Crystal structure of HutZ, a heme storage protein from Vibrio cholerae: A structural mismatch observed in the region of high sequence conservation

We report the first crystal structure of HutZ in a homodimer determined at 2.0 ？ resolution. The HutZ structure adopted a typical split-barrel fold. Through a docking study and site-directed mutagenesis, a heme-binding model for the HutZ dimer is proposed. Very interestingly, structural superimposition of HutZ and its homologous protein HugZ, a heme oxygenase from Helicobacter pylori, exhibited a structural mismatch of one amino acid residue in β6 of HutZ, although residues involved in this region are highly conserved in both proteins. Derived homologous models of different single point variants with model evaluations suggested that Pro140 of HutZ, corresponding to Phe215 of HugZ, might have been the main contributor to the structural mismatch. This mismatch initiates more divergent structural characteristics towards their C-terminal regions, which are essential features for the heme-binding of HugZ as a heme oxygenase.HutZ’s deficiency in heme oxygenase activity might derive from its residue shift relative to the heme oxygenase HugZ. This residue shift also emphasized a limitation of the traditional template selection criterion for homology modeling.Iron is an essential element for the Gram-negative pathogenic bacterium Vibrio cholerae. It plays important roles in the microbe’s survival and its ability to cause the diarrheal disease cholera of V. cholerae. Nevertheless, the concentration of free iron is extremely low in the environment as well as in the human hosts. Under iron starvation conditions, V. cholerae has evolved several high-affinity iron uptake systems [1]. Synthesis and secretion of the catechol-type siderophore vibriobactin is the main mechanism for obtaining iron [2]. Siderophores, such as schizokinen [3], enterobactin [4,5] and ferrichrome [6], produced by other microorganisms, can also be utilized by V. cholerae.Heme, an excellent iron source in the environment and human hosts, can be used by V. cholerae in the free form or with heme-binding protei