PDBsum entry 4gy5

Ligase

PDB id: 4gy5

Contents

Protein chains

215 a.a.

154 a.a.

Ligands

ALA-ARG-THR-LYS-GLN-THR-ALA-ARG-M3L-SER

ALA-ARG-THR-LYS-GLN-THR-ALA-ARG-M3L

Metals

_ZN ×7

Waters ×10

PDB id:

4gy5

Name:

Ligase

Title:

Crystal structure of the tandem tudor domain and plant homeodomain of uhrf1 with histone h3k9me3

Structure:

E3 ubiquitin-protein ligase uhrf1. Chain: a, b, c, d. Fragment: tudor phd domain, unp residues 134-366. Synonym: uhrf1. Engineered: yes. Peptide from histone h3.3. Chain: e, f. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: uhrf1. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: this sequence occurs naturally in humans

Resolution:

2.96Å R-factor: 0.257 R-free: 0.288

Authors:

J.Cheng,Y.Yang,J.Fang,J.Xiao,T.Zhu,F.Chen,P.Wang,Y.Xu

Key ref:

J.Cheng et al. (2013). Structural insight into coordinated recognition of trimethylated histone H3 lysine 9 (H3K9me3) by the plant homeodomain (PHD) and tandem tudor domain (TTD) of UHRF1 (ubiquitin-like, containing PHD and RING finger domains, 1) protein. J Biol Chem, 288, 1329-1339. PubMed id: 23161542

Date:

05-Sep-12 Release date: 14-Nov-12

Protein chains

Q96T88  (UHRF1_HUMAN) -  E3 ubiquitin-protein ligase UHRF1 from Homo sapiens

Seq: 793 a.a.

Struc: 215 a.a.*

Protein chains

Q96T88  (UHRF1_HUMAN) -  E3 ubiquitin-protein ligase UHRF1 from Homo sapiens

Seq: 793 a.a.

Struc: 154 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: Chains A, B, C, D: E.C.2.3.2.27 - RING-type E3 ubiquitin transferase.
• Reaction: S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N₆- ubiquitinyl-[acceptor protein]-L-lysine

J Biol Chem 288:1329-1339 (2013)

PubMed id: 23161542

Structural insight into coordinated recognition of trimethylated histone H3 lysine 9 (H3K9me3) by the plant homeodomain (PHD) and tandem tudor domain (TTD) of UHRF1 (ubiquitin-like, containing PHD and RING finger domains, 1) protein.

J.Cheng, Y.Yang, J.Fang, J.Xiao, T.Zhu, F.Chen, P.Wang, Z.Li, H.Yang, Y.Xu.

ABSTRACT

UHRF1 is an important epigenetic regulator connecting DNA methylation and histone methylations. UHRF1 is required for maintenance of DNA methylation through recruiting DNMT1 to DNA replication forks. Recent studies have shown that the plant homeodomain (PHD) of UHRF1 recognizes the N terminus of unmodified histone H3, and the interaction is inhibited by methylation of H3R2, whereas the tandem tudor domain (TTD) of UHRF1 recognizes trimethylated histone H3 lysine 9 (H3K9me3). However, how the two domains of UHRF1 coordinately recognize histone methylations remains elusive. In this report, we identified that PHD largely enhances the interaction between TTD and H3K9me3. We present the crystal structure of UHRF1 containing both TTD and PHD (TTD-PHD) in complex with H3K9m3 peptide at 3.0 Å resolution. The structure shows that TTD-PHD binds to the H3K9me3 peptide with 1:1 stoichiometry with the two domains connected by the H3K9me3 peptide and a linker region. The TTD interacts with residues Arg-8 and trimethylated Lys-9, and the PHD interacts with residues Ala-1, Arg-2, and Lys-4 of the H3K9me3 peptide. The biochemical experiments indicate that PHD-mediated recognition of unmodified H3 is independent of the TTD, whereas TTD-mediated recognition of H3K9me3 PHD. Thus, both TTD and PHD are essential for specific recognition of H3K9me3 by UHRF1. Interestingly, the H3K9me3 peptide induces conformational changes of TTD-PHD, which do not affect the autoubiquitination activity or hemimethylated DNA binding affinity of UHRF1 in vitro. Taken together, our studies provide structural insight into the coordinated recognition of H3K9me3 by the TTD and PHD of UHRF1.