Metal Binding Sites in Plant Soluble Inorganic Pyrophosphatases. An Example of the Use of ROSETTA Design and Hidden Markov Models to Guide the Homology Modeling of Proteins

Abstract

In contrast to their counterparts in bacteria and animals the soluble inorganic pyrophosphatases from plant cells are active as monomers. The isoforms 1 and 4 from <em>Arabidopsis thaliana</em> have been characterized with more detail, but their three-dimensional structure is unavailable. Here, a recently published protocol (ROSETTA design-HMMer), is used to guide well-known techniques for homology-modeling, in the production of reliable models for the three-dimensional structure of these two arabidopsis isoforms. Their interaction with magnesium ions and pyrophosphate is analyzed <em>in silico</em>in silico.

Phosphate monoester hydrolysis at tricopper site: The advantage and disadvantage of closely assembled trimetallic active sites

“…Due to the extreme stability, a series of metalloenzymes have been evolved in nature to accelerate the cleavage of phosphate ester bonds [1,[5][6][7][8]. Many enzymes contain a trimetallic active site, such as P1 nuclease [9,10], alkaline phosphatases [11,12], phospholipase C [6,13], and inorganic pyrophosphatases [14][15][16]. In addition, some proteins have only two metal ions in the active site in the absence of phosphates, like T5 flap endonuclease [17], but bind a third metal ion in the presence of substrate, which implies a template effect of phosphates in protein active sites.…”