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Phosphotransferase PDB id
1ndp
Jmol
Contents
Protein chains
150 a.a. *
Ligands
ADP ×2
Metals
_MG
Waters ×158
* Residue conservation analysis
PDB id:
1ndp
Name: Phosphotransferase
Title: Adenosine 5'-diphosphate binding and the active site of nucl diphosphate kinase
Structure: Nucleoside diphosphate kinase. Chain: a, b. Engineered: yes
Source: Dictyostelium discoideum. Organism_taxid: 44689
Biol. unit: Hexamer (from PQS)
Resolution:
2.20Å     R-factor:   0.193    
Authors: J.Janin,S.Morera,C.Dumas,I.Lascu,G.Lebras,M.Veron
Key ref:
S.Moréra et al. (1994). Adenosine 5'-diphosphate binding and the active site of nucleoside diphosphate kinase. Biochemistry, 33, 459-467. PubMed id: 8286376 DOI: 10.1021/bi00168a010
Date:
29-Nov-93     Release date:   30-Apr-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P22887  (NDKC_DICDI) -  Nucleoside diphosphate kinase, cytosolic
Seq:
Struc: 		155 a.a.
150 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
Bound ligand (Het Group name = ADP)
corresponds exactly 		+ 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    
 
 
DOI no: 10.1021/bi00168a010 Biochemistry 33:459-467 (1994)
PubMed id: 8286376  
 
 
Adenosine 5'-diphosphate binding and the active site of nucleoside diphosphate kinase.
S.Moréra, I.Lascu, C.Dumas, G.LeBras, P.Briozzo, M.Véron, J.Janin.
 
  ABSTRACT  
 
The X-ray structure of nucleoside diphosphate kinase (NDP kinase) from the slime mold Dictyostelium discoideum has been determined to 2.2-A resolution and refined to an R-factor of 0.19 with and without bound ADP-Mg2+. The nucleotide binds near His 122, a residue which becomes phosphorylated during the catalytic cycle. The mode of binding is different from that observed in other phosphokinases, and it involves no glycine-rich sequence. The adenine base makes only nonpolar contacts with the protein. It points outside, explaining the lack of specificity of NDP kinase toward the base. The ribose 2'- and 3'-hydroxyls and the pyrophosphate moiety are H-bonded to polar side chains. A Mg2+ ion bridges the alpha- to the beta-phosphate which approaches the imidazole group of His 122 from the N delta side. The geometry at the active site in the ADP-Mg2+ complex suggests a mechanism for catalysis whereby the gamma-phosphate of a nucleoside triphosphate can be transferred onto His 122 with a minimum of atomic motion.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19201797 J.Diao, and M.S.Hasson (2009).
Crystal structure of butyrate kinase 2 from Thermotoga maritima, a member of the ASKHA superfamily of phosphotransferases.
  J Bacteriol, 191, 2521-2529.
PDB code: 1saz
19387798 S.J.Annesley, and P.R.Fisher (2009).
Dictyostelium discoideum--a model for many reasons.
  Mol Cell Biochem, 329, 73-91.  
17285171 M.A.Boudreau, and J.C.Vederas (2007).
Synthesis and biological evaluation of nucleoside dicarboxylates as potential mimics of nucleoside diphosphates.
  Org Biomol Chem, 5, 627-635.  
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.  
12171931 S.Gallois-Montbrun, B.Schneider, Y.Chen, V.Giacomoni-Fernandes, L.Mulard, S.Morera, J.Janin, D.Deville-Bonne, and M.Veron (2002).
Improving nucleoside diphosphate kinase for antiviral nucleotide analogs activation.
  J Biol Chem, 277, 39953-39959.
PDB code: 1mn7
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.  
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
  9562560 A.Matte, L.W.Tari, and L.T.Delbaere (1998).
How do kinases transfer phosphoryl groups?
  Structure, 6, 413-419.  
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.  
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.  
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.  
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
9207061 Y.Xu, O.Sellam, S.Moréra, S.Sarfati, R.Biondi, M.Véron, and J.Janin (1997).
X-ray analysis of azido-thymidine diphosphate binding to nucleoside diphosphate kinase.
  Proc Natl Acad Sci U S A, 94, 7162-7165.
PDB code: 1lwx
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
8816286 C.Aguado-Velasco, M.Véron, J.A.Rambow, and E.R.Kuczmarski (1996).
NDP kinase can modulate contraction of Dictyostelium cytoskeletons.
  Cell Motil Cytoskeleton, 34, 194-205.  
  8805593 C.D.Mol, J.M.Harris, E.M.McIntosh, and J.A.Tainer (1996).
Human dUTP pyrophosphatase: uracil recognition by a beta hairpin and active sites formed by three separate subunits.
  Structure, 4, 1077-1092.
PDB codes: 1q5h 1q5u
  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.  
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.  
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.  
8557708 M.G.Surette, M.Levit, Y.Liu, G.Lukat, E.G.Ninfa, A.Ninfa, and J.B.Stock (1996).
Dimerization is required for the activity of the protein histidine kinase CheA that mediates signal transduction in bacterial chemotaxis.
  J Biol Chem, 271, 939-945.  
  8984006 S.Ananvoranich, J.Grandmaison, and P.J.Gulick (1996).
Molecular and biochemical characterization of two nucleoside diphosphate kinase cDNA clones from Flaveria bidentis.
  Genome, 39, 404-409.  
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.  
  7669582 M.Mandai, I.Konishi, T.Komatsu, T.Mori, S.Arao, H.Nomura, Y.Kanda, H.Hiai, and M.Fukumoto (1995).
Mutation of the nm23 gene, loss of heterozygosity at the nm23 locus and K-ras mutation in ovarian carcinoma: correlation with tumour progression and nm23 gene expression.
  Br J Cancer, 72, 691-695.  
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.  
  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
7634068 M.G.Swindells, and N.N.Alexandrov (1994).
Nucleotide binding in beta alpha beta--beta alpha beta topologies.
  Nat Struct Biol, 1, 677-678.  
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.