# The HD-Domain Metalloprotein Superfamily:
###### Abstract  
The histidine-aspartate (HD)-domain protein superfamily contains metalloprotein that share common structural features but catalyze vastly different reactions ranging from oxygenation to hydrolysis. This chemical diversion is afforded by (i) their ability to coordinate most biologically relevant transition metals in mono-, di-, and trinuclear configurations, (ii) sequence insertions or the addition of supernumerary ligands to their active sites, (iii) auxiliary substrate specificity residues vicinal to the catalytic site, (iv) additional protein domains that allosterically regulate their activities or have catalytic and sensory roles, and (v) their ability to work with protein partners. More than 500 structures of HD-domain proteins are available to date that lay out unique structural features which may be indicative of function. In this respect, we describe the three known classes of HD-domain proteins (hydrolases, oxygenases, and lyases) and identify their apparent traits with the aim to portray differences in the molecular details responsible for their functional divergence and reconcile existing notions that will help assign functions to yet-to-be characterized proteins. The present review collects data that exemplify how nature tinkers with the HD-domain scaffold to afford different chemistries and provides insight into the factors that can selectively modulate catalysis. HD-domain; metalloprotein; oxygenase; phosphatase; phosphodiesterase; hydratase; nucleic acid; phosphonate; diiron [  
sequence motif insertions or residues vicinal to the active site, (v) auxiliary domains with catalytic or regulatory roles, and (vi) interaction with protein partners. These six features appear to distinctly influence the range of chemistries these proteins perform. Despite variations in primary sequence, all HD-domain proteins share the HD residue dyad that coordinates transition metal ions such as Fe, Mn, Co, Mg, Cu, Zn, and Ni (Table 1) as well as a helical fold (Figure 1A) and functionally cluster based on sequence similarities (Figure 1B) [1; 3; 14]. Figure 1: **(A)** Helical structure of three HD-domain proteins. YqeK (PDB: 2008) is a phosphatase, PhnZ (PDB: 4N6W) is an oxygenase, and Ddi2 (PDB: 6 DKA) is a lyase. All exhibit a helical fold characteristic to HD-domain proteins despite their diverse functions. **(B)** Sequence similarity network (SSN) of the HD-domain superfamily depicting its size and functional clustering. The SSN was generated via the Enzyme Function Initiatives-Enzyme Similarity tool (EFI-EST) and visualized in Cytoscape. The SSN was generated by employing the IPR003607 family and tailored so that nodes represent sequences with \(\geq\) 50% identity and an e-value of 5. The SSN was further refined to contain the major protein clusters (size-wise), which amount to 183,015 unique protein sequences. Edges between nodes represent an alignment score of 70. HD-domain phosphohydrolases (SpoT/RelA, SAMHD1, deoxyguanosine phosphatases (dGTPases), nucleotidyltransferase) are represented in green and blue, while hydratasees are shown in yellow. PDEs are shown in red (HD-GYP proteins), light pink (exoribonucleases), orange (Cas proteins), and pink (PDEases). Oxygenases are shown in purple and their cluster, which consists of four nodes (372 sequences), is enlarged for visualization. Gray clusters contain proteins of unidentified function.