PDBsum entry 2nog

DNA binding protein

PDB id: 2nog

Contents

Protein chains

157 a.a. *

Metals

_MG ×2

Waters ×154

* Residue conservation analysis

PDB id:

2nog

Name:

DNA binding protein

Title:

Sant domain structure of xenopus remodeling factor iswi

Structure:

Iswi protein. Chain: a, b. Fragment: sant domain. Engineered: yes

Source:

Xenopus laevis. African clawed frog. Organism_taxid: 8355. Gene: iswi. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.00Å R-factor: 0.212 R-free: 0.274

Authors:

J.R.Horton,X.Cheng

Key ref:

J.R.Horton et al. (2007). Structure of the SANT domain from the Xenopus chromatin remodeling factor ISWI. Proteins, 67, 1198-1202. PubMed id: 17377988 DOI: 10.1002/prot.21352

Date:

25-Oct-06 Release date: 11-Sep-07

Protein chains

Q6DFM0  (Q6DFM0_XENLA) -  ISWI protein from Xenopus laevis

Seq: 1046 a.a.

Struc: 157 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1002/prot.21352

Proteins 67:1198-1202 (2007)

PubMed id: 17377988

Structure of the SANT domain from the Xenopus chromatin remodeling factor ISWI.

J.R.Horton, S.J.Elgar, S.I.Khan, X.Zhang, P.A.Wade, X.Cheng.

ABSTRACT

No abstract given.

Selected figure(s)

Figure 2.
Figure 2. Structure of Xenopus SANT. (A) A dimer of SANT domain formed in the crystallographic asymmetric unit. The dimer interface is formed between the N-terminal Pro-rich loop--hydrophobic interactions involving proline residues (P743, P746, P748, and P749) and helix A (Tyr775 and Tyr781) - and the helix D (two salt bridges between invariant Arg803 of one protomer and invariant Asp804 of another protomer). The Stokes radius of the domain was consistent with a solution dimer: the 21-kDa protein eluted from S75 gel filtration column with apparent molecular weight of 41 kDa. The total area of dimer interface of 707 Å^2 is within the limits, though at the lower end, of the 32 homodimers examined.[9] (B) A 90° rotated view from panel A. A Mg^2+ ion, required for crystallization, is bound at the loop region between helices E and F. Three main chain carbonyl oxygen atoms of Ala852, Val855, and Lys858 and two water molecules (w) coordinate the metal atom. (C) GRASP surface charge distribution is displayed with blue for positive, red for negative, and white for neutral. Filled circle indicates the opening of the concave L-surface. (D) Three views of the monomer structure of Xenopus SANT domain.

Figure 3.
Figure 3. Structural comparisons. (A) Xenopus and Drosophila SANT domains are colored in green and grey, respectively. The additional N-terminal helix in the Drosophila protein is in red, and the C-terminal SLIDE domain is shaded in yellow. The proteolytic cleavage site in the Xenopus protein is indicated. (B) Xenopus SANT domain and cMyb R2R3 are colored in green and magenta, respectively (middle panel). Structural alignment of helices D, E, and F of Xenopus SANT and that of R2 of c-Myb R2R3 (PDB 1GV2) derived the superimposition. The left panel shows the acidic surface patch of Xenopus SANT and the right panel shows the corresponding region of basic DNA binding surface of R2 of c-Myb R2R3. (C) X-ray structure of c-Myb R2R3[11] with the locations of three hydrophobic residues whose mutation to polar or charged side chains affecting the ability of v-Myb interaction with histone (left panel). A surface groove on the opposite side of the DNA binding might be the binding groove for histone H3 peptide.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2007, 67, 1198-1202) copyright 2007.

Figures were selected by an automated process.