The structure of the Escherichia coli nucleoside diphosphate kinase reveals a new quaternary architecture for this enzyme family

Abstract

Nucleoside diphosphate kinase (NDPK) catalyzes the transfer of gamma-phosphate from nucleoside triphosphates to nucleoside diphosphates. The subunit folding and the dimeric basic structural unit are remarkably the same for available structures but, depending on species, dimers self-associate to form hexamers or tetramers. The crystal structure of the Escherichia coli NDPK reveals a new tetrameric quaternary structure for this protein family. The two tetramers differ by the relative orientation of interacting dimers, which face either the convex or the concave side of their central sheet as in either Myxococcus xanthus (type I) or E. coli (type II), respectively. In the type II tetramer, the subunits interact by a new interface harboring a zone called the Kpn loop as in hexamers, but by the opposite face of this loop. The evolutionary conservation of the interface residues indicates that this new quaternary structure seems to be the most frequent assembly mode in bacterial tetrameric NDP kinases.

Hydrogen/Deuterium Exchange Mass Spectrometry Reveals Mechanistic Details of Activation of Nucleoside Diphosphate Kinases by Oligomerization

“…We show that in order to be active, hexameric Since not all NDPKs are hexameric, the question arises as to how bacterial tetrameric and dimeric ones are active. The analysis of crystal structures shows that in the type 2 tetramer, (46) the Kpn/α 0 foldon is located at the dimer-dimer interface and has the same control switch role. On the contrary, in type 1 tetramer (66) and dimer, (47,67,68) the Kpn/α 0 foldon is fully exposed and could not have such a regulatory role.…”

“…(42,43) NDPKs contain ferredoxin-like folds (45) which assemble first as dimers and then as tetramers or hexamers. (46)(47)(48) Tetramers are present in gram-negative bacteria and archaea, while hexamers are present in gram-positive bacteria and eukaryotes. Hexamers represent the most abundant type of oligomerization, which specifically relies on the well conserved surface loop that carries the site of the natural "Killer of prune" mutation (Kpn-loop) (Figures 1, S1).…”

A single Gly114Arg mutation stabilizes the hexameric subunit assembly and changes the substrate specificity of halo‐archaeal nucleoside diphosphate kinase

“…Since the crystal structure of HsNDK as well as a large volume of structure data exist for other NDKs [21][22][23], the observed mutation can be readily analyzed based on the three dimensional structure of the protein.…”

Dissecting the Unique Nucleotide Specificity of Mimivirus Nucleoside Diphosphate Kinase

“…They are most often hexameric enzymes, with a few occurrences of tetrameric and dimeric NDK structures in bacteria (19,25,26,31,38). They all catalyze the transfer of a phosphate group from an NTP onto a nucleotide diphosphate (NDP) through an Mg 2ϩ -dependent reaction.…”