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The pentameric nucleoplasmin fold is present in Drosophila FKBP39 and a large number of chromatin-related proteins.

Edlich-Muth C, Artero JB, Callow P, Przewloka MR, Watson AA, Zhang W, Glover DM, Debski J, Dadlez M, Round AR, Forsyth VT, Laue ED - J. Mol. Biol. (2015)

Bottom Line: The pentameric core domain, a doughnut-like structure with a central pore, is only found in the nucleoplasmin family.Furthermore, we show that two other chromatin proteins, Arabidopsis thaliana histone deacetylase type 2 (HD2) and Saccharomyces cerevisiae Fpr4, share the NPL fold and form pentamers, or a dimer of pentamers in the case of HD2.Thus, we propose a new family of proteins that share the pentameric nucleoplasmin-like NPL domain and are found in protists, fungi, plants and animals.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, United Kingdom.

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Structural alignment of NPL sequences. The structures of Xenopus nucleoplasmin (1KJ5, labelled “Xl NUP”) and FKBP39 were aligned and the other sequences were added based on sequence only. The two other proteins used in our experiments are yeast Fpr4 and A. thaliana HD2 (“A thali”). The residue numbering and the position of β-strands of FKBP39 are indicated above its sequence. The positions of the conserved and potentially catalytic histidine and aspartate are indicated, as well as the two dimer-promoting residues of nucleoplasmin. The yeast protein Fpr4, also an NPL-FKBP, contains a large insertion (residues 59–116, indicated by “z”) that has been omitted from the alignment. The other proteins are from the fungus Rhizopus oryzae; the insects Spodoptera frugiperda, Tribolium castaneum, A. mellifera and Aedes aegypti; the plants Glycine max, A. thaliana, Zea mays and Solanum chacoense; and the protozoa Leishmania braziliensis, Trypanosoma cruzi, Paramecium tetraurelia and Trypanosoma brucei.
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f0015: Structural alignment of NPL sequences. The structures of Xenopus nucleoplasmin (1KJ5, labelled “Xl NUP”) and FKBP39 were aligned and the other sequences were added based on sequence only. The two other proteins used in our experiments are yeast Fpr4 and A. thaliana HD2 (“A thali”). The residue numbering and the position of β-strands of FKBP39 are indicated above its sequence. The positions of the conserved and potentially catalytic histidine and aspartate are indicated, as well as the two dimer-promoting residues of nucleoplasmin. The yeast protein Fpr4, also an NPL-FKBP, contains a large insertion (residues 59–116, indicated by “z”) that has been omitted from the alignment. The other proteins are from the fungus Rhizopus oryzae; the insects Spodoptera frugiperda, Tribolium castaneum, A. mellifera and Aedes aegypti; the plants Glycine max, A. thaliana, Zea mays and Solanum chacoense; and the protozoa Leishmania braziliensis, Trypanosoma cruzi, Paramecium tetraurelia and Trypanosoma brucei.

Mentions: The phylogenetic tree of NPL sequences from plants, fungi and animals (Fig. 1) clearly shows that NPL-FKBPs and HD-tuins form their own well-separated clades. However, the major divide is between nucleoplasmins and the other two groups, with as little as 12% pairwise sequence identity between them. This can also be observed in the sequence alignment (Fig. 2) where only the hydrophobic character of some residues and the position of the β-strands are preserved between Xenopus nucleoplasmin (third to the last sequence in the alignment) and all the other proteins. In order to investigate whether all of these sequences share a common three-dimensional fold, we set out to determine the structure of a non-nucleoplasmin NPL.


The pentameric nucleoplasmin fold is present in Drosophila FKBP39 and a large number of chromatin-related proteins.

Edlich-Muth C, Artero JB, Callow P, Przewloka MR, Watson AA, Zhang W, Glover DM, Debski J, Dadlez M, Round AR, Forsyth VT, Laue ED - J. Mol. Biol. (2015)

Structural alignment of NPL sequences. The structures of Xenopus nucleoplasmin (1KJ5, labelled “Xl NUP”) and FKBP39 were aligned and the other sequences were added based on sequence only. The two other proteins used in our experiments are yeast Fpr4 and A. thaliana HD2 (“A thali”). The residue numbering and the position of β-strands of FKBP39 are indicated above its sequence. The positions of the conserved and potentially catalytic histidine and aspartate are indicated, as well as the two dimer-promoting residues of nucleoplasmin. The yeast protein Fpr4, also an NPL-FKBP, contains a large insertion (residues 59–116, indicated by “z”) that has been omitted from the alignment. The other proteins are from the fungus Rhizopus oryzae; the insects Spodoptera frugiperda, Tribolium castaneum, A. mellifera and Aedes aegypti; the plants Glycine max, A. thaliana, Zea mays and Solanum chacoense; and the protozoa Leishmania braziliensis, Trypanosoma cruzi, Paramecium tetraurelia and Trypanosoma brucei.
© Copyright Policy - CC BY
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4414354&req=5

f0015: Structural alignment of NPL sequences. The structures of Xenopus nucleoplasmin (1KJ5, labelled “Xl NUP”) and FKBP39 were aligned and the other sequences were added based on sequence only. The two other proteins used in our experiments are yeast Fpr4 and A. thaliana HD2 (“A thali”). The residue numbering and the position of β-strands of FKBP39 are indicated above its sequence. The positions of the conserved and potentially catalytic histidine and aspartate are indicated, as well as the two dimer-promoting residues of nucleoplasmin. The yeast protein Fpr4, also an NPL-FKBP, contains a large insertion (residues 59–116, indicated by “z”) that has been omitted from the alignment. The other proteins are from the fungus Rhizopus oryzae; the insects Spodoptera frugiperda, Tribolium castaneum, A. mellifera and Aedes aegypti; the plants Glycine max, A. thaliana, Zea mays and Solanum chacoense; and the protozoa Leishmania braziliensis, Trypanosoma cruzi, Paramecium tetraurelia and Trypanosoma brucei.
Mentions: The phylogenetic tree of NPL sequences from plants, fungi and animals (Fig. 1) clearly shows that NPL-FKBPs and HD-tuins form their own well-separated clades. However, the major divide is between nucleoplasmins and the other two groups, with as little as 12% pairwise sequence identity between them. This can also be observed in the sequence alignment (Fig. 2) where only the hydrophobic character of some residues and the position of the β-strands are preserved between Xenopus nucleoplasmin (third to the last sequence in the alignment) and all the other proteins. In order to investigate whether all of these sequences share a common three-dimensional fold, we set out to determine the structure of a non-nucleoplasmin NPL.

Bottom Line: The pentameric core domain, a doughnut-like structure with a central pore, is only found in the nucleoplasmin family.Furthermore, we show that two other chromatin proteins, Arabidopsis thaliana histone deacetylase type 2 (HD2) and Saccharomyces cerevisiae Fpr4, share the NPL fold and form pentamers, or a dimer of pentamers in the case of HD2.Thus, we propose a new family of proteins that share the pentameric nucleoplasmin-like NPL domain and are found in protists, fungi, plants and animals.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, United Kingdom.

Show MeSH