PMC

Stereo view of the PCBP2 KH3–DNA complex structure. The dense network of hydrogen bonds (yellow dashed bars) involved in DNA–protein interaction is shown. Red spheres represent structured water molecules that participate in the hydrogen-bonding network. The DNA and protein are colored orange and deep blue, respectively. Protein residues that participate in hydrogen bond interaction with the DNA are shown in stick representation.

(A) Comparison between the structure of Ade2 and Cyt3 of our crystallization DNA (top) and Ade 441 and Ade 442 from the crystal structure of the 50S ribosomal subunit of Haloarcula marismortui (bottom). Hydrogen bonds are depicted as yellow dashed bars, atoms are color-coded light blue, red, grey, white and dark blue for nitrogen, oxygen, carbon, hydrogen and phosphorous, respectively. (B) Top: Overlay of the structure of Ade2 and Cyt3 of our crystallization DNA (red) and Ade 441 and Ade 442 from the crystal structure of the 50S ribosomal subunit of H. marismortui (blue). Bottom: Overlay of our DNA (red) and Ade2532 and Cyt 2533 from the crystal structure of the 50S ribosomal subunit of H. marismortui (blue).

Stereo views of detailed hydrogen-bonding interactions between the DNA and PCBP2 KH3. Coloring schemes are identical to those in . 2Fo-Fc electron density map contoured at 1σ is shown in green for the DNA and light blue for the protein side chains that participate in intermolecular hydrogen bonds. (A), (B), (C) and (D) are for hydrogen bonds to Ade2/Cyt3, Cyt4, Cyt5 and Thy6/Ade7, respectively.

Surface representations of the three KH domains in the PCBP proteins. Left: crystal structure of the PCBP2 KH1 domain. Middle: a homologous model (built by the program Modeller based on the crystal structure of PCBP2 KH1) of the PCBP2 KH2 domain. Right: crystal structure of the PCBP2 KH3 domain from the present study. Positively charged, negatively charged, uncharged hydrophilic and hydrophobic residues are colored in blue, red, yellow and green, respectively. Note the large, continuous hydrophobic surface area (in green) of the KH1 and KH2 domains.

(A) Schematic diagram of the domain structure of human poly(C) binding protein-2 (PCBP2). Similar domain structures are observed in other members of the PCBP family. (B) Sequence alignment of the three KH domains from different PCBPs. Alignments were carried out using the program ClustalX. The sequence shown for PCBP2 KH3 corresponds to residues 285–359 in the full-length protein. The actual construct for crystallization has an artificial lysine before Ala285. Secondary structures of the KH3 domain were based on the crystal structure.

Overall structure of the PCBP2 KH3–DNA complex. (A) Structure of the complex in one asymmetric unit. The DNA and protein are colored orange and deep blue, respectively. (B) Surface representation of the protein showing the nucleic-acid-binding groove. Positively charged, negatively charged, uncharged hydrophilic and hydrophobic residues are colored blue, red, yellow and green, respectively. The floor of the nucleic-acid-binding groove is mainly defined by hydrophobic residues. The DNA in the complex is colored orange. The first three residues from a symmetry-related DNA (labeled A1*, A2* and C3*) are shown in dark teal and are stacking on top of the complex DNA. See text for details.