PDBsum entry 2i5o

Transferase

PDB id: 2i5o

Contents

Protein chain

34 a.a.

Metals

_ZN

References listed in PDB file

Key reference

Title

Structure of the ubiquitin-Binding zinc finger domain of human DNA y-Polymerase eta.

Authors

M.G.Bomar, M.T.Pai, S.R.Tzeng, S.S.Li, P.Zhou.

Ref.

EMBO Rep, 2007, 8, 247-251. [DOI no: 10.1038/sj.embor.7400901]

PubMed id

17304240

Abstract

The ubiquitin-binding zinc finger (UBZ) domain of human DNA Y-family polymerase (pol) eta is important in the recruitment of the polymerase to the stalled replication machinery in translesion synthesis. Here, we report the solution structure of the pol eta UBZ domain and its interaction with ubiquitin. We show that the UBZ domain adopts a classical C(2)H(2) zinc-finger structure characterized by a betabetaalpha fold. Nuclear magnetic resonance titration maps the binding interfaces between UBZ and ubiquitin to the alpha-helix of the UBZ domain and the canonical hydrophobic surface of ubiquitin defined by residues L8, I44 and V70. Although the UBZ domain binds ubiquitin through a single alpha-helix, in a manner similar to the inverted ubiquitin-interacting motif, its structure is distinct from previously characterized ubiquitin-binding domains. The pol eta UBZ domain represents a novel member of the C(2)H(2) zinc finger family that interacts with ubiquitin to regulate translesion synthesis.

Figure 2.
Figure 2 Nuclear magnetic resonance titration shows the binding interface between the polymerase UBZ domain and ubiquitin. (A) Chemical shift perturbations of the UBZ domain plotted against residue number. Residues with chemical shift changes greater than 2 and 1 are shown in orange (significantly perturbed) and yellow (perturbed), respectively. (B) A surface representation of the UBZ domain with significantly perturbed residues (labelled in black) shown in orange and perturbed residues in yellow. (C) 90° right-handed rotation of (B). (D) Chemical shift perturbations of residues in ubiquitin calculated and coloured as in (A). (E) A surface representation of ubiquitin. Significantly perturbed residues (shown in orange and labelled in black) and perturbed residues (shown in yellow) are distributed along the canonical hydrophobic surface defined by residues V70, I44 (both labelled in red) and L8. (F) 90° left-handed rotation of (E). Surface representations were generated by PyMol (DeLano, 2002). pol, polymerase; UBZ, ubiquitin-binding zinc finger.

Figure 3.
Figure 3 Proposed model of the polymerase UBZ domain–ubiquitin complex. (A) A ribbon diagram of the UIM–ubiquitin complex (PDB entry 1Q0W), with conserved residues shown in stick model. The orientation of the UIM -helix (pink) bound to ubiquitin (green) is indicated by an arrow, directed from the N to C terminus. (B) A ribbon diagram of the MIU/IUIM motif (brown) bound to ubiquitin (PDB entry 2FIF), with the orientation of the -helix and conserved residues indicated as in (A). (C) Alignment of the consensus sequences of the UBZ domain with MIU/IUIM and reversed UIM. The central invariant alanine is highlighted in purple, conserved hydrophobic residues in yellow, acidic residues in red, zinc ligands in blue and a highly conserved glutamine residue in grey. A serine residue at the +4 position in the UIM, which is replaced by an aspartate in the MIU/IUIM and the UBZ domains, is shown in blue. (D) A model of the UBZ domain–ubiquitin complex. The C-terminal cysteine of the UBZ domain, which was modified by the spin-label reagent MTSL (denoted as S), and ubiquitin residues, the resonances of which were severely attenuated during the spin-label titration, are coloured in blue. (E) Sections of ^1H-^15N HSQC spectra of ubiquitin, (F) in the presence of the spin-labelled UBZ domain and (G) after addition of 5 mM dithiothreitol. Note that the amide resonance of G75[Ub] disappears in the presence of the spin-labelled UBZ domain (F). IUIM; inverted UIM; MIU, motif interacting with ubiquitin; PDB, Protein Data Bank; UBZ, ubiquitin-binding zinc finger; UIM, ubiquitin-interacting motif.

The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO Rep (2007, 8, 247-251) copyright 2007.