Crystal Structure of the First KH Domain of Human Poly(C)-binding Protein-2 in Complex with a C-rich Strand of Human Telomeric DNA at 1.7 Å

Zhihua Du, John K. Lee, Richard Tjhen, Shang Li, Hu Pan, Robert M. Stroud, Thomas L. James
2005 Journal of Biological Chemistry  
Recognition of poly(C) DNA and RNA sequences in mammalian cells is achieved by a subfamily of the KH (hnRNP K homology) domain-containing proteins known as poly(C)-binding proteins (PCBPs). To reveal the molecular basis of poly(C) sequence recognition, we have determined the crystal structure, at 1.7-Å resolution, of PCBP2 KH1 in complex with a 7-nucleotide DNA sequence (5-AACCCTA-3) corresponding to one repeat of the human C-rich strand telomeric DNA. The protein-DNA interaction is mediated by
more » ... the combination of several stabilizing forces including hydrogen bonding, electrostatic interactions, van der Waals contacts, and shape complementarities. Specific recognition of the three cytosine residues is realized by a dense network of hydrogen bonds involving the side chains of two conserved lysines and one glutamic acid. The co-crystal structure also reveals a protein-protein dimerization interface of PCBP2 KH1 located on the opposite side of the protein from the DNA binding groove. Numerous stabilizing protein-protein interactions, including hydrophobic contacts, stacking of aromatic side chains, and a large number of hydrogen bonds, indicate that the protein-protein interaction interface is most likely genuine. Interaction of PCBP2 KH1 with the C-rich strand of human telomeric DNA suggests that PCBPs may participate in mechanisms involved in the regulation of telomere/telomerase functions. K-homology domain (KH 2 domain, originally identified in hnRNP-K) is one of the most frequently occurring and conserved nucleic acidbinding protein motifs. So far, a large number of KH domain-containing proteins have been identified in a wide variety of species ranging from bacteria to human. These KH domain proteins assume a wide spectrum of biological functions, including transcriptional and translational controls, mRNA stabilization, and mRNA splicing, among others. Different KH domains possess quite different nucleic acid binding specificities. Unveiling how different KH domains interact specifically with their nucleic acid targets and how these interactions contribute to the com-* This work was supported in part by National Institutes of Health Grants AI46967 (to T. L. J.) and GM51232 (to R. M. S.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact. The atomic coordinates and structure factors (code 2AXY) have been deposited in the Protein . 2 The abbreviations used are: KH domain, hnRNP-K homology domain; PCBP, poly(C)binding protein; KH1, the first KH domain of PCBP2; UTR, untranslated region; RMSD, root mean square deviation; nt, nucleotide; hnRNP, heterogeneous nuclear ribonucleoprotein; ssDNA, single-stranded DNA; htDNA, human telomeric DNA.
doi:10.1074/jbc.m508183200 pmid:16186123 fatcat:qvyde4j6qzhsjk33uacl6hwxlm