PDBsum entry 4jjn

DNA binding protein/DNA

PDB id: 4jjn

Contents

Protein chains

98 a.a.

89 a.a.

105 a.a.

95 a.a.

205 a.a.

211 a.a.

DNA/RNA

PDB id:

4jjn

Name:

DNA binding protein/DNA

Title:

Crystal structure of heterochromatin protein sir3 in complex with a silenced yeast nucleosome

Structure:

Histone h3. Chain: a, e. Engineered: yes. Histone h4. Chain: b, f. Engineered: yes. Histone h2a.2. Chain: c, g. Engineered: yes.

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 559292. Strain: atcc 204508 / s288c. Gene: hht1, hht2, histone h3, n2749, sin2, ybr010w, ybr0201, ynl031c. Expressed in: escherichia coli. Expression_system_taxid: 469008. Gene: hhf1, hhf2, histone h4, n2752, ybr009c, ybr0122, ynl030w.

Resolution:

3.09Å R-factor: 0.233 R-free: 0.255

Authors:

F.Wang,G.Li,A.Mohammed,C.Lu,M.Currie,A.Johnson,D.Moazed

Key ref:

F.Wang et al. (2013). Heterochromatin protein Sir3 induces contacts between the amino terminus of histone H4 and nucleosomal DNA. Proc Natl Acad Sci U S A, 110, 8495-8500. PubMed id: 23650358 DOI: 10.1073/pnas.1300126110

Date:

08-Mar-13 Release date: 15-May-13

Protein chains

P61830  (H3_YEAST) -  Histone H3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 136 a.a.

Struc: 98 a.a.

Protein chains

P02309  (H4_YEAST) -  Histone H4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 103 a.a.

Struc: 89 a.a.

Protein chains

P04912  (H2A2_YEAST) -  Histone H2A.2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 132 a.a.

Struc: 105 a.a.

Protein chains

P02294  (H2B2_YEAST) -  Histone H2B.2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 131 a.a.

Struc: 95 a.a.

Protein chain

P06701  (SIR3_YEAST) -  Regulatory protein SIR3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 978 a.a.

Struc: 205 a.a.*

Protein chain

P06701  (SIR3_YEAST) -  Regulatory protein SIR3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 978 a.a.

Struc: 211 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

DNA/RNA chains

T-C-G-A-G-A-A-T-C-C-C-G-G-T-G-C-C-G-A-G-G-C-C-G-C-T-C-A-A-T-T-G-G-T-C-G-T-A-G- 146 bases

A-T-C-G-G-A-T-G-T-A-T-A-T-A-T-C-T-G-A-C-A-C-G-T-G-C-C-T-G-G-A-G-A-C-T-A-G-G-G- 146 bases

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, F, G, H, K, L: E.C.?

DOI no: 10.1073/pnas.1300126110

Proc Natl Acad Sci U S A 110:8495-8500 (2013)

PubMed id: 23650358

Heterochromatin protein Sir3 induces contacts between the amino terminus of histone H4 and nucleosomal DNA.

F.Wang, G.Li, M.Altaf, C.Lu, M.A.Currie, A.Johnson, D.Moazed.

ABSTRACT

The regulated binding of effector proteins to the nucleosome plays a central role in the activation and silencing of eukaryotic genes. How this binding changes the properties of chromatin to mediate gene activation or silencing is not fully understood. Here we provide evidence that association of the budding yeast silent information regulator 3 (Sir3) silencing protein with the nucleosome induces a conformational change in the amino terminus of histone H4 that promotes interactions between the conserved H4 arginines 17 and 19 (R17 and R19) and nucleosomal DNA. Substitutions of H4R17 and R19 with alanine abolish silencing in vivo, but have little or no effect on binding of Sir3 to nucleosomes or histone H4 peptides in vitro. Furthermore, in both the previously reported crystal structure of the Sir3-bromo adjacent homology (BAH) domain bound to the Xenopus laevis nucleosome core particle and the crystal structure of the Sir3-BAH domain bound to the yeast nucleosome core particle described here, H4R17 and R19 make contacts with nucleosomal DNA rather than with Sir3. These results suggest that Sir3 binding generates a more stable nucleosome by clamping H4R17 and R19 to nucleosomal DNA, and raise the possibility that such induced changes in histone-DNA contacts play major roles in the regulation of chromatin structure.