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Molecular phylogeny and intricate evolutionary history of the three isofunctional enzymes involved in the oxidation of protoporphyrinogen IX.

Kobayashi K, Masuda T, Tajima N, Wada H, Sato N - Genome Biol Evol (2014)

Bottom Line: Land plants have a unique HemY homolog that is also shared by Chloroflexus species, in addition to the main HemY homolog originating from Cyanobacteria.Meanwhile, organisms missing any Protox can be classified into two groups; those lacking most heme synthetic genes, which necessarily depend on external heme supply, and those lacking only genes involved in the conversion of uroporphyrinogen III into heme, which would use a precorrin2-dependent alternative pathway.However, hemN encoding coproporphyrinogen IX oxidase was frequently found in organisms lacking Protox enzyme, which suggests a unique role of this gene other than in heme biosynthesis.

View Article: PubMed Central - PubMed

Affiliation: Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Japan kkobayashi@bio.c.u-tokyo.ac.jp naokisat@bio.c.u-tokyo.ac.jp.

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Comparison of the structures of various HemY proteins. Structures of various HemY proteins (shown on left and center) were estimated by homology modeling with Nicotiana tabacum PPO2, Bacillus subtilis HemY, and Myxococcus xanthus HemY. Characteristic structures are annotated with numbers, which correspond to the annotations in supplementary figure S7, Supplementary Material online. The rainbow color gradation from blue to red indicates direction from the N-terminus to C-terminus.
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evu170-F6: Comparison of the structures of various HemY proteins. Structures of various HemY proteins (shown on left and center) were estimated by homology modeling with Nicotiana tabacum PPO2, Bacillus subtilis HemY, and Myxococcus xanthus HemY. Characteristic structures are annotated with numbers, which correspond to the annotations in supplementary figure S7, Supplementary Material online. The rainbow color gradation from blue to red indicates direction from the N-terminus to C-terminus.

Mentions: Crystal structures of HemY from Nicotiana tabacum (ntPPO2) (Koch et al. 2004), Myxococcus xanthus (mxPPO) (Corradi et al. 2006), B. subtilis (bsPPO) (Qin et al. 2010), and Homo sapiens (hsPPO) (Qin et al. 2011) have revealed that the overall folding patterns are similar among HemY orthologs from these species (Qin et al. 2011). Amino acid residues involved in substrate- and FAD-binding were identified on the basis of their 3D structures and kinetic analyses of mutant proteins (Koch et al. 2004; Corradi et al. 2006; Heinemann et al. 2007; Qin et al. 2010, 2011; Hao et al. 2013). Multiple alignment of the HemY proteins showed that key amino acids of HemY are basically conserved across prokaryotes and eukaryotes (supplementary fig. S7, Supplementary Material online). However, some notable characteristics were found in each clade. 3D structures of HemY homologs of Arabidopsis thaliana (PPO1 and PPO2), Cyanidioschyzon merolae, C. aurantiacus, and R. castenholzii were modeled by using the known structures as templates. Figure 6 compares the structures of various HemY proteins. The loops that are characteristic to each protein are marked with a “#” plus an identification number, which are also shown in the alignment (supplementary fig. S7, Supplementary Material online).Fig. 6.—


Molecular phylogeny and intricate evolutionary history of the three isofunctional enzymes involved in the oxidation of protoporphyrinogen IX.

Kobayashi K, Masuda T, Tajima N, Wada H, Sato N - Genome Biol Evol (2014)

Comparison of the structures of various HemY proteins. Structures of various HemY proteins (shown on left and center) were estimated by homology modeling with Nicotiana tabacum PPO2, Bacillus subtilis HemY, and Myxococcus xanthus HemY. Characteristic structures are annotated with numbers, which correspond to the annotations in supplementary figure S7, Supplementary Material online. The rainbow color gradation from blue to red indicates direction from the N-terminus to C-terminus.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4231631&req=5

evu170-F6: Comparison of the structures of various HemY proteins. Structures of various HemY proteins (shown on left and center) were estimated by homology modeling with Nicotiana tabacum PPO2, Bacillus subtilis HemY, and Myxococcus xanthus HemY. Characteristic structures are annotated with numbers, which correspond to the annotations in supplementary figure S7, Supplementary Material online. The rainbow color gradation from blue to red indicates direction from the N-terminus to C-terminus.
Mentions: Crystal structures of HemY from Nicotiana tabacum (ntPPO2) (Koch et al. 2004), Myxococcus xanthus (mxPPO) (Corradi et al. 2006), B. subtilis (bsPPO) (Qin et al. 2010), and Homo sapiens (hsPPO) (Qin et al. 2011) have revealed that the overall folding patterns are similar among HemY orthologs from these species (Qin et al. 2011). Amino acid residues involved in substrate- and FAD-binding were identified on the basis of their 3D structures and kinetic analyses of mutant proteins (Koch et al. 2004; Corradi et al. 2006; Heinemann et al. 2007; Qin et al. 2010, 2011; Hao et al. 2013). Multiple alignment of the HemY proteins showed that key amino acids of HemY are basically conserved across prokaryotes and eukaryotes (supplementary fig. S7, Supplementary Material online). However, some notable characteristics were found in each clade. 3D structures of HemY homologs of Arabidopsis thaliana (PPO1 and PPO2), Cyanidioschyzon merolae, C. aurantiacus, and R. castenholzii were modeled by using the known structures as templates. Figure 6 compares the structures of various HemY proteins. The loops that are characteristic to each protein are marked with a “#” plus an identification number, which are also shown in the alignment (supplementary fig. S7, Supplementary Material online).Fig. 6.—

Bottom Line: Land plants have a unique HemY homolog that is also shared by Chloroflexus species, in addition to the main HemY homolog originating from Cyanobacteria.Meanwhile, organisms missing any Protox can be classified into two groups; those lacking most heme synthetic genes, which necessarily depend on external heme supply, and those lacking only genes involved in the conversion of uroporphyrinogen III into heme, which would use a precorrin2-dependent alternative pathway.However, hemN encoding coproporphyrinogen IX oxidase was frequently found in organisms lacking Protox enzyme, which suggests a unique role of this gene other than in heme biosynthesis.

View Article: PubMed Central - PubMed

Affiliation: Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Japan kkobayashi@bio.c.u-tokyo.ac.jp naokisat@bio.c.u-tokyo.ac.jp.

Show MeSH
Related in: MedlinePlus