PDBsum entry 1imh

Transcription/DNA

PDB id: 1imh

Contents

Protein chains

281 a.a. *

DNA/RNA

* Residue conservation analysis

PDB id:

1imh

Name:

Transcription/DNA

Title:

Tonebp/DNA complex

Structure:

5'-d( Tp Tp Gp Cp Tp Gp Gp Ap Ap Ap Ap Ap Tp Ap G)-3'. Chain: a. Engineered: yes. 5'-d( Ap Ap Cp Tp Ap Tp Tp Tp Tp Tp Cp Cp Ap Gp C)-3'. Chain: b. Engineered: yes. Nuclear factor of activated t cells 5. Chain: c, d. Fragment: DNA binding region.

Source:

Synthetic: yes. Other_details: solid phase DNA synthesis. Homo sapiens. Human. Organism_taxid: 9606. Gene: nfat5. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.86Å R-factor: 0.244 R-free: 0.290

Authors:

J.C.Stroud,C.Lopez-Rodriguez,A.Rao,L.Chen

Key ref:

J.C.Stroud et al. (2002). Structure of a TonEBP-DNA complex reveals DNA encircled by a transcription factor. Nat Struct Biol, 9, 90-94. PubMed id: 11780147 DOI: 10.1038/nsb749

Date:

10-May-01 Release date: 01-Feb-02

Protein chains

O94916  (NFAT5_HUMAN) -  Nuclear factor of activated T-cells 5 from Homo sapiens

Seq: 1531 a.a.

Struc: 281 a.a.

DNA/RNA chains

T-T-G-C-T-G-G-A-A-A-A-A-T-A-G 15 bases

A-A-C-T-A-T-T-T-T-T-C-C-A-G-C 15 bases

DOI no: 10.1038/nsb749

Nat Struct Biol 9:90-94 (2002)

PubMed id: 11780147

Structure of a TonEBP-DNA complex reveals DNA encircled by a transcription factor.

J.C.Stroud, C.Lopez-Rodriguez, A.Rao, L.Chen.

ABSTRACT

Tonicity-responsive enhancer binding protein (TonEBP), also known as NFAT5, is a unique member of the NFAT family of transcription factors that regulates gene expression induced by osmotic stress in mammalian cells. Unlike monomeric members of the NFAT family, TonEBP exists as a homodimer and binds asymmetric TonE DNA sites; furthermore, the affinity of TonEBP for DNA is much lower than that of other NFAT proteins. How TonEBP recognizes the TonE site and regulates the activation of hypertonicity response genes has not been clear. Here we show that TonEBP adopts a NF-kappaB-like structure upon binding to DNA, providing a direct structural link between the NFAT and NF-kappaB family of transcription factors. We also show that TonEBP completely encircles its DNA target and present biochemical evidence that the DNA encirclement may lead to increased kinetic stability of the TonEBP-DNA complex. Thus, the list of proteins that bind DNA by encirclement is now expanded to include sequence-specific transcription factors.

Selected figure(s)

Figure 1.
Figure 1. Structure of the TonEBP -DNA complex. a, Overall structure. The following scheme is used for all illustrations except Fig. 3c: the N-terminal (RHR-N) and C-terminal (RHR-C) domains of TonEBP are colored yellow and green, respectively. Strands and helices are labeled; the lettering corresponds to that used for NFAT1 (ref. 4). DNA is shown in the stick model. The sequence of the DNA used in the crystals is shown below the figure. b, Structure-based sequence alignment of human TonEBP (T), NFAT1(N), and NF- B p52 (P) in the DNA-binding region. The numbering for TonEBP is used. The secondary structure assignments for TonEBP are shown as colored bars ( -helices) and arrows ( -strands) above the aligned sequences; those for NF- B p52 are shown below the sequence. The colored blocks show residues that participate in contacts to DNA (magenta), RHR-C dimerization (green) and E'F loop dimerization (yellow).

Figure 3.
Figure 3. Dimerization in the TonEBP -DNA complex. a, The C-terminal dimer interface viewed in the same orientation as Fig. 1a. Hydrophobic residues Leu 372, Ile 390, Leu 422, Ile 429, and Phe 388 from each TonEBP monomer form the center of the interface. Polar residues Asn 426, His 424, His 427, Lys 373, Glu 386, and Ser 375 from each monomer form the peripheral of the interface through networks of hydrogen bonding and electrostatic interactions. b, The N-terminal dimer interface viewed from underneath the DNA with respect to Fig. 1a. The -helix of the E'F loop from each monomer supplies residues for dimerization, which include Arg 315, Ala 317, Asp 318, and Glu 320. The conformation of the -helix is stabilized by the DNA backbone (N-terminal capping) and by the hydrophobic interactions with the main body of the protein through residues Val 321, Leu 312, and Phe 267. c, Simulated-annealing omit map showing the electron density of the E'F dimer interface residues (Arg 315, Asn 316, Ala 317, Asp 318, Val 319, and Glu 320) in stereo. The 2.86 Å [A]-weighted F[o] - F[c] map is contoured at 2.0 level.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2002, 9, 90-94) copyright 2002.

Figures were selected by an automated process.