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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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Conformational comparison between Phe149of HutZ and thecorresponding residue Phe224of HugZ. HutZ is displayed in green ribbon and HugZ in magenta ribbon. Phe149 is labeled as blue stick, and its side chain points to hydrophobic pocket formed by residues in green. Phe224 is in yellow stick, and its side chain points in opposite direction.
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Figure 5: Conformational comparison between Phe149of HutZ and thecorresponding residue Phe224of HugZ. HutZ is displayed in green ribbon and HugZ in magenta ribbon. Phe149 is labeled as blue stick, and its side chain points to hydrophobic pocket formed by residues in green. Phe224 is in yellow stick, and its side chain points in opposite direction.

Mentions: Due to this structural mismatch, the side chains of all residues involved in this region pointed to opposite directions in HutZ and HugZ (Figure 4C). The side chain of Phe149 in HutZ protruded into a hydrophobic pocket formed by Ile18, Phe21, Lys91 and Leu93, whereas the side chain of corresponding residue Phe224 in HugZ turns to another hydrophobic pocket on the opposite side (Figure 5). Starting from this pair of residues, the conformations of the succeeding residues become significantly different between HutZ and HugZ.


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)

Conformational comparison between Phe149of HutZ and thecorresponding residue Phe224of HugZ. HutZ is displayed in green ribbon and HugZ in magenta ribbon. Phe149 is labeled as blue stick, and its side chain points to hydrophobic pocket formed by residues in green. Phe224 is in yellow stick, and its side chain points in opposite direction.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: Conformational comparison between Phe149of HutZ and thecorresponding residue Phe224of HugZ. HutZ is displayed in green ribbon and HugZ in magenta ribbon. Phe149 is labeled as blue stick, and its side chain points to hydrophobic pocket formed by residues in green. Phe224 is in yellow stick, and its side chain points in opposite direction.
Mentions: Due to this structural mismatch, the side chains of all residues involved in this region pointed to opposite directions in HutZ and HugZ (Figure 4C). The side chain of Phe149 in HutZ protruded into a hydrophobic pocket formed by Ile18, Phe21, Lys91 and Leu93, whereas the side chain of corresponding residue Phe224 in HugZ turns to another hydrophobic pocket on the opposite side (Figure 5). Starting from this pair of residues, the conformations of the succeeding residues become significantly different between HutZ and HugZ.

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