ABSTRACT
Specific Protein Catalytic Reaction Primary Reference PDB Entry
Anacystis nidulans DNA photolyase
Repairs pyrimidine dimers via photo-induced cleavage of the cyclobutane ring
71 1tez
G lucosy Itransferases
T4 bacteriophage BGT Transfers the glucose moiety of UDP-glucose to the 5-hydroxymethylC bases making p-glucosidic bond
16 1m5r
T4 bacteriophage AGT Transfers the glucose moiety of UDP-glucose to the 5-hydroxymethylC bases making a-glucosidic bond
112 1y8z
Sequence-specific endonucleases R.HinPII Cleaves phosphodiester bonds on both
strands of a recognition site 113 2flc
R.Ecl18kl Cleaves phosphodiester bonds on both strands of a recognition site
5 2fqz
R.PspGI Cleaves phosphodiester bonds on both strands of a recognition site
96 3bm3
Tn5 transposase Excises and integrates a transposon 114 Imuh
Other DNA binding proteins
SRA domain of UHRF1 (also known as ICBP90, Np95)
Directs Dnmtl methylation to hemi-methylated CpG sites
6-8 2zkf 3clz 2zo1
some other systems (see Table 1). Crystallographic studies showed that DNA base flipping comes in a variety of flavors (see Fig. 1) such as sole flipping of the target base itself,116 flipping of a base located on the opposite DNA strand to the target base (repair enzymes)17,18 or flipping of both nucleosides of a target base pair (repair enzymes, M.EcoDam, restriction endonucleases).5,19,20 In many cases, a concerted bending of the DNA helix is also observed.16,20
Although crystal structures reveal many structural details at atomic resolution, they provide only static snapshots, usually at the end of a flipping pathway; many dynamic and mechanistic aspects can only be discerned using other methods (see below). Thus, crystallography lays down a structural basis for further solution studies. An important extension of the method is the use of DNA substrates containing conformationally restricted nucleotide analogs, or mutant proteins to trap base-flipping intermediates.21,22 However, interpretation of such experiments requires utmost caution since chemical alterations to a system may cause unnatural conformations in the target nucleotide.
