PDBsum entry 1j5k

Transcription/DNA

PDB id: 1j5k

Contents

Protein chain

76 a.a. *

DNA/RNA

* Residue conservation analysis

PDB id:

1j5k

Name:

Transcription/DNA

Title:

Complex of the kh3 domain of hnrnp k with a single_stranded 10mer DNA oligonucleotide

Structure:

5'-d( Ap Tp Ap T Tp Cp Cp Cp Tp C)-3'. Chain: b. Engineered: yes. Heterogeneous nuclear ribonucleoprotein k. Chain: a. Fragment: kh3 domain, residues 379-463, numbered 5-89. Synonym: hnrnp k, dc-stretch binding protein, csbp, transformation upregulated nuclear protein, tunp. Engineered: yes

Source:

Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

1 models

Authors:

G.M.Clore,D.T.Braddock

Key ref:

D.T.Braddock et al. (2002). Molecular basis of sequence-specific single-stranded DNA recognition by KH domains: solution structure of a complex between hnRNP K KH3 and single-stranded DNA. EMBO J, 21, 3476-3485. PubMed id: 12093748 DOI: 10.1093/emboj/cdf352

Date:

13-May-02 Release date: 10-Jul-02

Protein chain

P61978  (HNRPK_HUMAN) -  Heterogeneous nuclear ribonucleoprotein K from Homo sapiens

Seq: 463 a.a.

Struc: 76 a.a.

DNA/RNA chain

T-C-C-C-T 5 bases

DOI no: 10.1093/emboj/cdf352

EMBO J 21:3476-3485 (2002)

PubMed id: 12093748

Molecular basis of sequence-specific single-stranded DNA recognition by KH domains: solution structure of a complex between hnRNP K KH3 and single-stranded DNA.

D.T.Braddock, J.L.Baber, D.Levens, G.M.Clore.

ABSTRACT

To elucidate the basis of sequence-specific single-stranded (ss) DNA recognition by K homology (KH) domains, we have solved the solution structure of a complex between the KH3 domain of the transcriptional regulator heterogeneous nuclear ribonucleoprotein K (hnRNP K) and a 10mer ssDNA. We show that hnRNP K KH3 specifically recognizes a tetrad of sequence 5'd-TCCC. The complex is stabilized by a dense network of methyl-oxygen hydrogen bonds involving the methyl groups of three isoleucine residues and the O2 and N3 atoms of the two central cytosine bases. Comparison with the recently solved structure of a specific protein-ssDNA complex involving the KH3 and KH4 domains of the far upstream element (FUSE) binding protein FBP suggests that the amino acid located five residues N-terminal of the invariant GXXG motif, which is characteristic of all KH domains, plays a crucial role in discrimination of the first two bases of the tetrad.

Selected figure(s)

Figure 2.
Figure 2 ssDNA binding by hnRNP K KH3. (A) Overall complex. The protein is displayed as a molecular surface (left) and as a backbone tube (right); hydrophobic, uncharged hydrophilic, positively charged and negatively charged residues located in the ssDNA binding site are depicted in green, magenta, blue and red, respectively; the ssDNA heavy atoms are in gold. (B) Detailed stereoview showing the hydrogen-bonding interactions of the methyl groups of Ile29, Ile36 and Ile49 with the O2 and N3 atoms of the cytosine bases. Nucleotide numbering is in italics.

Figure 4.
Figure 4 Discrimination of the first two first bases of the ssDNA recognition site by KH domains of hnRNP K and FBP. (A) hnRNP K KH3 recognizes TC, (B) FBP KH3 recognizes TT and (C) FBP KH4 recognizes TA. The protein backbone and side chains are shown in red and green, respectively, and the DNA in light blue. The numbering scheme employed is that of the hnRNP K KH3−ssDNA complex. Dashed lines indicate intermolecular hydrogen bonds. The residue at position 25 plays a key role in selection of the first two bases of the site. The coordinates of the FBP KH3/KH4 complex (accession code 1J4W) are taken from Braddock et al. (2002).

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2002, 21, 3476-3485) copyright 2002.

Figures were selected by an automated process.