Solution structure of the DNA- and RPA-binding domain of the human repair factor XPA

Abstract

The solution structure of the central domain of the human nucleotide excision repair protein XPA, which binds to damaged DNA and replication protein A (RPA), was determined by nuclear magnetic resonance (NMR) spectroscopy. The central domain consists of a zinc-containing subdomain and a C-terminal subdomain. The zinc-containing subdomain has a compact globular structure and is distinct from the zinc-fingers found in transcription factors. The C-terminal subdomain folds into a novel alpha/beta structure with a positively charged superficial cleft. From the NMR spectra of the complexes, DNA and RPA binding surfaces are suggested.

Domains in the XPA protein important in its role as a processivity factor

“…These were the N-terminal domain, which is needed for incision activity of the endonucleases involved in NER [20,21], and the central, DNA binding domain, which is needed for binding to damaged DNA (Fig. 4) [22][23][24]. Within the N-terminal domain of XPA is a region encoded by exon 2 that associates with ERCC1 and is essential for NER activity (Fig.…”

“…Within the central, DNA binding domain of the XPA protein (M98-F219) is the zinc-binding subdomain and a loop-rich subdomain (Figure 4) [22][23][24]26]. The zinc subdomain contains a zinc finger motif: Cys 105 -X 2 -Cys 108 -X 17 -Cys 126 -X 2 -Cys 129 [22][23][24]26].…”

“…The zinc subdomain contains a zinc finger motif: Cys 105 -X 2 -Cys 108 -X 17 -Cys 126 -X 2 -Cys 129 [22][23][24]26]. Replacement of any one of the cysteines by a serine leads to disruption of the zinc finger structure and NER [20,27].…”

“…4) [22][23][24]. It consists of a sheet-helix-loop region and a helix-turn-helix region, between which is a large basic cleft that plays an important role in DNA binding [23,24].…”

“…NMR studies indicate that the basic cleft in the loop-rich subdomain of the XPA binding domain could accommodate the phosphodiester backbone of double-stranded DNA [23,24]. Thus it is possible that the structure of XPA with its basic cleft could allow it to track along the DNA, searching for sites of damage in conjunction with XPC-hHR23B and RPA.…”