PDBsum entry 1vzp

DNA repair protein

PDB id: 1vzp

Contents

Protein chain

128 a.a.

Metals

_ZN

Theoretical model

PDB id:

1vzp

Name:

DNA repair protein

Title:

Nei like 2 DNA repair protein

Structure:

Hypothetical protein flj31644. Synonym: nei like 2. Chain: a. Fragment: c-terminal DNA binding domain, residues 192-319

Source:

Homo sapiens. Human

Authors:

V.S.Mathura

Key ref:

A.Das et al. (2004). Identification of a zinc finger domain in the human NEIL2 (Nei-like-2) protein. J Biol Chem, 279, 47132-47138. PubMed id: 15339932 DOI: 10.1074/jbc.M406224200

Date:

24-May-04 Release date: 14-Jun-04

Protein chain

Q969S2  (NEIL2_HUMAN) -  Endonuclease 8-like 2 from Homo sapiens

Seq: 332 a.a.

Struc: 128 a.a.

DOI no: 10.1074/jbc.M406224200

J Biol Chem 279:47132-47138 (2004)

PubMed id: 15339932

Identification of a zinc finger domain in the human NEIL2 (Nei-like-2) protein.

A.Das, L.Rajagopalan, V.S.Mathura, S.J.Rigby, S.Mitra, T.K.Hazra.

ABSTRACT

The recently identified human NEIL2 (Nei-like-2) protein, a DNA glycosylase/AP lyase specific for oxidatively damaged bases, shares structural features and reaction mechanism with the Escherichia coli DNA glycosylases, Nei and Fpg. Amino acid sequence analysis of NEIL2 suggested it to have a zinc finger-like Nei/Fpg. However, the Cys-X2-His-X16-Cys-X2-Cys (CHCC) motif present near the C terminus of NEIL2 is distinct from the zinc finger motifs of Nei/Fpg, which are of the C4 type. Here we show the presence of an equimolar amount of zinc in NEIL2 by inductively coupled plasma mass spectrometry. Individual mutations of Cys-291, His-295, Cys-315, and Cys-318, candidate residues for coordinating zinc, inactivated the enzyme by abolishing its DNA binding activity. H295A and C318S mutants were also shown to lack bound zinc, and a significant change in their secondary structure was revealed by CD spectra analysis. Molecular modeling revealed Arg-310 of NEIL2 to be a critical residue in its zinc binding pocket, which is highly conserved throughout the Fpg/Nei family. A R310Q mutation significantly reduced the activity of NEIL2. We thereby conclude that the zinc finger motif in NEIL2 is essential for its structural integrity and enzyme activity.

Selected figure(s)

Figure 1.
FIG. 1. Putative zinc finger domain of NEIL2. A, amino acid sequence alignment of NEIL2 with E. coli Nei and Fpg. The C termini of Nei and Fpg were aligned with the C-terminal sequence of NEIL2. The position of the helix two-turn helix motif (H2TH) is indicated, and the coordinating amino acid residues forming the zinc finger motif were boxed. B, schematic diagram of the C terminus of NEIL2 bearing the putative zinc finger motif.

Figure 6.
FIG. 6. Model of residues 192-319 of NEIL2. A, structural alignment for NEIL2 and E. coli Fpg (PDB code 1K82 [PDB] ) template generated by 3DPSSM. Identical residues are indicated by asterisks. Residues that participate in coordination of zinc ion are highlighted in red and boldface. B, ribbon diagram of a model of C-terminal region of NEIL2 generated using MOLMOL (49). The helices (shown in green) form the helix two-turn helix motif that binds to DNA. CHCC-type -hairpin zinc finger is highlighted with coordinating residues Cys-291, His-295, Cys-315, and Cys-318. C, ribbon diagram of model of C-terminal region of NEIL2 with DNA generated with MOLMOL. The helices (shown in blue) form the helix two-turn helix motif that binds to DNA. CHCC-type -hairpin zinc finger is highlighted with coordinating residues Cys-291, His-295, Cys-315, and Cys-318. The zinc ion stabilizes -strands (shown in green) that is critical to position of the catalytic residue Arg-310, which is conserved in E. coli Fpg.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 47132-47138) copyright 2004.

Figures were selected by an automated process.