5Y21

Crystal structure of AL2 PAL domain in complex with AtRing1a proximal site

Summary for 5Y21

• Entry DOI: 10.2210/pdb5y21/pdb
• Descriptor: PHD finger protein ALFIN-LIKE 2, AtRing1a proximal binding site peptide (3 entities in total)
• Functional Keywords: prc1 interactor, alfin-like family protein, complex, gene regulation
• Biological source: Arabidopsis thaliana (Mouse-ear cress); More
• Total number of polymer chains: 4
• Total formula weight: 34663.43

Authors

Peng, L.,Wang, L.L.,Huang, Y. (deposition date: 2017-07-22, release date: 2018-07-25, Last modification date: 2023-11-22)

Primary citation

Peng, L.,Wang, L.,Zhang, Y.,Dong, A.,Shen, W.H.,Huang, Y.
Structural Analysis of the Arabidopsis AL2-PAL and PRC1 Complex Provides Mechanistic Insight into Active-to-Repressive Chromatin State Switch
J. Mol. Biol., 430:4245-4259, 2018

PubMed Abstract: Polycomb group proteins play essential roles in transcriptional gene repression during both animal and plant development. Polycomb repression complex 1 (PRC1) is one of the key functional modules in polycomb group silencing. It acts as both a reader of H3K27me3 (histone H3 lysine 27 trimethylation) and a writer of H2Aub1 (histone H2A monoubiquitination) in establishing stable repression chromatin state. Intriguingly, a recent study showed that Arabidopsis PRC1 contains the H3K4me3-binding proteins of the ALFIN-like (AL) family, pointing to a chromatin state switch from active to repressive transcription of embryonic genes required for vegetative plant development. However, molecular and structural basis of AL-PRC1 complexes are lacking, which harmed insightful mechanistic understanding of AL-PRC1 complex function. In the present study, we report the crystal structures of the PAL domain (DUF3594 domain) of AL2 and AL7 proteins as well as their mechanistic binding to the PRC1 ring-finger proteins (RING1 and BMI1). We found that the PAL domain exists as a homodimer and represents a novel protein fold. We further determined the crystal structures of the PAL domain of AL2 (AL2-PAL) in complex with AtRING1a and AtBMI1b, the two core components of Arabidopsis PRC1. Interestingly, two PAL-binding sites were found on AtRING1a. Each of them can bind AL but with different affinities and distinct structural bases. Based on our results, we propose a mechanistic model to understand how AL proteins target PRC1 to active chromatin to undergo the transition from H3K4me3 to H2Aub1/H3K27me3 in establishing gene silencing.

PubMed: 30176245
DOI: 10.1016/j.jmb.2018.08.021

Experimental method

X-RAY DIFFRACTION (1.769 Å)