PDBsum entry 3f8j

Ligase/DNA

PDB id

3f8j

Loading ...

Contents

			Protein chain

					206 a.a. *

			DNA/RNA

			Ligands

					GOL ×9

			Waters ×161

* Residue conservation analysis

PDB id:

3f8j

Links

Name:

Ligase/DNA

Title:

Mouse uhrf1 sra domain bound with hemi-methylated cpg, crystal structure in space group c222(1)

Structure:

E3 ubiquitin-protein ligase uhrf1. Chain: b. Fragment: ydg domain: unp residues 417-628. Engineered: yes. 5'-d( Dcp Dcp Dap Dtp Dgp (5Cm)p Dgp Dcp Dtp Dgp Dap Dc)- 3'. Chain: 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:

1.99Å

R-factor:

0.198

R-free:

0.232

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

PROCHECK

	Headers

	References

Protein chain

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

Seq: Struc:

Seq: Struc:					782 a.a. 206 a.a.

Key:

PfamA domain

Secondary structure

CATH domain

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



		Enzyme reactions

Enzyme class:

E.C.2.3.2.27 - RING-type E3 ubiquitin transferase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

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.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21214517

A.L.Tien, S.Senbanerjee, A.Kulkarni, R.Mudbhary, B.Goudreau, S.Ganesan, K.C.Sadler, and C.Ukomadu (2011).
UHRF1 depletion causes a G2/M arrest, activation of DNA damage response and apoptosis.

Biochem J, 435, 175-185.

21339843

H.Hashimoto, P.M.Vertino, and X.Cheng (2010).
Molecular coupling of DNA methylation and histone methylation.

Epigenomics, 2, 657-669.

20886526

M.Joulie, B.Miotto, and P.A.Defossez (2010).
Mammalian methyl-binding proteins: what might they do?

Bioessays, 32, 1025-1032.

21029866

T.Bartke, M.Vermeulen, B.Xhemalce, S.C.Robson, M.Mann, and T.Kouzarides (2010).
Nucleosome-interacting proteins regulated by DNA and histone methylation.

Cell, 143, 470-484.

19943104

W.Jin, L.Chen, Y.Chen, S.G.Xu, G.H.Di, W.J.Yin, J.Wu, and Z.M.Shao (2010).
UHRF1 is associated with epigenetic silencing of BRCA1 in sporadic breast cancer.

Breast Cancer Res Treat, 123, 359-373.

19319879

M.Godmann, R.Lambrot, and S.Kimmins (2009).
The dynamic epigenetic program in male germ cells: Its role in spermatogenesis, testis cancer, and its response to the environment.

Microsc Res Tech, 72, 603-619.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.