PDBsum entry 2py9

RNA and DNA binding protein/RNA

PDB id: 2py9

Contents

Protein chains

72 a.a. *

DNA/RNA

Waters ×51

* Residue conservation analysis

PDB id:

2py9

Name:

RNA and DNA binding protein/RNA

Title:

Protein-RNA interaction involving kh1 domain from human poly(c)- binding protein-2

Structure:

12-mer c-rich strand of human telomeric RNA. Chain: e, f. Engineered: yes. Poly(rc)-binding protein 2. Chain: a, b, c, d. Synonym: alpha-cp2, hnrnp-e2. Engineered: yes

Source:

Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606. Gene: pcbp2. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.56Å R-factor: 0.220 R-free: 0.269

Authors:

T.L.James,Z.Du,J.K.Lee

Key ref:

Z.Du et al. (2007). X-ray crystallographic and NMR studies of protein-protein and protein-nucleic acid interactions involving the KH domains from human poly(C)-binding protein-2. Rna, 13, 1043-1051. PubMed id: 17526645

Date:

15-May-07 Release date: 12-Jun-07

Protein chains

Q15366  (PCBP2_HUMAN) -  Poly(rC)-binding protein 2 from Homo sapiens

Seq: 365 a.a.

Struc: 72 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains

A-A-C-C-C-U-A-A-C-C-C-U 12 bases

A-A-C-C-C-U-A-A-C-C-C-U 12 bases

Rna 13:1043-1051 (2007)

PubMed id: 17526645

X-ray crystallographic and NMR studies of protein-protein and protein-nucleic acid interactions involving the KH domains from human poly(C)-binding protein-2.

Z.Du, J.K.Lee, S.Fenn, R.Tjhen, R.M.Stroud, T.L.James.

ABSTRACT

Poly(C)-binding proteins (PCBPs) are KH (hnRNP K homology) domain-containing proteins that recognize poly(C) DNA and RNA sequences in mammalian cells. Binding poly(C) sequences via the KH domains is critical for PCBP functions. To reveal the mechanisms of KH domain-D/RNA recognition and its functional importance, we have determined the crystal structures of PCBP2 KH1 domain in complex with a 12-nucleotide DNA corresponding to two repeats of the human C-rich strand telomeric DNA and its RNA equivalent. The crystal structures reveal molecular details for not only KH1-DNA/RNA interaction but also protein-protein interaction between two KH1 domains. NMR studies on a protein construct containing two KH domains (KH1 + KH2) of PCBP2 indicate that KH1 interacts with KH2 in a way similar to the KH1-KH1 interaction. The crystal structures and NMR data suggest possible ways by which binding certain nucleic acid targets containing tandem poly(C) motifs may induce structural rearrangement of the KH domains in PCBPs; such structural rearrangement may be crucial for some PCBP functions.