_taxid: 7227
Biol. unit: Hexamer (from PQS)
Resolution:
2.40Å     R-factor:   0.167    
Authors: J.Janin,M.Chiadmi,C.Dumas,I.Lascu,G.Lebras,S.Morera,M.Veron
Key ref:
M.Chiadmi et al. (1993). Crystal structure of the Awd nucleotide diphosphate kinase from Drosophila. Structure, 1, 283-293. PubMed id: 8081741 DOI: 10.1016/0969-2126(93)90016-A
Date:
27-Nov-93     Release date:   30-Apr-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P08879  (NDKA_DROME) -  Nucleoside diphosphate kinase
Seq:
Struc: 		153 a.a.
152 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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     cytoplasm   5 terms 
  Biological process     microtubule-based process   16 terms 
  Biochemical function     nucleotide binding     9 terms  

 

 
    reference    
 
 
DOI no: 10.1016/0969-2126(93)90016-A Structure 1:283-293 (1993)
PubMed id: 8081741  
 
 
Crystal structure of the Awd nucleotide diphosphate kinase from Drosophila.
M.Chiadmi, S.Moréra, I.Lascu, C.Dumas, G.Le Bras, M.Véron, J.Janin.
 
  ABSTRACT  
 
BACKGROUND: Nucleotide diphosphate kinase (NDP kinase) is a phosphate transfer enzyme involved in cell regulation and in animal development. Drosophila NDP kinase is the product of the abnormal wing disc (awd) developmental gene, a point mutation in which can produce the killer of prune (K-pn) conditional lethal phenotype. The highly homologous mammalian genes control metastasis and a human NDP kinase acts as a transcription factor. RESULTS: The X-ray structure of the Awd protein prepared from Drosophila was solved at 2.4 A resolution by molecular replacement from the homologous Dictyostelium protein. Both are hexamers, and both have the same fold and the same active site. Subunit contacts differ as a result of sequence changes in the carboxy-terminal segment and in the loop that is the site of the K-pn mutation. CONCLUSIONS: Regulatory properties of animal NDP kinases depend on interactions with other macromolecules, such as DNA and the product of the Drosophila prune gene. The Awd structure suggests an allosteric mechanism of action of NDP kinase where DNA is the effector and the protein undergoes a major conformational change, possibly dissociating to dimers.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
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
  16511098 S.Jeudy, B.Coutard, R.Lebrun, and C.Abergel (2005).
Acanthamoeba polyphaga mimivirus NDK: preliminary crystallographic analysis of the first viral nucleoside diphosphate kinase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 569-572.  
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.  
14665452 X.Lin, C.Momany, and M.Momany (2003).
SwoHp, a nucleoside diphosphate kinase, is essential in Aspergillus nidulans.
  Eukaryot Cell, 2, 1169-1177.  
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
11274357 Y.Otsuki, M.Tanaka, S.Yoshii, N.Kawazoe, K.Nakaya, and H.Sugimura (2001).
Tumor metastasis suppressor nm23H1 regulates Rac1 GTPase by interaction with Tiam1.
  Proc Natl Acad Sci U S A, 98, 4385-4390.  
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.  
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.  
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
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.  
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.  
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.  
9305928 D.O.Lambeth, J.G.Mehus, M.A.Ivey, and B.I.Milavetz (1997).
Characterization and cloning of a nucleoside-diphosphate kinase targeted to matrix of mitochondria in pigeon.
  J Biol Chem, 272, 24604-24611.  
9038158 J.M.Freije, P.Blay, N.J.MacDonald, R.E.Manrow, and P.S.Steeg (1997).
Site-directed mutation of Nm23-H1. Mutations lacking motility suppressive capacity upon transfection are deficient in histidine-dependent protein phosphotransferase pathways in vitro.
  J Biol Chem, 272, 5525-5532.  
8663370 A.Giartosio, M.Erent, L.Cervoni, S.Moréra, J.Janin, M.Konrad, and I.Lascu (1996).
Thermal stability of hexameric and tetrameric nucleoside diphosphate kinases. Effect of subunit interaction.
  J Biol Chem, 271, 17845-17851.
PDB code: 1ncl
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
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.  
8706710 M.Brodbeck, A.Rohling, W.Wohlleben, C.J.Thompson, and U.Süsstrunk (1996).
Nucleoside-diphosphate kinase from Streptomyces coelicolor.
  Eur J Biochem, 239, 208-213.  
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.  
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.  
  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
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.