2P2R

Crystal structure of the third KH domain of human Poly(C)-Binding Protein-2 in complex with C-rich strand of human telomeric DNA

Summary for 2P2R

• Entry DOI: 10.2210/pdb2p2r/pdb
• Descriptor: C-rich strand of human telomeric DNA, Poly(rC)-binding protein 2, 6-AMINOPYRIMIDIN-2(1H)-ONE, ... (4 entities in total)
• Functional Keywords: protein-dna complex, rna and dna binding protein-dna complex, rna and dna binding protein/dna
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 2
• Total formula weight: 10312.55

Authors

James, T.L.,Stroud, R.M.,Du, Z.,Fenn, S.,Tjhen, R.,Lee, J.K. (deposition date: 2007-03-07, release date: 2007-06-12, Last modification date: 2024-10-30)

Primary citation

Fenn, S.,Du, Z.,Lee, J.K.,Tjhen, R.,Stroud, R.M.,James, T.L.
Crystal structure of the third KH domain of human poly(C)-binding protein-2 in complex with a C-rich strand of human telomeric DNA at 1.6 A resolution.
Nucleic Acids Res., 35:2651-2660, 2007

PubMed Abstract: KH (hnRNP K homology) domains, consisting of approximately 70 amino acid residues, are present in a variety of nucleic-acid-binding proteins. Among these are poly(C)-binding proteins (PCBPs), which are important regulators of mRNA stability and posttranscriptional regulation in general. All PCBPs contain three different KH domains and recognize poly(C)-sequences with high affinity and specificity. To reveal the molecular basis of poly(C)-sequence recognition, we have determined the crystal structure, at 1.6 A resolution, of PCBP2 KH3 domain in complex with a 7-nt DNA sequence (5'-AACCCTA-3') corresponding to one repeat of the C-rich strand of human telomeric DNA. The domain assumes a type-I KH fold in a betaalphaalphabetabetaalpha configuration. The protein-DNA interface could be studied in unprecedented detail and is made up of a series of direct and water-mediated hydrogen bonds between the protein and the DNA, revealing an especially dense network involving several structural water molecules for the last 2 nt in the core recognition sequence. Unlike published KH domain structures, the protein crystallizes without protein-protein contacts, yielding new insights into the dimerization properties of different KH domains. A nucleotide platform, an interesting feature found in some RNA molecules, was identified, evidently for the first time in DNA.

PubMed: 17426136
DOI: 10.1093/nar/gkm139

Experimental method

X-RAY DIFFRACTION (1.6 Å)