PDBsum entry 1v1q

DNA binding

PDB id: 1v1q

Contents

Protein chains

111 a.a.

Ligands

CYS ×3

Waters ×134

References listed in PDB file

Key reference

Title

Crystal structure of prib, A primosomal DNA replication protein of escherichia coli.

Authors

J.H.Liu, T.W.Chang, C.Y.Huang, S.U.Chen, H.N.Wu, M.C.Chang, C.D.Hsiao.

Ref.

J Biol Chem, 2004, 279, 50465-50471. [DOI no: 10.1074/jbc.M406773200]

PubMed id

15383524

Abstract

PriB is one of the Escherichia coli varphiX-type primosome proteins that are required for assembly of the primosome, a mobile multi-enzyme complex responsible for the initiation of DNA replication. Here we report the crystal structure of the E. coli PriB at 2.1 A resolution by multi-wavelength anomalous diffraction using a mercury derivative. The polypeptide chain of PriB is structurally similar to that of single-stranded DNA-binding protein (SSB). However, the biological unit of PriB is a dimer, not a homotetramer like SSB. Electrophoretic mobility shift assays demonstrated that PriB binds single-stranded DNA and single-stranded RNA with comparable affinity. We also show that PriB binds single-stranded DNA with certain base preferences. Based on the PriB structural information and biochemical studies, we propose that the potential tetramer formation surface and several other regions of PriB may participate in protein-protein interaction during DNA replication. These findings may illuminate the role of PriB in varphiX-type primosome assembly.

Figure 2.
FIG. 2. A, ribbon diagram of a PriB dimer compared with those of EcoSSB and HsmtSSB tetramers. The monomers are colored differently. Side chains of Val-6 in the PriB dimer, Ile-9 in the EcoSSB tetramer, and His-18 in the HsmtSSB tetramer are shown as stick models. B, electrostatic potential comparison of the dimer-dimer interfaces of EcoSSB and HsmtSSB, as well as the putative region of the PriB dimer. For simplicity, the L[23] of each dimer is omitted in this diagram. Positive and negative potentials are shown in blue and red, respectively, whereas charge residues of one monomer are labeled in yellow. The black dotted line indicates the monomer-monomer interface of each dimer. Single letter amino acid abbreviations are used with position numbers. MSMS (58) was used to calculate the molecular surface contours, and the surface electrostatic potential was calculated using MEAD (59).

Figure 5.
FIG. 5. Comparisons of cysteinylated and free cysteine residues on a PriB dimer. Cys-12 (C12) and Cys-27 (C27) of monomer A (designated by the letter A in parentheses) are shown in panels A and B, respectively. Cys-12 and Cys-27 of monomer B (designated by the letter B in parentheses) are shown in panels C and D, respectively, for comparison. Cysteinyl moieties are shown as ball-and-stick models, whereas residues surrounding those cysteinyl moieties are shown as stick models and labeled using single letter amino acid abbreviations with position numbers. The electron density maps contoured at 1 show cysteinylated cysteines as orange mesh. The coordinating waters are presented as cyan balls. The disulfide bonds are shown as yellow dotted lines, and the hydrogen bonds are shown as brown dotted lines. In panel D, which shows the free Cys-27 of monomer B, a stick model of Cys-27 of monomer A is presented in brown as a comparison.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 50465-50471) copyright 2004.