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

Liu X, Gong J, Wei T, Wang Z, Du Q, Zhu D, Huang Y, Xu S, Gu L - BMC Struct. Biol. (2012)

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, 250100, China.

ABSTRACT

Background: HutZ is the sole heme storage protein identified in the pathogenic bacterium Vibrio cholerae and is required for optimal heme utilization. However, no heme oxygenase activity has been observed with this protein. Thus far, HutZ's structure and heme-binding mechanism are unknown.

Results: We report the first crystal structure of HutZ in a homodimer determined at 2.0 Å 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.

Conclusions: 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.

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Overall structure of HutZ(A) and stereoview ofHutZ monomer (B). (A) There are two dimers in an asymmetric unit, termed A (green), B (cyan), C (magenta) and D (yellow) for clarification. (B) Rainbow-colored scheme representation of HutZ monomer. Four α-helices and six β-strands are labeled.
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Figure 1: Overall structure of HutZ(A) and stereoview ofHutZ monomer (B). (A) There are two dimers in an asymmetric unit, termed A (green), B (cyan), C (magenta) and D (yellow) for clarification. (B) Rainbow-colored scheme representation of HutZ monomer. Four α-helices and six β-strands are labeled.

Mentions: The structure of HutZ contains four monomer molecules (A, B, C and D) in an asymmetric unit that form two homodimers (AB and CD) (Figure 1A). Each monomer includes amino acid residues 13–150 of the entire HutZ protein (residues 1–176). Protein interface analysis with CCP4i showed that the interface area between monomers A and B was 1575.1 Å2 and 1569.4 Å2 for C and D, covering approximately 18% of the total solvent accessible surface area of 17208 Å2. This suggested that the homodimer forms, which represent the aggregation state of most split-barrel proteins in solution, were stable for HutZ. The existence of HutZ homodimers in solution was further confirmed by gel filtration chromatography on a Superdex-200 column (Additional file 1).


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

Liu X, Gong J, Wei T, Wang Z, Du Q, Zhu D, Huang Y, Xu S, Gu L - BMC Struct. Biol. (2012)

Overall structure of HutZ(A) and stereoview ofHutZ monomer (B). (A) There are two dimers in an asymmetric unit, termed A (green), B (cyan), C (magenta) and D (yellow) for clarification. (B) Rainbow-colored scheme representation of HutZ monomer. Four α-helices and six β-strands are labeled.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3472187&req=5

Figure 1: Overall structure of HutZ(A) and stereoview ofHutZ monomer (B). (A) There are two dimers in an asymmetric unit, termed A (green), B (cyan), C (magenta) and D (yellow) for clarification. (B) Rainbow-colored scheme representation of HutZ monomer. Four α-helices and six β-strands are labeled.
Mentions: The structure of HutZ contains four monomer molecules (A, B, C and D) in an asymmetric unit that form two homodimers (AB and CD) (Figure 1A). Each monomer includes amino acid residues 13–150 of the entire HutZ protein (residues 1–176). Protein interface analysis with CCP4i showed that the interface area between monomers A and B was 1575.1 Å2 and 1569.4 Å2 for C and D, covering approximately 18% of the total solvent accessible surface area of 17208 Å2. This suggested that the homodimer forms, which represent the aggregation state of most split-barrel proteins in solution, were stable for HutZ. The existence of HutZ homodimers in solution was further confirmed by gel filtration chromatography on a Superdex-200 column (Additional file 1).

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, 250100, China.

ABSTRACT

Background: HutZ is the sole heme storage protein identified in the pathogenic bacterium Vibrio cholerae and is required for optimal heme utilization. However, no heme oxygenase activity has been observed with this protein. Thus far, HutZ's structure and heme-binding mechanism are unknown.

Results: We report the first crystal structure of HutZ in a homodimer determined at 2.0 Å 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.

Conclusions: 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.

Show MeSH
Related in: MedlinePlus