PDBsum entry 1khc

Transferase

PDB id: 1khc

Contents

Protein chain

137 a.a. *

Ligands

UNX-UNX-UNX-UNX

UNX-UNX ×4

UNX-UNX-UNX ×2

UNX ×4

Waters ×162

* Residue conservation analysis

References listed in PDB file

Key reference

Title

The pwwp domain of mammalian DNA methyltransferase dnmt3b defines a new family of DNA-Binding folds.

Authors

C.Qiu, K.Sawada, X.Zhang, X.Cheng.

Ref.

Nat Struct Biol, 2002, 9, 217-224. [DOI no: 10.1038/nsb759]

PubMed id

11836534

Abstract

The PWWP domain is a weakly conserved sequence motif found in > 60 eukaryotic proteins, including the mammalian DNA methyltransferases Dnmt3a and Dnmt3b. These proteins often contain other chromatin-association domains. A 135-residue PWWP domain from mouse Dnmt3b (amino acids 223--357) has been structurally characterized at 1.8 A resolution. The N-terminal half of this domain resembles a barrel-like five-stranded structure, whereas the C-terminal half contains a five-helix bundle. The two halves are packed against each other to form a single structural module that exhibits a prominent positive electrostatic potential. The PWWP domain alone binds DNA in vitro, probably through its basic surface. We also show that recombinant Dnmt3b2 protein (a splice variant of Dnmt3b) and two N-terminal deletion mutants (Delta218 and Delta369) have approximately equal methyl transfer activity on unmethylated and hemimethylated CpG-containing oligonucleotides. The Delta218 protein, which includes the PWWP domain, binds DNA more strongly than Delta369, which lacks the PWWP domain.

Figure 2.
Figure 2. Structure of Dnmt3b2 PWWP domain. a, RIBBON^49 diagram, with invariant amino acids in cyan, conserved in yellow and varied in gray. The SWWP motif is colored in magenta. In the crystal packing contacts, strand 6 from one molecule interacts with strand 4, which is the edge strand of the -sheet (4 3 2 1 5), of a neighboring molecule through backbone−backbone hydrogen bonds in an antiparallel arrangement. b, Molecular surface and charge distribution. The view is oriented similarly to that in (a). The surface is colored according to charge: positively charged groups (Arg and Lys) are blue, negatively charged groups (Glu and Asp) are red and uncharged groups are white. c, Contours of the electrostatic potential at 2 KT e^-1 calculated and displayed in two orientations as a mesh surface. The positive potential is shown in blue, and the negative potential in red. Panels (b,c) were done using GRASP^50.

Figure 4.
Figure 4. Comparison of PWWP domain with its structural homologs. a, Ribbon diagram and stereo view of the superimposition of PWWP (yellow) and Sp100b SAND domain (PDB 1H5P)^33 (orange). For clarity, the C-terminal helix of SAND domain is not shown in the superimposition. The structural similarity between the two domains was detected manually. Below is the structure-based sequence alignment between the -barrel structure of PWWP and SAND. The line between the two sequences indicates the residues used in superimposition. b, Ribbon diagram and stereo view of the superimposition of PWWP (yellow) and the SMN Tudor domain (PDB 1G5V)^34 (orange). The r.m.s. deviation is 0.8 Å when 43 C atoms (out of total 56 residues in Tudor) are structurally aligned between the two domains (DALI Z-score of 6.3). The largest difference lies in the loop between strands 2 and 3. In comparison, the five-stranded -barrel of PWWP is remotely similar to the SH3 structures (DALI Z-score of 3.3), a small basic folding unit. The structure-based sequence alignment between the -barrel structure of PWWP and Tudor is shown below, with the line between the two sequences indicating the residues used in superimposition.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2002, 9, 217-224) copyright 2002.