Evolutionary Genomics of the HAD Superfamily: Understanding the Structural Adaptations and Catalytic Diversity in a Superfamily of Phosphoesterases and Allied Enzymes

Abstract

The HAD (haloacid dehalogenase) superfamily includes phosphoesterases, ATPases, phosphonatases, dehalogenases, and sugar phosphomutases acting on a remarkably diverse set of substrates. The availability of numerous crystal structures of representatives belonging to diverse branches of the HAD superfamily provides us with a unique opportunity to reconstruct their evolutionary history and uncover the principal determinants that led to their diversification of structure and function. To this end we present a comprehensive analysis of the HAD superfamily that identifies their unique structural features and provides a detailed classification of the entire superfamily. We show that at the highest level the HAD superfamily is unified with several other superfamilies, namely the DHH, receiver (CheY-like), von Willebrand A, TOPRIM, classical histone deacetylases and PIN/FLAP nuclease domains, all of which contain a specific form of the Rossmannoid fold. These Rossmannoid folds are distinguished from others by the presence of equivalently placed acidic catalytic residues, including one at the end of the first core β-strand of the central sheet. The HAD domain is distinguished from these related Rossmannoid folds by two key structural signatures, a "squiggle" (a single helical turn) and a "flap" (a beta hairpin motif) located immediately downstream of the first β-strand of their core Rossmanoid fold. The squiggle and the flap motifs are predicted to provide the necessary mobility to these enzymes for them to alternate between the "open" and "closed" conformations. In addition, most members of the HAD superfamily contains inserts, termed caps, occurring at either of two positions in the core Rossmannoid fold. We show that the cap modules have been independently inserted into these two stereotypic positions on multiple occasions in evolution and display extensive evolutionary diversification independent of the core catalytic domain. The first group of caps, the C1 caps, is directly inserted into the flap motif and regulates access of reactants to the active site. The second group, the C2 caps, forms a roof over the active site, and access to their internal cavities might be in part regulated by the movement of the flap. The diversification of the cap module was a major factor in the exploration of a vast substrate space in the course of the evolution of this superfamily. We show that the HAD superfamily contains 33 major families distributed across the three superkingdoms of life. Analysis of the phyletic patterns suggests that at least five distinct HAD proteins are traceable to the last universal common ancestor (LUCA) of all extant organisms. While these prototypes diverged prior to the emergence Abbreviations used: HAD, haloacid dehalogenase; PNKP, polynucleotide kinase phosphatase; KDO 8-P, deoxy-Dmannose-octulosonate 8-phosphate; CTD, carboxyl-terminal domain; PNKP, polynucleotide kinase phosphatase; LUCA, last universal common ancestor.E-mail address of the corresponding author: aravind@ncbi.nlm.nih.gov of the LUCA, t...

The Phosphate Fast-Responsive Genes PECP1 and PPsPase1 Affect Phosphocholine and Phosphoethanolamine Content

“…The superfamily of HAD phosphatases is a very large and divergent group of enzymes, with very little overall homology but great diversity in substrates (Burroughs et al, 2006). These phosphatases are subdivided into different classes based on the overall structural arrangement of their active core (Burroughs et al, 2006).…”

“…These phosphatases are subdivided into different classes based on the overall structural arrangement of their active core (Burroughs et al, 2006). Interestingly, the InterPro predictive modeling software recently assigned PPsPase1, PECP1, and ThMPase1 to the PHOSPHO1/2 subgroup within the HAD-like superfamily (Stewart et al, 2003;Hunter et al, 2009;Seifried et al, 2013).…”

“…Indeed, in Arabidopsis, the in vivo role of these overexpressors seems more directly linked to the degradation of PCho and PEth polar heads, the by-products of phospholipid degradation triggered in response to Pi starvation. We have demonstrated that their induction is largely under the control of PHR1/PHL1, adding them to the list of proteins involved in lipid metabolism under the control of these transcription factors (Rouached et al, 2010;Pant et al, 2015).The superfamily of HAD phosphatases is a very large and divergent group of enzymes, with very little overall homology but great diversity in substrates (Burroughs et al, 2006). These phosphatases are subdivided into different classes based on the overall structural arrangement of their active core (Burroughs et al, 2006).…”

Insights into the Catalytic Mechanism of Human sEH Phosphatase by Site-Directed Mutagenesis and LC–MS/MS Analysis

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Functional Diversity of Haloacid Dehalogenase Superfamily Phosphatases from Saccharomyces cerevisiae

“…These families represent a challenge for functional annotation because their catalytic activities and substrates are likely to be very similar. One such family are haloacid dehalogenase (HAD) 2 -like hydrolases, which represent one of the largest enzyme superfamilies found in all organisms, with 479,051 sequences in databases (InterPro IPR023214) and 33 major families (24,25). Most genomes are predicted to contain multiple HAD-like proteins, including 28 genes in E. coli, 45 genes in S. cerevisiae, and 183 genes in humans (26).…”