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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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Structure comparison of HutZand HugZ monomers. Overall HutZ monomer folding (green) is very similar to the homologous protein HugZ (magenta). HugZ N-terminal domain which is absent in HutZ is labeled in blue, and HugZ variable C-terminal region is in yellow. Secondary structural assignment for HutZ was labeled in green and HugZ in magenta.
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Figure 2: Structure comparison of HutZand HugZ monomers. Overall HutZ monomer folding (green) is very similar to the homologous protein HugZ (magenta). HugZ N-terminal domain which is absent in HutZ is labeled in blue, and HugZ variable C-terminal region is in yellow. Secondary structural assignment for HutZ was labeled in green and HugZ in magenta.

Mentions: Although the HutZ homodimer adopted a typical split-barrel fold that is commonly conserved in FMN-binding proteins, no such activity was observed for HutZ (data not shown). Superimposition of both monomers from each dimer produces an RMSD of 0.294 Å for all corresponding Cα atoms. A HutZ monomer consisted of four α-helices interwoven with six β-strands (Figure 1B), a structure similar to the C-terminal domain of HugZ (PDB code: 3GAS) (Figure 2) [13]. Six antiparallel strands, β1-β6, produced a β-barrel of a Greek key topology (Additional file 2). Helices α1 and α2 were packed against the β-barrel and blocked each opening of the β-barrel. Helices α3 and α4 were loaded on one side of the β-barrel, with the HutZ dimer bound mainly through interactions of exposed β-barrel from each monomer. The two β-barrels were packed with each other side by side, bringing together surfaces distant from helices α3 and α4 on the loading side.


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)

Structure comparison of HutZand HugZ monomers. Overall HutZ monomer folding (green) is very similar to the homologous protein HugZ (magenta). HugZ N-terminal domain which is absent in HutZ is labeled in blue, and HugZ variable C-terminal region is in yellow. Secondary structural assignment for HutZ was labeled in green and HugZ in magenta.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Structure comparison of HutZand HugZ monomers. Overall HutZ monomer folding (green) is very similar to the homologous protein HugZ (magenta). HugZ N-terminal domain which is absent in HutZ is labeled in blue, and HugZ variable C-terminal region is in yellow. Secondary structural assignment for HutZ was labeled in green and HugZ in magenta.
Mentions: Although the HutZ homodimer adopted a typical split-barrel fold that is commonly conserved in FMN-binding proteins, no such activity was observed for HutZ (data not shown). Superimposition of both monomers from each dimer produces an RMSD of 0.294 Å for all corresponding Cα atoms. A HutZ monomer consisted of four α-helices interwoven with six β-strands (Figure 1B), a structure similar to the C-terminal domain of HugZ (PDB code: 3GAS) (Figure 2) [13]. Six antiparallel strands, β1-β6, produced a β-barrel of a Greek key topology (Additional file 2). Helices α1 and α2 were packed against the β-barrel and blocked each opening of the β-barrel. Helices α3 and α4 were loaded on one side of the β-barrel, with the HutZ dimer bound mainly through interactions of exposed β-barrel from each monomer. The two β-barrels were packed with each other side by side, bringing together surfaces distant from helices α3 and α4 on the loading side.

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