Structural Insight into the DNA-Binding Mode of the Primosomal Proteins PriA, PriB, and DnaT
Figure 3
(a) Amino acid sequence alignment of KpPriA. An alignment consensus of 150 sequenced PriA homologs by the program ConSurf reveals the degree of variability at each position along the primary sequence. Highly variable amino acids are colored teal, whereas those highly conserved are colored burgundy. A consensus sequence was established by determining the most commonly found amino acid residue at each position relative to the primary sequence of KpPriA. The N-terminal 19–219 amino acid residues in PriA are not highly conserved. Asp17, located in the 3′BD of EcPriA, is crucial for the 3′ base-non-selective recognition of DNA, and Arg697, located in the CTD of KpPriA, is crucial for the SSB-Ct binding and induction of structural changes in the SSB-DNA complex; both are significantly invariable. (b) Crystal structure of KpPriA. KpPriA has six subdomains (Protein Data Bank entry: 4NL4), namely, a 3′ DNA-binding domain (3′BD; orange), a winged-helix domain (WH; green), two lobes of the helicase core (colored hot pink and blue, resp.), a Cys-rich region (CRR; dark blue), and a C-terminal domain (CTD; red). 3′BD and WH comprise the N-terminal DNA-binding domain (DBD), and the other four subdomains (two lobes of the helicase core, CRR, and CTD) comprise the helicase domain (HD). (c) Putative DNA-binding mode of KpPriA. The DNA-binding models of KpPriA are directly constructed by manually superimposing the KpPriA with DNA-bound crystal structure of Hel308 (Protein Data Bank entry: 2P6R), RecQ1 (Protein Data Bank entry: 2WWY), PcrA (Protein Data Bank entry: 3PJR), and RecG (Protein Data Bank entry: 1GM5). Considering the known ssDNA-binding site at DBD and the putative wedge element in KpPriA located at CRR, KpPriA may use the Hel308-based model to bind DNA. The β-hairpin, an important motif for DNA strand separation by helicase, is colored in magenta.
