PDBsum entry 2zo1

Ligase/DNA

PDB id: 2zo1

Contents

Protein chain

206 a.a. *

DNA/RNA

Ligands

EDO ×2

Waters ×97

* Residue conservation analysis

PDB id:

2zo1

Name:

Ligase/DNA

Title:

Mouse np95 sra domain DNA specific complex 2

Structure:

DNA (5'- d( Dtp Dcp Dcp Dap Dtp Dgp Dcp Dgp Dcp Dtp Dgp Dap Dc)-3'). Chain: d. Engineered: yes. Other_details: 12 base pair DNA duplex. DNA (5'-d( Dgp Dtp Dcp Dap Dgp (5Cm) p Dgp Dcp Dap Dap Dtp Dgp Dg)-3'). Chain: e. Engineered: yes.

Source:

Synthetic: yes. Mus musculus. Mouse. Organism_taxid: 10090. Gene: np95. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.96Å R-factor: 0.221 R-free: 0.246

Authors:

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

Key ref:

H.Hashimoto et al. (2008). The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix. Nature, 455, 826-829. PubMed id: 18772888 DOI: 10.1038/nature07280

Date:

05-May-08 Release date: 09-Sep-08

Protein chain

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

T-G-C-G-C-T-G-A-C 9 bases

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

DOI no: 10.1038/nature07280

Nature 455:826-829 (2008)

PubMed id: 18772888

The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix.

H.Hashimoto, J.R.Horton, X.Zhang, M.Bostick, S.E.Jacobsen, X.Cheng.

ABSTRACT

Maintenance methylation of hemimethylated CpG dinucleotides at DNA replication forks is the key to faithful mitotic inheritance of genomic methylation patterns. UHRF1 (ubiquitin-like, containing PHD and RING finger domains 1) is required for maintenance methylation by interacting with DNA nucleotide methyltransferase 1 (DNMT1), the maintenance methyltransferase, and with hemimethylated CpG, the substrate for DNMT1 (refs 1 and 2). Here we present the crystal structure of the SET and RING-associated (SRA) domain of mouse UHRF1 in complex with DNA containing a hemimethylated CpG site. The DNA is contacted in both the major and minor grooves by two loops that penetrate into the middle of the DNA helix. The 5-methylcytosine has flipped completely out of the DNA helix and is positioned in a binding pocket with planar stacking contacts, Watson-Crick polar hydrogen bonds and van der Waals interactions specific for 5-methylcytosine. Hence, UHRF1 contains a previously unknown DNA-binding module and is the first example of a non-enzymatic, sequence-specific DNA-binding protein domain to use the base flipping mechanism to interact with DNA.

Selected figure(s)

Figure 1.
Figure 1: Structure of SRA–DNA complex. a, Summary of the SRA–DNA interactions; mc, main-chain-atom-mediated contacts; w, water-mediated hydrogen bonds. Black boxes represent CpG recognition sequence and K495-associated dotted lines represent weak hydrogen bonds. b, The side chains of V451 of the base flipping loop and R496 of the CpG recognition loop are in direct van der Waals contact. c, The two loops—CpG recognition and base flipping—penetrate into the DNA helix from opposite directions. d, The 5mC flips out and binds in a cage-like pocket. e, The surface charge at neutral pH is displayed as blue for positive (20 k[B]T), red for negative (-20 k[B]T), and white for neutral, where k[B] is the Boltzmann's constant and T is the temperature.

Figure 2.
Figure 2: Details of SRA–DNA interactions. a, The 5mC G base pair is shown in the front, and the adjoining G C base pair is in the back. b, Planar stacking contacts of the extrahelical 5mC with Y471 and Y483 (left image). Omit electron densities, contoured at 4 and 5 above the mean, respectively, are shown for omitting 5mC (blue) or the methyl group (red) (right image). c, The hydrogen bond interactions with the polar atoms of 5mC. The double-dotted lines indicate van der Waals contacts with the methyl group of ring carbon C5. d, H450 forms a hydrogen bond from the minor groove side with cytosine of G C pair at position 5 (see Fig. 1a). e, Network of internal polar interactions centred on residues H447 and S464. Gua, guanine. f, Network of internal charged interactions centred on residues R541 and D560. Distances are shown in angstroms.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: Nature (2008, 455, 826-829) copyright 2008.

Figures were selected by the author.