B subunit of UvrABC (DNA repair system) complexed with a DNA strand
Bacillus caldotenax (bacteria)
DNA repair, which recognizes unwanted damages in DNA and correcting them, is one of the indispensable systems for all organisms. Nucleotide excision repair (NER) is one of the well-conserved system among living organisms. Compared to other DNA repair system, NER has distinct ability to repair relatively bulky damages such as thymine dimers.
In prokaryotes, NER cascade is a complex and multistep process, mediated by Uvr proteins, UvrA, UvrB and UvrC. At the beginning of the NER cascade, complex of damaged DNA, UvrA, and UvrB is formed. After damage identification, UvrA dissociates, whereas UvrB remains bound to the DNA and forms a stable preincision complex. And in the last step, UvrC binds to this complex and mediates the incision of both sides of the damaged region. UvrB is essential to NER system and plays a central role, involving recognition of damaged DNA directly and guiding damaged DNA to following incision. Although several crystal structure of UvrB DNA-free form have already solved, structural information of DNA recognition by UvrB had been lacking.
The structure shown here is the complex of UvrB and DNA from Bacillus caldotenax. This complex shows tight binding of UvrB and hairpin shape DNA, which is dramatically bent and forms a DNA hairpin (hpDNA). UvrB consists of 5 domains, 1a, 1b, 2, 3 and 4, whereas domain 4 is disordered in this complex. A highly conserved and flexible beta-hairpin connecting domains 1a and 1b is inserted between the DNA strands, and the 3’ DNA overhang of “inner” strand is behind the beta-hairpin and clamped by beta-hairpin and domain 1b. The base just behind the beta hairpin is flipped out and inserted in a narrow hydrophobic binding pocket formed by a beta hairpin and domain 1b, which gives a enough space for pi-stacking interaction between next base and Tyr96, the residue essential for formation of preincision complex. Tyr96 may stabilize the opening of the dsDNA by substituting for the space of flipped out base.
Although the authors of this paper admit that it is not clear whether the damage is located on the “inner” or “outer” strand, it is more easily explained if the damage is located on the inner strand at the position of G17.
Figure 1: The base alignment of binging hairpin shaped DNA strand. Black letters indicate disordered nucleotides. The F letter indicates fluorescein-adducted thymine (FldT, F11), which is partially ordered.
Figure 2: The structure of UvrB with cartoon expression, binding DNA strand with ball and stick (for backbone) and stick expression (for sidechain). White numbers indicate the base number of DNA strand. The outer strand consists of bases from 1 to 5, and the inner strand consists of bases from 13 to 19. The partial structure of base 11 (F11) is also shown. The double strand stem consists of 6 bases, from 1 to 3 and from 15 to 17. The important residue Tyr96 stablizing the separated DNA strands.
Protein Data Bank (PDB)
author: Miho Higurashi