PDBsum entry 1xna

DNA binding protein

PDB id: 1xna

Contents

Protein chain

151 a.a. *

* Residue conservation analysis

PDB id:

1xna

Name:

DNA binding protein

Title:

Nmr solution structure of the single-strand break repair protein xrcc1-n-terminal domain

Structure:

Protein (DNA-repair protein xrcc1). Chain: a. Fragment: n-terminal domain, residues 1-183. Residues 152-183 are disordered and not shown.. Synonym: xrcc1-ntd. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Cellular_location: nucleus. Gene: xrcc1. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

1 models

Authors:

A.Marintchev,G.P.Mullen

Key ref:

A.Marintchev et al. (1999). Solution structure of the single-strand break repair protein XRCC1 N-terminal domain. Nat Struct Biol, 6, 884-893. PubMed id: 10467102 DOI: 10.1038/12347

Date:

27-Feb-99 Release date: 01-Sep-99

Protein chain

P18887  (XRCC1_HUMAN) -  DNA repair protein XRCC1 from Homo sapiens

Seq: 633 a.a.

Struc: 151 a.a.

DOI no: 10.1038/12347

Nat Struct Biol 6:884-893 (1999)

PubMed id: 10467102

Solution structure of the single-strand break repair protein XRCC1 N-terminal domain.

A.Marintchev, M.A.Mullen, M.W.Maciejewski, B.Pan, M.R.Gryk, G.P.Mullen.

ABSTRACT

XRCC1 functions in the repair of single-strand DNA breaks in mammalian cells and forms a repair complex with beta-Pol, ligase III and PARP. Here we describe the NMR solution structure of the XRCC1 N-terminal domain (XRCC1 NTD). The structural core is a beta-sandwich with beta-strands connected by loops, three helices and two short two-stranded beta-sheets at each connection side. We show, for the first time, that the XRCC1 NTD specifically binds single-strand break DNA (gapped and nicked). We also show that the XRCC1 NTD binds a gapped DNA-beta-Pol complex. The DNA binding and beta-Pol binding surfaces were mapped by NMR and found to be well suited for interaction with single-strand gap DNA containing a 90 degrees bend, and for simultaneously making contacts with the palm-thumb of beta-Pol in a ternary complex. The findings suggest a mechanism for preferential binding of the XRCC1 NTD to flexible single-strand break DNA.

Selected figure(s)

Figure 2.
Figure 2. The NMR solution structure of the XRCC1 NTD. a, Overlay of the 23 structural conformers for residues 3−151 in stereo. The superimposition utilized all -strands. Residues 1, 2 and 152−183 are disordered. b, Ribbon representation of the average solution structure for residues 3−151. c, Overlay of the 23 NMR conformers showing the packing of hydrophobic side chains. Structures were displayed using the molecular graphics program MOLMOL^46.

Figure 9.
Figure 9. Ribbon overlay of the -strands in the XRCC1 NTD (violet) and the galactose binding domain (yellow) from sialidase (accession code 1EUU). The XRCC1 NTD shows no sequence homology with the galactose binding domains. The bulged residue 89 in the XRCC1 NTD was not included in the superimposition. Dali (version 2.0) was used in the search for structural neighbors^47.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (1999, 6, 884-893) copyright 1999.

Figures were selected by an automated process.