PDBsum entry 1zfd

Zinc finger DNA binding domain

PDB id: 1zfd

Contents

Protein chain

32 a.a. *

Metals

_ZN

* Residue conservation analysis

PDB id:

1zfd

Name:

Zinc finger DNA binding domain

Title:

Swi5 zinc finger domain 2, nmr, 45 structures

Structure:

Swi5. Chain: a. Fragment: zinc finger domain 2. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: t7 promoter

NMR struc:

45 models

Authors:

D.Neuhaus,Y.Nakaseko,J.W.R.Schwabe,D.Rhodes,A.Klug

Key ref:

D.Neuhaus et al. (1992). Solution structures of two zinc-finger domains from SWI5 obtained using two-dimensional 1H nuclear magnetic resonance spectroscopy. A zinc-finger structure with a third strand of beta-sheet. J Mol Biol, 228, 637-651. PubMed id: 1453468 DOI: 10.1016/0022-2836(92)90846-C

Date:

04-Apr-96 Release date: 14-Oct-96

Protein chain

P08153  (SWI5_YEAST) -  Transcriptional factor SWI5 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 709 a.a.

Struc: 32 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1016/0022-2836(92)90846-C

J Mol Biol 228:637-651 (1992)

PubMed id: 1453468

Solution structures of two zinc-finger domains from SWI5 obtained using two-dimensional 1H nuclear magnetic resonance spectroscopy. A zinc-finger structure with a third strand of beta-sheet.

D.Neuhaus, Y.Nakaseko, J.W.Schwabe, A.Klug.

ABSTRACT

This paper describes the detailed three-dimensional structures of two zinc-finger domains from the yeast transcription factor SWI5, calculated using the results of the n.m.r. experiments described in the accompanying paper. The structure of finger 2 is essentially similar to those previously obtained by others for isolated, synthetic single zinc-finger domains in solution, and for the three zinc-finger peptide Zif268 in its crystalline complex with DNA. The N-terminal half of the sequence forms a two-stranded, irregular beta-sheet containing both of the metal-binding cysteine residues, while the remainder of the structure forms a helix. Approximately the first half of this helix is alpha-helical, whereas the C-terminal portion, including the two metal-binding histidine residues, is 3(10) helical. Four invariant hydrophobic residues form a core to the structure. In contrast to all previously described structures of zinc-finger domains, finger 1 has an additional strand in the beta-sheet, formed by residues N-terminal to the formal start of the finger motif. This additional strand plays a role in stabilising the folded form of finger 1, since a two-finger peptide lacking the N-terminal residues showed folded structure in finger 2 but not in finger 1.

Selected figure(s)

Figure 5.
Figure 5. Schematic representation of the structures of ingers 1 panels and B) and 2 (panels C and D) from SW15, prepared using the program Molscript (Kraulis, 1991). In each case, the structure having the lowest NOE violations is shown. iews A and C are related to views B and D by a 90'' rotation bout the vertical. In addition to the schematic representtion of the backbone, bonds are shown between the non-hydrogen atoms of the side-chains of the metal binding an conserved hydrophobic residues, nd these rsidues are labelled (not that, because the arrows representing the /3sheet do not necessarily pass through the actual c'' atom positions, the C''-CB bonds of some side-chains have been extended with broken lines so as to meet the bacbone representation artificially).

Figure 6.
Figure 6. Stereoview of a local ackbone superimposition in the turn regio (Cvs44 to Cys49) between the two P-strands of fingr 2 of SWIS; as in Fig. 3,45 structures are shown. Atoms Nj: NH, C'', e and 0' re shown for all residues, tog&her with the zinc ions and he non-hydrogen side-chain atoms of Cys44, Pro47 and Cys49. The conformation is clearly that of tpe II p-turn, characterized by the hydrogen bond between His46 C = 0 and Cys49 ?u'H (indicated hy the broken line) and by the relative orientation of the Pro47-Gly48 peptide bond.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1992, 228, 637-651) copyright 1992.

Figures were selected by an automated process.