X-ray structure of human nucleoside diphosphate kinase B complexed with GDP at 2 å resolution

Abstract

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.

Single Strand DNA Specificity Analysis of Human Nucleoside Diphosphate Kinase B

“…They catalyze the transfer of a phosphate from a nucleoside triphosphate to a nucleoside diphosphate via the formation of an enzymatic intermediate phosphorylated on a catalytic histidine residue (1). The crystal structures of NDP 1 kinases from several organisms including prokaryotes (2) and eukaryotes (3)(4)(5) have been determined. They all share a common subunit fold, built around a ␤␣␤␤␣␤ motif, also present in the "palm domain" of DNA polymerases (5).…”

“…The crystal structures of NDP 1 kinases from several organisms including prokaryotes (2) and eukaryotes (3)(4)(5) have been determined. They all share a common subunit fold, built around a ␤␣␤␤␣␤ motif, also present in the "palm domain" of DNA polymerases (5). Although the prokaryotic enzyme from Myxococcus xanthus is a tetramer (6), all eukaryotic enzymes known to date are hexamers composed of identical subunits each containing an active site.…”

X‐ray structure of Mycobacterium tuberculosis nucleoside diphosphate kinase

“…The data, evaluated with DENZO and SCALEPACK, 4 were 99.5% complete, with I/ ϭ 11.7 and a redundancy of 5.7 at 2.6 Å resolution. Molecular replacement was performed with AMoRe 5 by using the human NDP kinase B monomer (entry 1NUE 6 ) as a search model. Refinement by CNS 7 yielded a model with R cryst ϭ 20.5% and R free ϭ 24.6% for all data at 2.6 Å resolution, and good geometry.…”

“…In the human protein, the chain is 15 residues longer, and the C-terminal Glu152 interacts with another subunit in the hexamer. 6 Subunit Interactions. Despite its divergent sequence in the Kpn loop and shorter C-terminus, M. tuberculosis NDP kinase is a hexamer like its eukaryotic homologs.…”

“…Arg4, linked by a salt bridge to the terminal carboxylate of Ala136, and Ala 97 inserted in the Kpn loop are drawn in full bonds. A GDP molecule bound to the human B subunit 6 locates the substrate-binding site.…”