High-Resolution Analysis of Zn2+ Coordination in the Alkaline Phosphatase Superfamily by EXAFS and X-ray Crystallography

• Published in: Journal of molecular biology Vol. 415; no. 1; pp. 102 - 117
• Main Authors: Bobyr, Elena, Lassila, Jonathan K., Wiersma-Koch, Helen I., Fenn, Timothy D., Lee, Jason J., Nikolic-Hughes, Ivana, Hodgson, Keith O., Rees, Douglas C., Hedman, Britt, Herschlag, Daniel
• Format: Journal Article
• Language: English
• Published: Elsevier Ltd 01-01-2012
• Subjects: absorption; adenosine monophosphate; alkaline phosphatase; catalytic activity; catalytic promiscuity; crystal structure; Escherichia coli; hydrolysis; nucleotide pyrophosphatase/phosphodiesterase; phosphates; phosphoryl transfer; spectroscopy; X-radiation; x-ray absorption spectroscopy; X-ray diffraction; Xanthomonas axonopodis; zinc; x-ray absorption spectroscopy; XAS; nucleotide pyrophosphatase/phosphodiesterase; EXAFS; FT; AP; NPP; PEG; crystal structure; phosphoryl transfer; SSRL; BVS; catalytic promiscuity
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/j.jmb.2011.10.040

Comparisons among evolutionarily related enzymes offer opportunities to reveal how structural differences produce different catalytic activities. Two structurally related enzymes, Escherichia coli alkaline phosphatase (AP) and Xanthomonas axonopodis nucleotide pyrophosphatase/phosphodiesterase (NPP), have nearly identical binuclear Zn2+ catalytic centers but show tremendous differential specificity for hydrolysis of phosphate monoesters or phosphate diesters. To determine if there are differences in Zn2+ coordination in the two enzymes that might contribute to catalytic specificity, we analyzed both x-ray absorption spectroscopic and x-ray crystallographic data. We report a 1.29-Å crystal structure of AP with bound phosphate, allowing evaluation of interactions at the AP metal site with high resolution. To make systematic comparisons between AP and NPP, we measured zinc extended x-ray absorption fine structure for AP and NPP in the free-enzyme forms, with AMP and inorganic phosphate ground-state analogs and with vanadate transition-state analogs. These studies yielded average zinc–ligand distances in AP and NPP free-enzyme forms and ground-state analog forms that were identical within error, suggesting little difference in metal ion coordination among these forms. Upon binding of vanadate to both enzymes, small increases in average metal–ligand distances were observed, consistent with an increased coordination number. Slightly longer increases were observed in NPP relative to AP, which could arise from subtle rearrangements of the active site or differences in the geometry of the bound vanadyl species. Overall, the results suggest that the binuclear Zn2+ catalytic site remains very similar between AP and NPP during the course of a reaction cycle.
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► We report a 1. 29-Å structure of E. coli AP, a model phosphoryl transfer enzyme. ► An evolutionarily related phosphodiesterase has a similar binuclear zinc site. ► X-ray absorption spectroscopy allowed direct comparison of the two enzymes.