PDBsum entry 6b9m

Transferase

PDB id: 6b9m

Contents

Protein chains

150 a.a.

17 a.a.

Waters ×535

PDB id:

6b9m

Name:

Transferase

Title:

Crystal structure of uhrf1 ttd domain in complex with the polybasic region

Structure:

E3 ubiquitin-protein ligase uhrf1. Chain: a, b, c. Fragment: unp residues 129-280. Synonym: ring-type e3 ubiquitin transferase uhrf1,ubiquitin-like phd and ring finger domain-containing protein 1,ubiquitin-like-containing phd and ring finger domains protein 1. Engineered: yes. E3 ubiquitin-protein ligase uhrf1. Chain: d.

Source:

Danio rerio. Zebrafish. Organism_taxid: 7955. Gene: uhrf1. Expressed in: escherichia coli k-12. Expression_system_taxid: 83333. Homo sapiens. Human. Organism_taxid: 9606.

Resolution:

1.68Å R-factor: 0.183 R-free: 0.207

Authors:

J.Song,X.Tan

Key ref:

L.Gao et al. (2018). An Intramolecular Interaction of UHRF1 Reveals Dual Control for Its Histone Association. Structure, 26, 304. PubMed id: 29395786

Date:

10-Oct-17 Release date: 14-Feb-18

Protein chains

E7EZF3  (UHRF1_DANRE) -  E3 ubiquitin-protein ligase UHRF1 from Danio rerio

Seq: 776 a.a.

Struc: 150 a.a.*

Protein chain

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

Seq: 793 a.a.

Struc: 17 a.a.

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

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

Structure 26:304 (2018)

PubMed id: 29395786

An Intramolecular Interaction of UHRF1 Reveals Dual Control for Its Histone Association.

L.Gao, X.F.Tan, S.Zhang, T.Wu, Z.M.Zhang, H.W.Ai, J.Song.

ABSTRACT

UHRF1 (ubiquitin-like, containing PHD and RING finger domains, 1) is one of the essential components of mammalian DNA methylation machinery. Chromatin association of UHRF1 is controlled via an interplay between its intramolecular interaction and dual recognition of histone H3 trimethylated at lysine 9 (H3K9me3) and hemimethylated DNA. Here, we report the crystal structure of the N-terminal tandem Tudor domain (TTD) of UHRF1 in complex with the C-terminal polybasic region (PBR). Structural analysis reveals that PBR binding leads to displacement of the TTD-plant homeodomain (PHD) linker, as well as blockage of the H3K9me3-engaging cage, both of which contribute to a chromatin-occluded UHRF1 conformation. Disruption of the TTD-PBR interaction, which is facilitated by the binding of UHRF1 to hemimethylated DNA or regulatory protein USP7, shifts the UHRF1 conformation toward an open state, allowing for efficient H3K9me3 binding. Together, this study provides structural basis for the allosteric regulation of UHRF1.