PDBsum entry 2zkf

Ligase

PDB id: 2zkf

Contents

Protein chain

209 a.a. *

DNA/RNA

Waters ×45

* Residue conservation analysis

PDB id:

2zkf

Name:

Ligase

Title:

Crystal structure of the sra domain of mouse np95 in complex with hemi-methylated cpg DNA

Structure:

E3 ubiquitin-protein ligase uhrf1. Chain: a. Fragment: unp residues 404-613. Synonym: ubiquitin-like phd and ring finger domain-containing protein 1, ubiquitin-like-containing phd and ring finger domains protein 1, nuclear zinc finger protein np95, nuclear protein 95. Engineered: yes. DNA (5'-d(p Dcp Dap Dcp Dcp Dgp Dgp Dap Dtp Dap Dgp Da)- 3').

Source:

Mus musculus. Mouse. Organism_taxid: 10090. Gene: uhrf1, np95. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: nucleotide synthesis. Other_details: nucleotide synthesis

Resolution:

2.55Å R-factor: 0.217 R-free: 0.275

Authors:

K.Arita,M.Ariyoshi,H.Tochio,Y.Nakamura,M.Shirakawa

Key ref:

K.Arita et al. (2008). Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism. Nature, 455, 818-821. PubMed id: 18772891 DOI: 10.1038/nature07249

Date:

19-Mar-08 Release date: 09-Sep-08

Protein chain

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

Seq: 782 a.a.

Struc: 209 a.a.

DNA/RNA chains

C-A-C-C-G-G-A-T-A-G-A 11 bases

C-T-A-T-C-5CM-G-G-T-G-A 11 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

DOI no: 10.1038/nature07249

Nature 455:818-821 (2008)

PubMed id: 18772891

Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism.

K.Arita, M.Ariyoshi, H.Tochio, Y.Nakamura, M.Shirakawa.

ABSTRACT

DNA methylation of CpG dinucleotides is an important epigenetic modification of mammalian genomes and is essential for the regulation of chromatin structure, of gene expression and of genome stability. Differences in DNA methylation patterns underlie a wide range of biological processes, such as genomic imprinting, inactivation of the X chromosome, embryogenesis, and carcinogenesis. Inheritance of the epigenetic methylation pattern is mediated by the enzyme DNA methyltransferase 1 (Dnmt1), which methylates newly synthesized CpG sequences during DNA replication, depending on the methylation status of the template strands. The protein UHRF1 (also known as Np95 and ICBP90) recognizes hemi-methylation sites via a SET and RING-associated (SRA) domain and directs Dnmt1 to these sites. Here we report the crystal structures of the SRA domain in free and hemi-methylated DNA-bound states. The SRA domain folds into a globular structure with a basic concave surface formed by highly conserved residues. Binding of DNA to the concave surface causes a loop and an amino-terminal tail of the SRA domain to fold into DNA interfaces at the major and minor grooves of the methylation site. In contrast to fully methylated CpG sites recognized by the methyl-CpG-binding domain, the methylcytosine base at the hemi-methylated site is flipped out of the DNA helix in the SRA-DNA complex and fits tightly into a protein pocket on the concave surface. The complex structure suggests that the successive flip out of the pre-existing methylated cytosine and the target cytosine to be methylated is associated with the coordinated transfer of the hemi-methylated CpG site from UHRF1 to Dnmt1.

Selected figure(s)

Figure 2.
Figure 2: Overall structure of the SRA–hemi-methylated CpG DNA complex. a, Ribbon representation of the SRA–DNA complex in the same orientations as in Fig. 1a: grey, SRA; orange, N-tail and finger loop; light blue, loop L3; light green, DNA; magenta, flipped-out base 5mC[7]. b, Schematic representation of the protein–DNA interactions observed in the crystal structure. Hydrogen bonds between SRA and DNA are shown by red lines: dotted, main-chain contacts; solid, side-chain contacts. Van der Waals contacts between SRA and DNA are shown by blue lines. W, water molecules mediating indirect interactions.

Figure 3.
Figure 3: Specific recognition of a hemi-methylated CpG site by SRA. The colour codes for the protein and DNA are same as in Fig. 2a. Red dotted lines show hydrogen-bond contacts within 4 Å. a, Close-up view of the flipped-out 5mC[7] recognition site. The composite-omit electron density map for 5mC[7] (more than 6.0 ) is shown in blue. b, The orphaned guanidine G[7]' base is retained near a canonical position in the DNA duplex by interactions with the SRA residues. c, Interactions between the G8 C8' base pair adjacent to the flipped-out base and the SRA residues. Wat, water. d, The model of fully methylated DNA bound to the SRA. The methyl group of 5mC[8]' (shown as a green sphere) causes steric interference with Asn 494 (orange spheres) in the finger loop. The hydrogen-bond distances between these bases and the SRA residues are listed in Supplementary Tables 2 and 3.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2008, 455, 818-821) copyright 2008.

Figures were selected by an automated process.