PDBsum entry 2d5v

Transcription/DNA

PDB id: 2d5v

Contents

Protein chains

135 a.a. *

DNA/RNA

Ligands

ACT ×2

GOL ×2

Waters ×195

* Residue conservation analysis

PDB id:

2d5v

Name:

Transcription/DNA

Title:

Crystal structure of hnf-6alpha DNA-binding domain in complex with the ttr promoter

Structure:

5'-d( Tp Cp Tp Ap Ap Gp Tp Cp Ap Ap Tp Ap Ap T)-3'. Chain: c, e. Engineered: yes. 5'-d( Ap Tp Tp Ap Tp Tp Gp Ap Cp Tp Tp Ap Gp A)-3'. Chain: d, f. Engineered: yes. Hepatocyte nuclear factor 6. Chain: a, b. Fragment: residues 1-156.

Source:

Synthetic: yes. Rattus norvegicus. Norway rat. Organism_taxid: 10116. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Trimer (from PQS)

Resolution:

2.00Å R-factor: 0.245 R-free: 0.269

Authors:

D.Iyaguchi,M.Yao,N.Watanabe,J.Nishihira,I.Tanaka

Key ref:

D.Iyaguchi et al. (2007). DNA recognition mechanism of the ONECUT homeodomain of transcription factor HNF-6. Structure, 15, 75-83. PubMed id: 17223534 DOI: 10.1016/j.str.2006.11.004

Date:

07-Nov-05 Release date: 05-Dec-06

Protein chains

P70512  (HNF6_RAT) -  Hepatocyte nuclear factor 6 from Rattus norvegicus

Seq: 465 a.a.

Struc: 135 a.a.

DNA/RNA chains

T-C-T-A-A-G-T-C-A-A-T-A-A-T 14 bases

A-T-T-A-T-T-G-A-C-T-T-A-G 13 bases

T-C-T-A-A-G-T-C-A-A-T-A-A-T 14 bases

A-T-T-A-T-T-G-A-C-T-T-A 12 bases

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1016/j.str.2006.11.004

Structure 15:75-83 (2007)

PubMed id: 17223534

DNA recognition mechanism of the ONECUT homeodomain of transcription factor HNF-6.

D.Iyaguchi, M.Yao, N.Watanabe, J.Nishihira, I.Tanaka.

ABSTRACT

Hepatocyte nuclear factor-6 (HNF-6), a liver-enriched transcription factor, controls the development of various tissues, such as the pancreas and liver, and regulates the expression of several hepatic genes. This protein belongs to the ONECUT class of homeodomain proteins and contains a bipartite DNA-binding domain composed of a single cut domain and a characteristic homeodomain. This transcription factor has two distinct modes of DNA binding and transcriptional activation that use different coactivators depending on the target gene. The crystal structure of the bipartite DNA-binding domain of HNF-6alpha complexed with the HNF-6-binding site of the TTR promoter revealed the DNA recognition mechanism of this protein. Comparing our structure with the DNA-free structure of HNF-6 or the structure of Oct-1, we discuss characteristic features associated with DNA binding and the structural basis for the dual mode of action of this protein, and we suggest a strategy for variability of transcriptional activation of the target gene.

Selected figure(s)

Figure 5.
Figure 5. Protein-DNA Contacts
Schematic diagram of protein-DNA contacts. Residues from the cut domain are shown in light blue, and the homeodomain is shown in yellow. The bases, phosphates, and sugars contacted by each domain are indicated in the corresponding colors. The bases contacted by both domains are shown in red. Solid black lines indicate hydrogen bonds. van der Waals interactions are indicated as dashed blue lines. Water molecules are shown as green spheres.

Figure 6.
Figure 6. Detailed View of the Homeodomain-DNA Interactions
Interactions of Asn-143, Met-146, Asn-147, and Arg-150 with DNA are shown. Dashed red lines indicate hydrogen bonds. van der Waals interactions are indicated as dashed blue lines. Water molecules are shown as green spheres. Residue numbers and base numbers are labeled.

The above figures are reprinted by permission from Cell Press: Structure (2007, 15, 75-83) copyright 2007.

Figures were selected by an automated process.