The crystal structures of the enzyme hydroxymethylbilane synthase, also known as porphobilinogen deaminase

Abstract

The enzyme hydroxymethylbilane synthase (HMBS; EC 4.3.1.8), also known as porphobilinogen deaminase, catalyses the stepwise addition of four molecules of porphobilinogen to form the linear tetrapyrrole 1-hydroxymethylbilane. Thirty years of crystal structures are surveyed in this topical review. These crystal structures aim at the elucidation of the structural basis of the complex reaction mechanism involving the formation of tetrapyrrole from individual porphobilinogen units. The consistency between the various structures is assessed. This includes an evaluation of the precision of each molecular model and what was not modelled. A survey is also made of the crystallization conditions used in the context of the operational pH of the enzyme. The combination of 3D structural techniques, seeking accuracy, has also been a feature of this research effort. Thus, SAXS, NMR and computational molecular dynamics have also been applied. The general framework is also a considerable chemistry research effort to understand the function of the enzyme and its medical pathologies in acute intermittent porphyria (AIP). Mutational studies and their impact on the catalytic reaction provide insight into the basis of AIP and are also invaluable for guiding the understanding of the crystal structure results. Future directions for research on HMBS are described, including the need to determine the protonation states of key amino-acid residues identified as being catalytically important. The question remains – what is the molecular engine for this complex reaction? Thermal fluctuations are the only suggestion thus far.

One ring closer to a closure: the crystal structure of the ES3 hydroxymethylbilane synthase intermediate

“…Our previous work on the crystal structure of the p.Arg173Trp variant demonstrated the potential of using variants to obtain snapshots of reaction intermediates, in that case the ES 2 [13], however, risking that the variant conformation could be forced in an unnatural conformation. This is also applicable for the p.Arg167Gln ES 3 structure presented here; nonetheless, the justification for using substitution variants has recently been discussed in a review by Helliwell [33]. The structural homology showed remarkably consistent least-square values of superimposed models of the known wt-HMBS and variant ES 2 structures and supports that the overall structure of the variant is correct.…”

Reactivity of a fluorine-containing dirhodium tetracarboxylate compound with proteins

“…The presence of tfa ligand close to dirhodium centre in structure 1 was further validated refining the structure with Phenix.refine, as suggested by other authors. 39…”

“…The presence of tfa ligand close to dirhodium centre in structure 1 was further validated refining the structure with Phenix.refine, as suggested by other authors. 39 In the structure of HEWL, radiation damage was observed. Coordinates and structure factors were deposited in the Protein Data Bank (PDB codes 7QPW, 7QQ0, 7QPY and 7QPZ for the Rh/RNase A adducts, 7QQ1 for the adduct with HEWL).…”

Characterisation of a common hotspot variant in acute intermittent porphyria sheds light on the mechanism of hydroxymethylbilane synthase function

“…However, for many variants, the effect on the HMBS enzyme has not been clearly described and the knowledge of the HMBS mechanism at the molecular level is still limited. Even with the numerous HMBS crystal structures and molecular dynamic (MD) simulations published in the last decades, the exact mechanisms of polypyrrole elongation are not yet completed through to the stage of Michaelis complex EP [32]. From the earliest studies, it was recognised that the enzyme in the crystal had to be with the cofactor in its active form [33].…”