Human nucleotide excision repair protein XPA: H-1 NMR and CD solution studies of a synthetic peptide fragment corresponding to the zinc-binding domain (101-141)

A peptide corresponding to residues 101-141 of the human nucleotide excision repair protein XPA was synthesized with an isoleucine substituted for L138 and its solution structure studied by circular dichroism and homonuclear H-1 NMR spectroscopy. The peptide, (XPA-41), contains a C-4-type zinc-binding motif, C105-(X)(2)-C108-(X)(17)-C126-(X)(2)-C129, which XPA requires for damaged-DNA binding activity. The proton resonances of XPA-41 without zinc (apoXPA-41) were assigned using homonuclear TOCSY, NOESY and DQF-COSY data and show the ape-zinc peptide is a random coil. The peptide was folded with the addition of 1.2 equivalents of ZnCl2 in dilute solution at pH 4.0. Electrospray ionization mass spectroscopy illustrated an increase in the molecular weight of XPA-41 by 65 amu. Circular dichroism spectra of the zinc-folded peptide (zXPA-41) showed the acquisition of elements of secondary structure. Such a conclusion was confirmed with H-1 NMR data collected at 25 degrees C, pH 6.3. H-alpha-secondary shifts and NOE patterns indicate that regions V102-C105 and G109-F112 form an anti-parallel beta-sheet and residues N128-K137 form a nascent alpha-helix. Rapid exchange of most amide resonances between S115-C126 prohibited unambiguous assignment of all the proton resonances in this region. However, a 1.19 ppm downfield shift of the H-alpha resonance of T125 relative to the ape-zinc peptide, together with downfield shifted H-alpha resonances for the adjacent residues (P124 and L123), suggest a second beta-sheet is present in the S115-C126 region. On the basis of structural similarities to GATA-1 (Science 261:438-446), a homology generated structure for zXPA-41 was made, using GATA-1 as the template, which satisfied all the observed NOEs. Using the hybrid homology-NMR based zXPA-41 structure and analogy to GATA-1, models for the role played by the zinc-binding core (101-141) of XPA in DNA damage recognition are proposed.