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

Citation:
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.
PDB ID: 2P2RDownload
MMDB ID: 64917
PDB Deposition Date: 2007/3/7
Updated in MMDB: 2017/10
Experimental Method:
x-ray diffraction
Resolution: 1.6  Å
Source Organism:
Homo sapiens
Similar Structures:
Biological Unit for 2P2R: dimeric; determined by author
Molecular Components in 2P2R
Label Count Molecule
Protein (1 molecule)
1
Poly(rc)-binding Protein 2(Gene symbol: PCBP2)
Molecule annotation
Nucleotide(1 molecule)
1
C-rich Strand of Human Telomeric DNA
Molecule annotation
Chemical (1 molecule)
1
1
* Click molecule labels to explore molecular sequence information.

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