PDBsum entry 1ncs

Transcription regulation

PDB id: 1ncs

Contents

Protein chain

47 a.a. *

Metals

_ZN

* Residue conservation analysis

PDB id:

1ncs

Name:

Transcription regulation

Title:

Nmr study of swi5 zinc finger domain 1

Structure:

Transcriptional factor swi5. Chain: a. Fragment: zinc finger DNA binding domain 1 of swi5. Synonym: peptide m30f. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: t7. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: t7 polymerase expression system

NMR struc:

46 models

Authors:

R.N.Dutnall,D.Neuhaus,D.Rhodes

Key ref:

R.N.Dutnall et al. (1996). The solution structure of the first zinc finger domain of SWI5: a novel structural extension to a common fold. Structure, 4, 599-611. PubMed id: 8736557 DOI: 10.1016/S0969-2126(96)00064-0

Date:

26-Feb-96 Release date: 10-Jun-96

Protein chain

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

Seq: 709 a.a.

Struc: 47 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1016/S0969-2126(96)00064-0

Structure 4:599-611 (1996)

PubMed id: 8736557

The solution structure of the first zinc finger domain of SWI5: a novel structural extension to a common fold.

R.N.Dutnall, D.Neuhaus, D.Rhodes.

ABSTRACT

BACKGROUND: The 2Cys-2His (C2-H2) zinc finger is a protein domain commonly used for sequence-specific DNA recognition. The zinc fingers of the yeast transcription factors SWI5 and ACE2 share strong sequence homology, which extends into a region N-terminal to the first finger, suggesting that the DNA-binding domains of these two proteins include additional structural elements. RESULTS: Structural analysis of the zinc fingers of SWI5 reveals that a 15 residue region N-terminal to the finger motifs forms part of the structure of the first finger domain, adding a beta strand and a helix not previously observed in other zinc finger structures. Sequence analysis suggests that other zinc finger proteins may also have this structure. Biochemical studies show that this additional structure increases DNA-binding affinity. CONCLUSIONS: The structural analysis presented reveals a novel zinc finger structure in which additional structural elements have been added to the C2-H2 zinc finger fold. This additional structure may enhance stability and has implications for DNA recognition by extending the potential DNA-binding surface of a single zinc finger domain.

Selected figure(s)

Figure 5.
Figure 5. Stereo view of backbone N, Cα, C atom trace of the lowest energy structure of peptide m30F. The Cα atom of every fifth residue is shown as a black sphere and the backbone N atoms of slowly exchanging NH groups are shown in cyan. The side chain heavy atoms of the zinc ligands are coloured as in Figure 4a. Figure 5. Stereo view of backbone N, Cα, C atom trace of the lowest energy structure of peptide m30F. The Cα atom of every fifth residue is shown as a black sphere and the backbone N atoms of slowly exchanging NH groups are shown in cyan. The side chain heavy atoms of the zinc ligands are coloured as in [3]Figure 4a.

Figure 8.
Figure 8. Model of the first zinc finger of SWI5 docked to B-form DNA. A schematic representation of the zinc finger structure is shown prepared as in Figure 4a. The sequence of the DNA is that of the primary binding site of SWI5 and the two DNA-strands are coloured differently for contrast. The protein N and C termini and zinc ion are marked as well as the 5′ and 3′ ends of the DNA strand (dark blue) to which the additional helix makes its closest approach. The DNA-recognition helix of the canonical zinc finger is positioned to contact a base triplet on the cyan strand. This arrangement positions the additional helix near the opposite (dark blue) strand across the major groove, at a suitable distance (≈7 å) for basic residues on the surface of the helix to reach phosphate groups of the DNA backbone. Figure 8. Model of the first zinc finger of SWI5 docked to B-form DNA. A schematic representation of the zinc finger structure is shown prepared as in [3]Figure 4a. The sequence of the DNA is that of the primary binding site of SWI5 and the two DNA-strands are coloured differently for contrast. The protein N and C termini and zinc ion are marked as well as the 5′ and 3′ ends of the DNA strand (dark blue) to which the additional helix makes its closest approach. The DNA-recognition helix of the canonical zinc finger is positioned to contact a base triplet on the cyan strand. This arrangement positions the additional helix near the opposite (dark blue) strand across the major groove, at a suitable distance (≈7 å) for basic residues on the surface of the helix to reach phosphate groups of the DNA backbone.

The above figures are reprinted by permission from Cell Press: Structure (1996, 4, 599-611) copyright 1996.

Figures were selected by an automated process.