PDBsum entry 1pl5

DNA binding protein/transcription

PDB id: 1pl5

Contents

Protein chains

75 a.a.

Waters ×40

PDB id:

1pl5

Name:

DNA binding protein/transcription

Title:

Crystal structure analysis of the sir4p c-terminal coiled coil

Structure:

Regulatory protein sir4. Chain: a, s. Fragment: residues 1217-1358. Synonym: silent information regulator 4. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: sir4. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.50Å R-factor: 0.261 R-free: 0.288

Authors:

G.A.Murphy,E.J.Spedale,S.T.Powell,L.Pillus,S.C.Schultz,L.Chen

Key ref:

G.A.Murphy et al. (2003). The Sir4 C-terminal coiled coil is required for telomeric and mating type silencing in Saccharomyces cerevisiae. J Mol Biol, 334, 769-780. PubMed id: 14636601 DOI: 10.1016/j.jmb.2003.09.066

Date:

06-Jun-03 Release date: 01-Jun-04

Protein chains

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

Seq: 1358 a.a.

Struc: 75 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1016/j.jmb.2003.09.066

J Mol Biol 334:769-780 (2003)

PubMed id: 14636601

The Sir4 C-terminal coiled coil is required for telomeric and mating type silencing in Saccharomyces cerevisiae.

G.A.Murphy, E.J.Spedale, S.T.Powell, L.Pillus, S.C.Schultz, L.Chen.

ABSTRACT

Saccharomyces cerevisiae Sir4p plays important roles in silent chromatin at telomeric and silent mating type loci. The C terminus of Sir4p (Sir4CT) is critical for its functions in vivo because over-expression or deletion of Sir4CT fragments disrupts normal telomeric structure and abolishes the telomere position effect. The 2.5A resolution X-ray crystal structure of an Sir4CT fragment (Sir4p 1217-1358) reveals a 72 residue homodimeric, parallel coiled coil, burying an extensive 3600A(2) of surface area. The crystal structure is consistent with results of protein cross-linking and analytical ultracentrifugation results demonstrating that Sir4CT exists as a dimer in solution. Disruption of the coiled coil in vivo by point mutagenesis results in total derepression of telomeric and HML silent mating marker genes, suggesting that coiled coil dimerization is essential for Sir4p-mediated silencing. In addition to the coiled coil dimerization interface (Sir4CC interface), a crystallographic interface between pairs of coiled coils is significantly hydrophobic and buries 1228A(2) of surface area (interface II). Remarkably, interface II mutants are deficient in telomeric silencing but not in mating type silencing in vivo. However, point mutants of interface II do not affect the oligomerization state of Sir4CT in solution. These results are consistent with the hypothesis that interface II mimics a protein interface between Sir4p and one of its protein partners that is essential for telomeric silencing but not mating type silencing.

Selected figure(s)

Figure 1.
Figure 1. The X-ray crystal structure of Sir4p residues 1272-1347. (a) Two C-terminal Sir4 fragments combine to form a 72 residue homodimeric parallel coiled coil, including amino acid residues V1274 to L1344 (strand A, cyan) or M1345 (strand S, magenta). Residues in positions a and d are drawn in stick model. (b) A helical wheel diagram with a and d residues listed. b-Branching residues are shown in bold, colored are charged or polar residues (d positions K1288, N1309, T1323, and K1337). (c) Residues in the coiled coil. Mutations to disrupt the coiled coil are in bold, and underlined when combined. Interface II mutants are red.

Figure 4.
Figure 4. A large hydrophobic interface exists between symmetry-related coiled coils. (a) The surface of the N terminus of the coiled coil (NT-surface) (green and rose) contacts a C-terminal surface of its symmetry-related neighbor (CT-surface) (cyan and magenta). This interface, interface II, has a hydrophobic core, seven ordered water molecules and a hydrogen bonding network. For clarity, only hydrogen bonding involving water molecules is shown. (b) Surface complementarity of interface II. A coiled coil's NT-surface (molecular surface representation) has a large hole into which Phe1322 from another coiled coil's CT-surface nestles (cyan and magenta). Interface residues from the CT-surface are shown. (c) and (d) Molecular surfaces colored by hydrophobicity (F, V, I, L, A are yellow) show the two interaction surfaces. A stick model is placed atop the surface representation to indicate the position of the interface. (c) The NT-surface. (d) The CT-surface.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 334, 769-780) copyright 2003.

Figures were selected by an automated process.