X-ray structure of human nucleoside diphosphate kinase B complexed with GDP at 2 A resolution.
BACKGROUND
Nucleoside diphosphate (NDP) kinases provide precursors for DNA and RNA synthesis. In mammals, these enzymes are also involved in cell regulations. Human NDP kinase B, product of the human nm23-H2 gene, is both an enzyme and a transcription factor. It activates transcription of the c-myc oncogene independently of its catalytic function, by binding to its promoter DNA. How do the two functions coexist?


RESULTS
Recombinant human NDP kinase B was co-crystallized with GDP. The X-ray structure was solved at 2.0 A resolution by molecular replacement from the homologous Drosophila Awd protein. Both enzymes are homo-hexamers with a characteristic beta alpha beta beta alpha beta fold. GDP binds near the active site His118. The guanine base is in a surface cleft and interacts with the C terminus of another subunit.


CONCLUSIONS
The beta alpha beta beta alpha beta fold, also present in the 'palm' domain of Escherichia coli DNA polymerase I and HIV reverse transcriptase, is both a mononucleotide- and a polynucleotide-binding fold. If NDP kinase B binds DNA in the same way as the polymerases, the enzyme must undergo a conformation change in order to carry out gene activation.
Moréra
S
S
Laboratoire de Biologie Structurale, UMR 9920 CNRS-Université Paris-Sud, Gif-sur-Yvette, France.
Lacombe
M L
ML
Xu
Y
Y
LeBras
G
G
Janin
J
J
D000595:Amino Acid Sequence; D000818:Animals; D018360:Crystallography, X-Ray; D004256:DNA Polymerase I / Q000737:chemistry; D029721:Drosophila Proteins; D004331:Drosophila melanogaster / Q000201:enzymology; D005786:Gene Expression Regulation; D006153:Guanosine Diphosphate / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D007301:Insect Hormones / Q000737:chemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D020559:Monomeric GTP-Binding Proteins; D054778:NM23 Nucleoside Diphosphate Kinases; D009701:Nucleoside-Diphosphate Kinase / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D055503:Protein Multimerization; D012194:RNA-Directed DNA Polymerase / Q000737:chemistry; D011993:Recombinant Fusion Proteins / Q000737:chemistry / Q000378:metabolism; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D014157:Transcription Factors / Q000737:chemistry* / Q000378:metabolism; D015533:Transcriptional Activation
D029721:Drosophila Proteins; D007301:Insect Hormones; D054778:NM23 Nucleoside Diphosphate Kinases; D011993:Recombinant Fusion Proteins; D014157:Transcription Factors; D006153:Guanosine Diphosphate; C517938:NME1 protein, human; C517940:NME2 protein, human; D009701:Nucleoside-Diphosphate Kinase; C061642:awd protein, Drosophila; D012194:RNA-Directed DNA Polymerase; D004256:DNA Polymerase I; D020559:Monomeric GTP-Binding Proteins