PDBsum entry 3clz

Ligase

PDB id: 3clz

Contents

Protein chains

204 a.a. *

DNA/RNA

Waters ×652

* Residue conservation analysis

PDB id:

3clz

Name:

Ligase

Title:

The set and ring associated (sra) domain of uhrf1 bound to methylated DNA

Structure:

E3 ubiquitin-protein ligase uhrf1. Chain: a, b, c, d. Fragment: sra domain (unp residues 414-617). Synonym: ubiquitin-like phd and ring finger domain-containing protein 1, ubiquitin-like-containing phd and ring finger domains protein 1, inverted ccaat box-binding protein of 90 kda, transcription factor icbp90, nuclear zinc finger protein np95, nuclear protein 95, hunp95, ring finger protein 106. Engineered: yes.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: uhrf1, icbp90, np95, rnf106. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Synthetic: yes

Resolution:

2.20Å R-factor: 0.191 R-free: 0.231

Authors:

J.R.Walker,G.V.Avvakumov,S.Xue,A.Dong,Y.Li,C.Bountra,J.Weigelt, C.H.Arrowsmith,A.M.Edwards,A.Bochkarev,S.Dhe-Paganon,Structural Genomics Consortium (Sgc)

Key ref:

G.V.Avvakumov et al. (2008). Structural basis for recognition of hemi-methylated DNA by the SRA domain of human UHRF1. Nature, 455, 822-825. PubMed id: 18772889 DOI: 10.1038/nature07273

Date:

20-Mar-08 Release date: 29-Apr-08

Protein chains

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

Seq: 793 a.a.

Struc: 204 a.a.*

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

DNA/RNA chains

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

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

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

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

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

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

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

C-C-C-T-G-C-G-G-G-C-C-C 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/nature07273

Nature 455:822-825 (2008)

PubMed id: 18772889

Structural basis for recognition of hemi-methylated DNA by the SRA domain of human UHRF1.

G.V.Avvakumov, J.R.Walker, S.Xue, Y.Li, S.Duan, C.Bronner, C.H.Arrowsmith, S.Dhe-Paganon.

ABSTRACT

Epigenetic inheritance in mammals is characterized by high-fidelity replication of CpG methylation patterns during development. UHRF1 (also known as ICBP90 in humans and Np95 in mouse) is an E3 ligase important for the maintenance of global and local DNA methylation in vivo. The preferential affinity of UHRF1 for hemi-methylated DNA over symmetrically methylated DNA by means of its SET and RING-associated (SRA) domain and its association with the maintenance DNA methyltransferase 1 (DNMT1) suggests a role in replication of the epigenetic code. Here we report the 1.7 A crystal structure of the apo SRA domain of human UHRF1 and a 2.2 A structure of its complex with hemi-methylated DNA, revealing a previously unknown reading mechanism for methylated CpG sites (mCpG). The SRA-DNA complex has several notable structural features including a binding pocket that accommodates the 5-methylcytosine that is flipped out of the duplex DNA. Two specialized loops reach through the resulting gap in the DNA from both the major and the minor grooves to read the other three bases of the CpG duplex. The major groove loop confers both specificity for the CpG dinucleotide and discrimination against methylation of deoxycytidine of the complementary strand. The structure, along with mutagenesis data, suggests how UHRF1 acts as a key factor for DNMT1 maintenance methylation through recognition of a fundamental unit of epigenetic inheritance, mCpG.

Selected figure(s)

Figure 2.
Figure 2: The methylcytosine-binding pocket. A three-dimensional, close-up stereo image of the methylcytosine (mC6, coloured in cyan) in the binding pocket, showing interacting residues in stick format. Also included is the phosphate group of mC6 and two well-defined water molecules (red spheres) in the pocket. The 5-methyl group is shown as a small sphere. Hydrogen bonds are shown as dashed lines and labelled with distances (Å). Nearby secondary structure elements are drawn and labelled. The deoxyribose of mC6 and the remaining double-stranded DNA are not shown for clarity.

Figure 4.
Figure 4: Role of the NKR finger in the DNA binding. a, Schematic representation of the interactions with the DNA. Van der Waals contacts to DNA are shown as a series of short, parallel lines, and hydrogen bonds are shown as arrows. The carbon atom at position 5 of C7' is marked with an asterisk in this and subsequent panels. b, Close-up view of the finger–double-stranded DNA interface in three-dimensional stereo view. The NKR finger and thumb, coloured as in Fig. 1, and bases (green) are shown in stick format. The double-stranded DNA backbone is coloured brown and adjacent bases are represented in PyMol cartoon format. Three water molecules shown as red spheres mediate interactions, two of which are between the finger and G7 and the other molecule coordinates the backbone of the DNA and the side chains of Asn 489 and Arg 491. The C5 carbon atom of the non-methylated C7' (marked with an asterisk) is buried by the NKR finger and is within van der Waals distances from side chain and backbone atoms of Asn 489. For clarity, the side chain of Lys 490, which is solvent exposed, is not shown.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2008, 455, 822-825) copyright 2008.

Figures were selected by an automated process.