PDBsum entry: 1ozj

Transcription/DNA

PDB id: 1ozj

Contents

Protein chains

126 a.a. *

DNA/RNA

Metals

_ZN ×2

Waters ×47

* Residue conservation analysis

PDB id:

1ozj

Name:

Transcription/DNA

Title:

Crystal structure of smad3-mh1 bound to DNA at 2.4 a resolution

Structure:

Smad binding element. Chain: c. Engineered: yes. Smad binding element. Chain: d. Engineered: yes. Smad 3. Chain: a, b. Fragment: dwa domain.

Source:

Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606. Gene: madh3 or smad3 or mad3. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Tetramer (from PQS)

Resolution:

2.40Å R-factor: 0.210 R-free: 0.270

Authors:

J.Chai,J.-W.Wu,N.Yan,J.Massague,N.P.Pavletich,Y.Shi

Key ref:

J.Chai et al. (2003). Features of a Smad3 MH1-DNA complex. Roles of water and zinc in DNA binding. J Biol Chem, 278, 20327-20331. PubMed id: 12686552 DOI: 10.1074/jbc.C300134200

Date:

09-Apr-03 Release date: 23-Mar-04

Protein chains

P84022  (SMAD3_HUMAN) -  Mothers against decapentaplegic homolog 3

Seq: 425 a.a.

Struc: 126 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: intracellular (2 terms)
• Biological process: regulation of transcription, DNA-dependent (2 terms)
• Biochemical function: protein binding (2 terms)

DOI no: 10.1074/jbc.C300134200

J Biol Chem 278:20327-20331 (2003)

PubMed id: 12686552

Features of a Smad3 MH1-DNA complex. Roles of water and zinc in DNA binding.

J.Chai, J.W.Wu, N.Yan, J.Massagué, N.P.Pavletich, Y.Shi.

ABSTRACT

The Smad family of proteins mediates transforming growth factor-beta signaling from cell membrane to the nucleus. In the nucleus, Smads serve as transcription factors by directly binding to specific DNA sequences and regulating the expression of ligand-response genes. A previous structural analysis, at 2.8-A resolution, revealed a novel DNA-binding mode for the Smad MH1 domain but did not allow accurate assignment of the fines features of protein-DNA interactions. The crystal structure of a Smad3 MH1 domain bound to a palindromic DNA sequence, determined at 2.4-A resolution, reveals a surprisingly important role for water molecules. The asymmetric placement of the DNA-binding motif (a conserved 11-residue beta-hairpin) in the major groove of DNA is buttressed by seven well ordered water molecules. These water molecules make specific hydrogen bonds to the DNA bases, the DNA phosphate backbones, and several critical Smad3 residues. In addition, the MH1 domain is found to contain a bound zinc atom using four invariant residues among Smad proteins, three cysteines and one histidine. Removal of the zinc atom results in compromised DNA binding activity. These results define the Smad MH1 domain as a zinc-coordinating module that exhibits unique DNA binding properties.

Selected figure(s)

Figure 1.
FIG. 1. Structural features of the Smad3 MH1 domain bound to SBE. A, overall structure of the Smad3 MH1 domain bound to SBE. The palindromic DNA and the MH1 domain are colored purple and cyan, respectively. The DNA-binding motif is highlighted in orange. The bound zinc atom is shown in red, and its coordinating residues are colored yellow. B, a stereo view of the ordered water molecules between the DNA bases and the -hairpin. The electron density "omit" map on the water molecules, shown in red and labeled, was calculated by omitting these solvents and contoured at 3 . The -hairpin is shown in cyan, and DNA-binding residues are highlighted in yellow. This figure, Fig. 2A, and Fig. 3B were prepared using MOLSCRIPT (28).

Figure 2.
FIG. 2. Specific DNA contacts mediated by water molecules. A, a stereo view of the specific contacts between the -hairpin and the DNA. Hydrogen bonds are represented by red dashed lines. Water molecules are shown as green spheres. B, a summary of the specific DNA recognition by the -hairpin and water molecules. Hydrogen bonds are represented by arrows.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 20327-20331) copyright 2003.

Figures were selected by the author.