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Crystal structure of malaria parasite nucleosome assembly protein: distinct modes of protein localization and histone recognition.

Gill J, Yogavel M, Kumar A, Belrhali H, Jain SK, Rug M, Brown M, Maier AG, Sharma A - J. Biol. Chem. (2009)

Bottom Line: Expression of green fluorescent protein-tagged PfNapL confirmed its exclusive localization to the parasite cytoplasm.A detailed analysis of PfNapL structure suggests unique histone binding properties.The crucial structural differences observed between parasite and yeast NAPs shed light on possible new modes of histone recognition by nucleosome assembly proteins.

View Article: PubMed Central - PubMed

Affiliation: Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Road, New Delhi 110067, India.

ABSTRACT
Nucleosome assembly proteins (NAPs) are histone chaperones that are essential for the transfer and incorporation of histones into nucleosomes. NAPs participate in assembly and disassembly of nucleosomes and in chromatin structure organization. Human malaria parasite Plasmodium falciparum contains two nucleosome assembly proteins termed PfNapL and PfNapS. To gain structural insights into the mechanism of NAPs, we have determined and analyzed the crystal structure of PfNapL at 2.3 A resolution. PfNapL, an ortholog of eukaryotic NAPs, is dimeric in nature and adopts a characteristic fold seen previously for yeast NAP-1 and Vps75 and for human SET/TAF-1b (beta)/INHAT. The PfNapL monomer is comprised of domain I, containing a dimerization alpha-helix, and a domain II, composed of alpha-helices and a beta-subdomain. Structural comparisons reveal that the "accessory domain," which is inserted between the domain I and domain II in yeast NAP-1 and other eukaryotic NAPs, is surprisingly absent in PfNapL. Expression of green fluorescent protein-tagged PfNapL confirmed its exclusive localization to the parasite cytoplasm. Attempts to disrupt the PfNapL gene were not successful, indicating its essential role for the malaria parasite. A detailed analysis of PfNapL structure suggests unique histone binding properties. The crucial structural differences observed between parasite and yeast NAPs shed light on possible new modes of histone recognition by nucleosome assembly proteins.

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Comparison of PfNapL structure with yNAP-1 (Protein Data Bank code 2AYU) and hSET (Protein Data Bank code 2E50). a, superimposition of PfNapL monomer (purple) onto yNAP-1 (blue) and hSET (orange). Accessory domain of yNAP-1 is colored yellow. NES and NLS in yNAP-1 and PfNapL are indicated. b, superimposition of PfNapL and yNAP-1 dimers. The lower half shows superimposition of domain I and II from PfNapL and yNAP-1 monomers. yNAP-1 is colored blue, and the accessory domain is colored yellow. PfNapL is colored purple. The extra residues in domain II of yNAP-1 are colored cyan and are disordered in PfNapL. c, superimposition of PfNapL and hSET dimers. The lower half shows superimposition of domain I and II from PfNapL and hSET monomers. The extra residues of PfNapL are colored cyan and are disordered in hSET.
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fig2: Comparison of PfNapL structure with yNAP-1 (Protein Data Bank code 2AYU) and hSET (Protein Data Bank code 2E50). a, superimposition of PfNapL monomer (purple) onto yNAP-1 (blue) and hSET (orange). Accessory domain of yNAP-1 is colored yellow. NES and NLS in yNAP-1 and PfNapL are indicated. b, superimposition of PfNapL and yNAP-1 dimers. The lower half shows superimposition of domain I and II from PfNapL and yNAP-1 monomers. yNAP-1 is colored blue, and the accessory domain is colored yellow. PfNapL is colored purple. The extra residues in domain II of yNAP-1 are colored cyan and are disordered in PfNapL. c, superimposition of PfNapL and hSET dimers. The lower half shows superimposition of domain I and II from PfNapL and hSET monomers. The extra residues of PfNapL are colored cyan and are disordered in hSET.

Mentions: Structural Conservation with yNAP-1, hSET, and Vps75—The root mean square (r.m.s.) deviation derived from the least square fittings of 191 Cα of PfNapL with the corresponding Cα of yNAP-1, hSET, and Vps75 is 1.9, 1.8, and 1.8 Å, respectively (Fig. 2a and Fig. S3). The dimerization helix α2 of PfNapL shows an r.m.s. deviation of 1.4 and 1.1 Å with the corresponding dimerization helices of yNAP-1 and hSET (Fig. 2, b and c). The core domain II of PfNapL is also similar to yNAP-1 and hSET, with an average r.m.s. deviation of 1.1 and 1.0 Å, respectively (Fig. 2, b and c). The dimerization helix α2 of PfNapL has high sequence similarity with the corresponding dimerization helices of hSET/yNAP-1 for a total of ∼50 residues (Fig. 2, b and c). In the β subdomain, PfNapL has 16 of 24 identical and 5 of 8 conserved residues with the corresponding β subdomains of hSET/yNAP-1. The residues 290-295 of this antiparallel β-sheet region of yNAP-1 had been previously identified as the nuclear localization signal (NLS) (15) (Figs. 1c and 2, b and c). Residues 200-221 in PfNapL corresponding to this short anti-parallel β-sheet region (β5 and β6) in yNAP-1 are disordered (Fig. 2b). However, the NLS sequences between yeast and PfNapL are highly conserved (Figs. 1c and 2b).


Crystal structure of malaria parasite nucleosome assembly protein: distinct modes of protein localization and histone recognition.

Gill J, Yogavel M, Kumar A, Belrhali H, Jain SK, Rug M, Brown M, Maier AG, Sharma A - J. Biol. Chem. (2009)

Comparison of PfNapL structure with yNAP-1 (Protein Data Bank code 2AYU) and hSET (Protein Data Bank code 2E50). a, superimposition of PfNapL monomer (purple) onto yNAP-1 (blue) and hSET (orange). Accessory domain of yNAP-1 is colored yellow. NES and NLS in yNAP-1 and PfNapL are indicated. b, superimposition of PfNapL and yNAP-1 dimers. The lower half shows superimposition of domain I and II from PfNapL and yNAP-1 monomers. yNAP-1 is colored blue, and the accessory domain is colored yellow. PfNapL is colored purple. The extra residues in domain II of yNAP-1 are colored cyan and are disordered in PfNapL. c, superimposition of PfNapL and hSET dimers. The lower half shows superimposition of domain I and II from PfNapL and hSET monomers. The extra residues of PfNapL are colored cyan and are disordered in hSET.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2665062&req=5

fig2: Comparison of PfNapL structure with yNAP-1 (Protein Data Bank code 2AYU) and hSET (Protein Data Bank code 2E50). a, superimposition of PfNapL monomer (purple) onto yNAP-1 (blue) and hSET (orange). Accessory domain of yNAP-1 is colored yellow. NES and NLS in yNAP-1 and PfNapL are indicated. b, superimposition of PfNapL and yNAP-1 dimers. The lower half shows superimposition of domain I and II from PfNapL and yNAP-1 monomers. yNAP-1 is colored blue, and the accessory domain is colored yellow. PfNapL is colored purple. The extra residues in domain II of yNAP-1 are colored cyan and are disordered in PfNapL. c, superimposition of PfNapL and hSET dimers. The lower half shows superimposition of domain I and II from PfNapL and hSET monomers. The extra residues of PfNapL are colored cyan and are disordered in hSET.
Mentions: Structural Conservation with yNAP-1, hSET, and Vps75—The root mean square (r.m.s.) deviation derived from the least square fittings of 191 Cα of PfNapL with the corresponding Cα of yNAP-1, hSET, and Vps75 is 1.9, 1.8, and 1.8 Å, respectively (Fig. 2a and Fig. S3). The dimerization helix α2 of PfNapL shows an r.m.s. deviation of 1.4 and 1.1 Å with the corresponding dimerization helices of yNAP-1 and hSET (Fig. 2, b and c). The core domain II of PfNapL is also similar to yNAP-1 and hSET, with an average r.m.s. deviation of 1.1 and 1.0 Å, respectively (Fig. 2, b and c). The dimerization helix α2 of PfNapL has high sequence similarity with the corresponding dimerization helices of hSET/yNAP-1 for a total of ∼50 residues (Fig. 2, b and c). In the β subdomain, PfNapL has 16 of 24 identical and 5 of 8 conserved residues with the corresponding β subdomains of hSET/yNAP-1. The residues 290-295 of this antiparallel β-sheet region of yNAP-1 had been previously identified as the nuclear localization signal (NLS) (15) (Figs. 1c and 2, b and c). Residues 200-221 in PfNapL corresponding to this short anti-parallel β-sheet region (β5 and β6) in yNAP-1 are disordered (Fig. 2b). However, the NLS sequences between yeast and PfNapL are highly conserved (Figs. 1c and 2b).

Bottom Line: Expression of green fluorescent protein-tagged PfNapL confirmed its exclusive localization to the parasite cytoplasm.A detailed analysis of PfNapL structure suggests unique histone binding properties.The crucial structural differences observed between parasite and yeast NAPs shed light on possible new modes of histone recognition by nucleosome assembly proteins.

View Article: PubMed Central - PubMed

Affiliation: Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Road, New Delhi 110067, India.

ABSTRACT
Nucleosome assembly proteins (NAPs) are histone chaperones that are essential for the transfer and incorporation of histones into nucleosomes. NAPs participate in assembly and disassembly of nucleosomes and in chromatin structure organization. Human malaria parasite Plasmodium falciparum contains two nucleosome assembly proteins termed PfNapL and PfNapS. To gain structural insights into the mechanism of NAPs, we have determined and analyzed the crystal structure of PfNapL at 2.3 A resolution. PfNapL, an ortholog of eukaryotic NAPs, is dimeric in nature and adopts a characteristic fold seen previously for yeast NAP-1 and Vps75 and for human SET/TAF-1b (beta)/INHAT. The PfNapL monomer is comprised of domain I, containing a dimerization alpha-helix, and a domain II, composed of alpha-helices and a beta-subdomain. Structural comparisons reveal that the "accessory domain," which is inserted between the domain I and domain II in yeast NAP-1 and other eukaryotic NAPs, is surprisingly absent in PfNapL. Expression of green fluorescent protein-tagged PfNapL confirmed its exclusive localization to the parasite cytoplasm. Attempts to disrupt the PfNapL gene were not successful, indicating its essential role for the malaria parasite. A detailed analysis of PfNapL structure suggests unique histone binding properties. The crucial structural differences observed between parasite and yeast NAPs shed light on possible new modes of histone recognition by nucleosome assembly proteins.

Show MeSH
Related in: MedlinePlus