PDBsum entry 1k1v

DNA binding protein

PDB id: 1k1v

Contents

Protein chain

41 a.a. *

* Residue conservation analysis

PDB id:

1k1v

Name:

DNA binding protein

Title:

Solution structure of the DNA-binding domain of mafg

Structure:

Mafg. Chain: a. Fragment: residues 24-64. Synonym: transcription factor mafg. Engineered: yes

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

20 models

Authors:

H.Kusunoki,H.Motohashi,F.Katsuoka,A.Morohashi,M.Yamamoto,T.Tanaka

Key ref:

H.Kusunoki et al. (2002). Solution structure of the DNA-binding domain of MafG. Nat Struct Biol, 9, 252-256. PubMed id: 11875518 DOI: 10.1038/nsb771

Date:

25-Sep-01 Release date: 10-Apr-02

Protein chain

O54790  (MAFG_MOUSE) -  Transcription factor MafG from Mus musculus

Seq: 162 a.a.

Struc: 41 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1038/nsb771

Nat Struct Biol 9:252-256 (2002)

PubMed id: 11875518

Solution structure of the DNA-binding domain of MafG.

H.Kusunoki, H.Motohashi, F.Katsuoka, A.Morohashi, M.Yamamoto, T.Tanaka.

ABSTRACT

The Maf family proteins, which constitute a subgroup of basic region-leucine zipper (bZIP) proteins, function as transcriptional regulators of cellular differentiation. Together with the basic region, the Maf extended homology region (EHR), conserved only within the Maf family, defines the DNA binding specific to Mafs. Here we present the first NMR-derived structure of the DNA-binding domain (residues 1-76) of MafG, which contains the EHR and the basic region. The structure consists of three alpha-helices and resembles the fold of the DNA-binding domain of Skn-1, a developmental transcription factor of Caenorhabditis elegans. The structural similarity between MafG and Skn-1 enables us to propose a possible mechanism by which Maf family proteins recognize their consensus DNA sequences.

Selected figure(s)

Figure 2.
Figure 2. 3D structure of MafG(1 -76). a, Stereo view of a best-fit superposition of the backbone atoms (N, C and C') of the 20 NMR-derived structures of MafG(1 -76). The main chain atoms of the 20 structures are superimposed against the energy-minimized average structure using residues 24 -64. The 23 N-terminal and 12 C-terminal residues, which are not well defined because they lack many experimental restraints, are omitted throughout panels (a -d). b, Ribbon diagram of the energy- minimized average structure of MafG(1 -76). The -helices are shown in purple and labeled. c,d, Electrostatic potential surfaces of MafG(1 -76). Positive and negative potentials are in blue and red, respectively. The orientation of the image (d) is the same as that in panel (b). The image in (c) is related to that in (d) by a 180° rotation along the vertical axis.

Figure 4.
Figure 4. Comparison of MafG(1 -76) with the Skn-1 DNA-binding domain. a, DNA-binding domains of MafG (left) and Skn-1 (right) (PDB accession code 1SKN). The helices of MafG and the corresponding regions of Skn-1 are in purple; the other helical regions of Skn-1 are in cyan. b, DNA-binding surfaces of MafG (left) and Skn-1 (right). The basic residues of MafG (Lys 53, Arg 56, Arg 57 and Lys 60) and Skn-1 (Arg 503, Arg 506, Arg 507, Arg 508 and Lys 510) are in blue. The five residues of Skn-1 that interact with the DNA bases and the corresponding residues of MafG (only Asn 61 and Tyr 64 in this panel) are in green. Val 34, Arg 35 and Asn 38 of MafG and the corresponding residues of Skn-1 are shown in red. c, Sequence alignment of the MafG and Skn-1 DNA-binding domains (SWISS-PROT accession number P34707). Secondary structure elements of MafG (upper) and Skn-1 (lower) are shown. The residues that form the hydrophobic cores of MafG and Skn-1 are underlined. The residues corresponding to the colored residues in panel (b) are highlighted in a matching color. The capping box sequences are indicated with asterisks. Open and closed circles show the residues of Skn-1 that interact with the bases and phosphate backbones of DNA, respectively. d, DNA sequence used in the structure determination of the Skn-1 -DNA complex and its interaction with the NXXAAXXCR sequence of Skn-1. The consensus recognition site of Skn-1 is boxed. The AP-1 core region is in green. Hydrogen bonds and van der Waals contacts are indicated by solid and dotted lines, respectively. e, EMSA of MafG(1 -76) and its mutants using an oligonucleotide containing the T-MARE-like sequence (probe #25 in ref. 5). The concentrations of purified protein were 0 M (lanes 1, 5, 9 and 13), 0.2 M (lanes 2, 6, 10 and 14), 0.8 M (lanes 3, 7, 11 and 15), and 3 M (lanes 4, 8, 12 and 16).

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2002, 9, 252-256) copyright 2002.

Figures were selected by the author.