PDBsum entry 1nyh

Transcription repressor

PDB id: 1nyh

Contents

Protein chain

76 a.a.

PDB id:

1nyh

Name:

Transcription repressor

Title:

Crystal structure of the coiled-coil dimerization motif of sir4

Structure:

Regulatory protein sir4. Chain: a. Fragment: coiled-coil dimerization domain, residue 1198-1358. Synonym: silent information regulator 4. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: sir4. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PDB file)

Resolution:

3.10Å R-factor: 0.273 R-free: 0.288

Authors:

J.F.Chang,B.E.Hall,J.C.Tanny,D.Moazed,D.Filman,T.Ellenberger

Key ref:

J.F.Chang et al. (2003). Structure of the coiled-coil dimerization motif of Sir4 and its interaction with Sir3. Structure, 11, 637-649. PubMed id: 12791253 DOI: 10.1016/S0969-2126(03)00093-5

Date:

12-Feb-03 Release date: 24-Jun-03

Protein chain

P11978  (SIR4_YEAST) -  Regulatory protein SIR4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 1358 a.a.

Struc: 76 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1016/S0969-2126(03)00093-5

Structure 11:637-649 (2003)

PubMed id: 12791253

Structure of the coiled-coil dimerization motif of Sir4 and its interaction with Sir3.

J.F.Chang, B.E.Hall, J.C.Tanny, D.Moazed, D.Filman, T.Ellenberger.

ABSTRACT

The yeast silent information regulators Sir2, Sir3, and Sir4 physically interact with one another to establish a transcriptionally silent state by forming repressive chromatin structures. The Sir4 protein contains binding sites for both Sir2 and Sir3, and these protein-protein interactions are required for gene silencing. Here, we report the X-ray structure of the coiled-coil dimerization motif within the C-terminus of Sir4 and show that it forms a stable 1:1 complex with a dimeric fragment of Sir3 (residues 464-978). We have identified a cluster of residues on the surface of the Sir4 coiled coil required for specific interactions with Sir3. The histone deacetylase Sir2 can also bind to this complex, forming a ternary complex with the truncated Sir3 and Sir4 proteins. The dual interactions of Sir4 with Sir3 and Sir2 suggest a physical basis for recruiting Sir3 to chromatin by virtue of its interactions with Sir4 and with deacetylated histones in chromatin.

Selected figure(s)

Figure 5.
Figure 5. A Hydrophobic Patch of Residues on the Surface of the Sir4 Coiled Coil Binds Sir3(A) A series of mutant Sir4-C2 proteins with amino acid substitutions at the exposed positions along the length of the coiled coil were constructed and tested for interaction with Sir3T by the GST pull-down assay with a 1:1 molar ratio of Sir3T and each Sir4-C2 mutant. Mutation of residues M1307 and I1311 prevent binding to Sir3T, and mutation of the neighboring residue E1310 strongly interferes with binding to Sir3T.(B) The locations of the Sir4 residues that are required for interaction with Sir3 are shown, colored as in Figure 1B. The Sir3 binding site is present on each subunit of the coiled-coil dimer, suggesting that two Sir3 molecules interact with the Sir4 dimer (cf. Figure 6).(C) A series of N-terminally truncated Sir3 proteins were tested for interaction with the GST-Sir4-C2 coiled-coil domain. The Sir3 proteins were expressed in E. coli and purified with a C-terminal His[6] affinity tag prior to use in the pull-down experiment. The efficiency of the interaction with Sir4-C2 is shown.(D) Pull-down assays are shown that test the interaction of Sir4 with a series of N-terminally truncated Sir3 proteins. The results show that the region of Sir3 between residues 495 and 522 is crucial for efficient binding to Sir4. This region is exposed and proteolytically sensitive in the absence of Sir4 (see text for details).

The above figure is reprinted by permission from Cell Press: Structure (2003, 11, 637-649) copyright 2003.

Figure was selected by an automated process.