PDBsum entry 3f8i

Ligase/DNA

PDB id: 3f8i

Contents

Protein chains

206 a.a. *

DNA/RNA

Waters ×135

* Residue conservation analysis

PDB id:

3f8i

Name:

Ligase/DNA

Title:

Mouse uhrf1 sra domain bound with hemi-methylated cpg, crystal structure in space group p21

Structure:

E3 ubiquitin-protein ligase uhrf1. Chain: a, b. Fragment: ydg domain: unp residues 419-628. Engineered: yes. 5'-d( Dcp Dcp Dap Dtp Dgp (5Cm)p Dgp Dcp Dtp Dgp Dap Dc)- 3'. Chain: d, f. Engineered: yes. 5'-d( Dgp Dtp Dcp Dap Dgp Dcp Dgp Dcp Dap Dtp Dgp Dg)-3'.

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Gene: uhrf1. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: synthetic DNA oligo. Other_details: synthetic DNA oligo

Resolution:

2.29Å R-factor: 0.223 R-free: 0.268

Authors:

H.Hashimoto,J.R.Horton,X.Zhang,X.Cheng

Key ref:

H.Hashimoto et al. (2009). UHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications. Epigenetics, 4, 8. PubMed id: 19077538

Date:

12-Nov-08 Release date: 06-Jan-09

Protein chains

Q8VDF2  (UHRF1_MOUSE) -  E3 ubiquitin-protein ligase UHRF1 from Mus musculus

Seq: 782 a.a.

Struc: 206 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DNA/RNA chains

C-C-A-T-G-5CM-G-C-T-G-A-C 12 bases

G-T-C-A-G-C-G-C-A-T-G-G 12 bases

C-C-A-T-G-5CM-G-C-T-G-A-C 12 bases

G-T-C-A-G-C-G-C-A-T-G-G 12 bases

Enzyme reactions

• Enzyme class: 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

Epigenetics 4:8 (2009)

PubMed id: 19077538

UHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications.

H.Hashimoto, J.R.Horton, X.Zhang, X.Cheng.

ABSTRACT

Cytosine methylation in DNA is a major epigenetic signal, and plays a central role in propagating chromatin status during cell division. However the mechanistic links between DNA methylation and histone methylation are poorly understood. A multi-domain protein UHRF1 (ubiquitin-like, containing PHD and RING finger domains 1) is required for DNA CpG maintenance methylation at replication forks, and mouse UHRF1-null cells show enhanced susceptibility to DNA replication arrest and DNA damaging agents. Recent data demonstrated that the SET and RING associated (SRA) domain of UHRF1 binds hemimethylated CpG and flips 5-methylcytosine out of the DNA helix, whereas its tandom tudor domain and PHD domain bind the tail of histone H3 in a highly methylation sensitive manner. We hypothesize that UHRF1 brings the two components (histones and DNA) carrying appropriate markers (on the tails of H3 and hemimethylated CpG sites) ready to be assembled into a nucleosome after replication.