The Nuclease A-Inhibitor Complex Is Characterized by a Novel Metal Ion Bridge

Abstract

Nonspecific, extracellular nucleases have received enhanced attention recently as a consequence of the critical role that these enzymes can play in infectivity by overcoming the host neutrophil defense system. The activity of the cyanobacterial nuclease NucA, a member of the ␤␤␣ Me superfamily, is controlled by the specific nuclease inhibitor, NuiA. Here we report the 2.3-Å resolution crystal structure of the NucA-NuiA complex, showing that NucA inhibition by NuiA involves an unusual divalent metal ion bridge that connects the nuclease with its inhibitor. The C-terminal Thr-135 NuiA hydroxyl oxygen is directly coordinated with the catalytic Mg 2؉ of the nuclease active site, and Glu-24 NuiA also extends into the active site, mimicking the charge of a scissile phosphate. NuiA residues Asp-75 and Trp-76 form a second interaction site, contributing to the strength and specificity of the interaction. The crystallographically defined interface is shown to be consistent with results of studies using site-directed NuiA mutants. This mode of inhibition differs dramatically from the exosite mechanism of inhibition seen with the DNase colicins E7/E9 and from other nuclease-inhibitor complexes that have been studied. The structure of this complex provides valuable insights for the development of inhibitors for related nonspecific nucleases that share the DRGH active site motif such as the Streptococcus pneumoniae nuclease EndA, which mediates infectivity of this pathogen, and mitochondrial EndoG, which is involved in recombination and apoptosis.Nonspecific nucleases are involved in a broad range of functions that include extra-and intracellular digestion, programmed cell death, defense, replication, recombination, and repair (1-3). They also have proven useful for determining nucleic acid structures, mapping mutations, studying the interaction of DNA and RNA with various ligands (4), and sequencing of RNA (5). Most recently, an important role for these nucleases in microbial infectivity has been demonstrated, based on their ability to digest the DNA component of host neutrophil extracellular traps (6 -8). Consequently, these nucleases are now recognized as significant drug targets, and information related to the inhibition of these enzymes is of potential use for inhibitor development. As a result of their ability to degrade nucleic acids nonspecifically, they also represent an endogenous toxic challenge. Therefore, regulation of their activity is critical for the cells that produce them.The ␤␤␣ Me superfamily of nucleases (9) comprises nonspecific, structure-specific, and sequence-specific enzymes that share a structurally conserved active site scaffold and utilize a divalent metal ion. They can be grouped according to sequence motifs into three families: His-Cys box nucleases (e.g. I-PpoI (10)), HNH nucleases (e.g. colicins E7 and E9 (11, 12) and I-HmuI (13)), and DRGH nucleases (e.g. the extracellular nuclease from Serratia marcescens (14), the DNA entry nuclease EndA from Streptococcus pneumoniae (15), the Syncephalast...

Structural insights into catalytic and substrate binding mechanisms of the strategic EndA nuclease from Streptococcus pneumoniae

“…Structural comparisons by the Dali server (31) demonstrate some core features are conserved with the DRGH nucleases: NucA (32,33), Serratia nuclease (34,35), and EndoG (36) (Figure 2). The SM endonuclease from Serratia marcescens showed the greatest similarity to EndA, with an RMSD of 2.9 Å (over 137 out of 235 Cα atoms).…”

Mutational and biochemical analysis of the DNA-entry nuclease EndA from Streptococcus pneumoniae

“…Asp157, Arg158 and His160 from the conserved DRGH-motif, all localized in one of the two β-strands of the ββα-Me finger structure, were exchanged for alanine (7,24,25). His160 within the DRG H -motif corresponds to the first histidine residue in the H - N-H-motif and plays an essential role in catalysis acting as the general base (26,27).…”

Nucleases Encoded by the Integrated Elements CJIE2 and CJIE4 Inhibit Natural Transformation of Campylobacter jejuni

“…(Fig. 1), a member of the Serratia nuclease family which belongs to the group of DNA/RNA nonspecific endonucleases (14,28). CJE0566 and CJE1441 are very similar at the amino acid level and display considerable similarity to Cla_0934 from C. lari RM2100.…”