PDBsum entry: 1irf

Transcription regulation

PDB id: 1irf

Contents

Protein chain

112 a.a. *

* Residue conservation analysis

PDB id:

1irf

Name:

Transcription regulation

Title:

Interferon regulatory factor-2 DNA binding domain, nmr, minimized average structure

Structure:

Interferon regulatory factor-2. Chain: a. Fragment: residues 2-113. Engineered: yes

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Cell_line: bl21. Cellular_location: nucleus. Gene: potential. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

1 models

Authors:

J.Furui,K.Uegaki,T.Yamazaki,M.Shirakawa,M.B.Swindells, H.Harada,T.Taniguchi,Y.Kyogoku

Key ref:

J.Furui et al. (1998). Solution structure of the IRF-2 DNA-binding domain: a novel subgroup of the winged helix-turn-helix family. Structure, 6, 491-500. PubMed id: 9562558 DOI: 10.1016/S0969-2126(98)00050-1

Date:

24-Nov-97 Release date: 28-Jan-98

Protein chain

P23906  (IRF2_MOUSE) -  Interferon regulatory factor 2

Seq: 349 a.a.

Struc: 112 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: regulation of transcription, DNA-dependent (1 term)
• Biochemical function: regulatory region DNA binding (2 terms)

DOI no: 10.1016/S0969-2126(98)00050-1

Structure 6:491-500 (1998)

PubMed id: 9562558

Solution structure of the IRF-2 DNA-binding domain: a novel subgroup of the winged helix-turn-helix family.

J.Furui, K.Uegaki, T.Yamazaki, M.Shirakawa, M.B.Swindells, H.Harada, T.Taniguchi, Y.Kyogoku.

ABSTRACT

BACKGROUND: The transcription of interferon (IFN) and IFN-inducible genes is mainly regulated by the interferon regulatory factor (IRF) family of proteins, which recognize a unique AAGTGA hexamer repeat motif in the regulatory region of IFN genes. A DNA-binding domain of approximately 100 amino acids has been commonly found in the IRF family of proteins, but it has no sequence homology to known DNA-binding motifs. Elucidation of the structures of members of the IRF family is therefore useful to the understanding of the regulation and evolution of the immune system at the structural level. RESULTS: The solution structure of the DNA-binding domain of interferon regulatory factor-2 (IRF-2) has been determined by NMR spectroscopy. It is composed of a four-stranded antiparallel beta sheet and three alpha helices, and its global fold is similar to those of the winged helix-turn-helix (wHTH) family of proteins. A long loop (Pro37-Asp51) is found immediately before the HTH motif, which is not found in other wHTH proteins. The NMR signals of residues in this long loop, as well as the second helix of the HTH motif, are strongly affected upon the addition of the hexamer repeat DNA, suggesting that these structural elements participate in DNA recognition and binding. CONCLUSIONS: The structural similarity of the DNA-binding domain of IRF-2 with those of proteins in the wHTH family shows that the IRF proteins belong to the wHTH family, even though there is no apparent sequence homology among proteins of the two families. The sequential structure alignment program (SSAP) shows that IRF-2 has a slightly different structure from typical wHTH proteins, mainly in the orientation of helix 2. The IRF family of proteins should therefore be categorized into a subfamily of the wHTH family. The evidence here implies that the evolutional pathway of the IRF family is distinct from that of the other wHTH proteins, in other words, the immune system diverged from an evolutional stem at an early stage.

Selected figure(s)

Figure 3.
Figure 3. Hydrophobic core residues in IRF-2(113). The sidechains of hydrophobic residues that play important roles in construction of the hydrophobic core are shown. The sidechains of hydrophobic residues in the a helices and b sheet are colored green and yellow, respectively.

The above figure is reprinted by permission from Cell Press: Structure (1998, 6, 491-500) copyright 1998.

Figure was selected by an automated process.