Structural biology

Enzyme–chromatin complex visualized

The structure of an enzyme that is bound to a nucleosome — a protein complex around which DNA is wrapped — reveals how contacts between the two orient the enzyme so that it can modify a specific amino-acid residue. See Article p.591

In the nucleus, genomic DNA is organized in a highly compact protein–DNA complex called chromatin. The basic building block of chromatin is the nucleosome, an eight-subunit core comprised of two copies of each of the histone proteins H2A, H2B, H3 and H4, around which DNA is wrapped in two helical turns. Many nucleosome-remodelling and histone-modifying enzymes modulate chromatin structure and thereby affect the transcription, replication and repair of genomic DNA. However, despite the importance of these enzymes, we have only a limited understanding of how they interact physically with nucleosomes. On page 591 of this issue, McGinty et al.1 describe the crystal structure of the H2A-modifying module of an enzyme called Polycomb repressive complex 1, bound to a nucleosome. For the first time, the structure reveals how a histone-modifying enzyme recognizes its nucleosomal substrate.

Polycomb repressive complex 1 (PRC1) acts with other protein complexes of the Polycomb group to repress the transcription of many of the genes that control developmental processes in animals. PRC1 can compact chromatin and inhibit nucleosome remodelling through a non-enzymatic mechanism2. But the complex also has 'E3' ubiquitin-ligase enzyme activity, which links a single ubiquitin molecule to an amino-acid residue, lysine (Lys) 119, in H2A3 — a process called monoubiquitylation. The function of this protein modification in transcriptional repression is not well understood. However, studies published this year4,5 found that Lys 119 ubiquitylation creates a binding site for one form of the histone-methyltransferase enzyme complex PRC2, and thereby promotes the addition of three methyl groups to H3 at Lys 27, a modification that is crucial for the transcriptional repression of Polycomb target genes.

Six forms of mammalian PRC1 have been identified. All contain two proteins that have RING fingers — domains that bind zinc and are often found in proteins involved in ubiquitylation. One protein is a subunit of E3 ubiquitin ligase, either Ring1B or the closely related protein Ring1A, and the other is either the Polycomb-group RING finger (PCGF) protein Bmi1 or one of five other PCGF-related proteins6. In vitro studies7,8,9 have established that Ring1B alone shows only poor E3 activity on nucleosomes, but that a Ring1B–Bmi1 complex functions as an E3 ligase, and acts with the 'E2' enzyme UbcH5c to monoubiquitylate nucleosomal H2A at Lys 119 (E2 enzymes provide the ubiquitin molecule for ubiquitylation).

Building on previous structural studies7,8,9,10, McGinty and colleagues obtained crystals of the human Ring1B–Bmi1–UbcH5c complex bound to a nucleosome. They found that the complex binds to the flat sides of the nucleosome disc (Fig. 1), forming a crescent shape. Half of the crescent, the Ring1B–Bmi1 RING-finger dimer, binds the central histone surface, and the other half, UbcH5c, is positioned directly above the carboxy-terminal end of H2A, which contains the target of the complex, Lys 119. The researchers' structure does not contain the ubiquitin molecule that is transferred to H2A, but the location of the active-site cysteine amino acid of UbcH5c suggests that only Lys 119 or the adjacent residue, Lys 118, would be close enough to become ubiquitylated.

Figure 1: Enzyme–nucleosome contacts dictate substrate specificity.
figure1

a, This schematic diagram shows the disc face of the nucleosome and the acidic patch formed by histone proteins H2A and H2B. The H2A lysine (Lys) amino-acid residues Lys 119, Lys 124, Lys 127 and Lys 129 are indicated by yellow circles. b, McGinty et al.1 report that the Ring1B–Bmi1 E3 ubiquitin-ligase enzyme, which is part of the Polycomb repressive complex PRC1, positions another enzyme, UbcH5c, just above Lys 119, enabling monoubiquitylation of H2A at this residue. c, A hypothetical model of how the BRCA1–BARD1 E3 ligase positions the UbcH5c enzyme above Lys 124, Lys 127 and Lys 129.

Although UbcH5c is in contact with the nucleosomal DNA, it barely touches the histones in the nucleosome. Rather, the precise orientation of UbcH5c is controlled by the position of the Ring1B–Bmi1 dimer on the nucleosome surface. Here, a recurring theme of nucleosome recognition comes into play. McGinty and colleagues report that Ring1B uses a positively charged arginine amino-acid residue as an anchor to contact an 'acidic patch' formed by H2A and H2B. The acidic patch is implicated in nucleosome–nucleosome interactions10, and has also been identified as the crucial interaction site in all other nucleosome–protein complexes that have been structurally determined so far. As the authors note, LANA peptide and RCC1, CENP-C and Sir3 proteins all use an arginine residue to make contact with this acidic patch (see Fig. 4 of the Extended Data for the paper1).

In the case of the Ring1B–Bmi1 complex, McGinty et al. found that other positively charged Ring1B residues also interact with the acidic patch, extending the Ring1B–nucleosome interaction surface. Nevertheless, a mutational analysis performed by the authors shows that the arginine anchor is primarily responsible for binding. Mutating this residue resulted in a 50-fold decrease in binding affinity and H2A monoubiquitylation, whereas mutating adjacent positively charged residues had less-dramatic effects. The Bmi1 subunit seems to make a lesser contribution to nucleosome binding affinity, although contact with the amino-terminal helix of H3 is crucial for binding, and presumably also for fixing the orientation of the complex on the nucleosome surface.

What predictions can be made on the basis of the authors' structure? The BRCA1–BARD1 RING-finger dimer is an E3 ligase that is related to Ring1B–Bmi1, but BRCA1–BARD1 ubiquitylates Lys 124, Lys 127 or Lys 129, which are located nearer to the C terminus of H2A than residues modified by Ring1B–Bmi1 (ref. 11). McGinty and colleagues found that, like Ring1B–Bmi1, the BRCA1–BARD1 dimer seems to act with UbcH5c, and that the nucleosome-binding region of Ring1B and the corresponding region in BRCA1 are evolutionarily conserved — a confirmation of findings from another study11. Moreover, they show that mutation of the acidic patch eliminates BRCA1-mediated H2A monoubiquitylation in nucleosomes. These observations make it likely that BRCA1–BARD1 binds the acidic patch in a similar fashion to Ring1B–Bmi1. However, the overall geometry probably differs, such that only H2A residues Lys 124, Lys 127 or Lys 129 can become modified (Fig. 1).

Only some of the six different Ring1B–PCGF complexes seem to be able to monoubiquitylate H2A at Lys 119 in vivo5. This raises the possibility that one or more subunits of the other PRC1-type complexes occupy different interfaces on the E3 ligase or on the nucleosome in a way that precludes either the binding of an E2 enzyme or the transfer of ubiquitin to H2A. Undoubtedly, McGinty and colleagues' study will serve as the foundation for future structural investigations that will resolve how other E3 ligases or larger PRC1 assemblies interact with nucleosomes.

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Correspondence to Jürg Müller or Christoph W. Müller.

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Müller, J., Müller, C. Enzyme–chromatin complex visualized. Nature 514, 572–573 (2014). https://doi.org/10.1038/514572a

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