spacer
spacer

PDBsum entry 2d5v

Go to PDB code: 
protein dna_rna ligands links
Transcription/DNA PDB id
2d5v
Jmol
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 comple 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    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
A4II00  (A4II00_XENTR) -  DNA-binding protein SATB
Seq:
Struc:
493 a.a.
135 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     regulation of transcription, DNA-dependent   1 term 
  Biochemical function     DNA binding     3 terms  

 

 
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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18095340 R.P.Matthews, K.Lorent, and M.Pack (2008).
Transcription factor onecut3 regulates intrahepatic biliary development in zebrafish.
  Dev Dyn, 237, 124-131.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.