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

doi:10.1074/jbc.m508183200

Zhihua Du, John K Lee + Show 5 more

Open Access

https://doi.org/10.1074/jbc.m508183200

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Abstract

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-A 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 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.

Highlights

Plex regulatory processes is of central importance to a better understanding of how KH domain proteins function
One of the most distinctive nucleic acid binding specificities achieved by the KH domains is manifested by a subfamily of KH domain-containing proteins known as poly(C)-binding proteins (PCBPs)
We report the 1.7-Å resolution crystal structure of the PCBP2 KH1 domain in complex with a seven-nucleotide single-stranded DNA sequence (5Ј-AACCCTA-3Ј) corresponding to one repeat of the C-rich strand of human telomeric DNA

Summary

Structure of KH Domain in Complex with Human Telomeric DNA

It should be noted that PCBP functions are diverse, they are most dependent on the ability of the KH domains to recognize single-stranded C-rich RNA or DNA sequences with high specificity and affinity. We report the 1.7-Å resolution crystal structure of the PCBP2 KH1 domain in complex with a seven-nucleotide single-stranded DNA sequence (5Ј-AACCCTA-3Ј) corresponding to one repeat of the C-rich strand of human telomeric DNA (htDNA). Each of the three cystosines is recognized by a network of strong hydrogen bonds to the Watson-Crick positions involving the side chain functional group of a particular amino acid. Another outstanding feature of the PCBP KH1 domain is the presence of a protein-protein dimerization interface located on the other side of KH1 domain from the DNA binding interface. Insights into mechanisms of PCBP functions, in the context of comparison with other available KH domain-nucleic acids complex structures, are discussed

EXPERIMENTAL PROCEDURES

Reflections in working set

RESULTS

DISCUSSION