Bioinformatics & Structural Biology

1. Bioinformatics & Structural Biology M93360008 生技所 研一 劉怡萱

2. Crystal Structure of PriB, a Component of the Escherichia coli Replication Restart Primosome • Structure, Vol. 12, 1967–1975, November, 2004 • Matthew Lopper,1 James M. Holton,2 • and James L. Keck1,* • ( 1Department of Biomolecular Chemistry • University of Wisconsin Medical School • 2Physical Biosciences Division • Lawrence Berkeley National Laboratory ) • The PDB ID of PriB: 1TXY

3. The PDB Structure summary of PriB PDB Code: 1txy Classification: DNA binding protein Exp. Method: X-ray Diffraction Structure : Primosomal replication protein N Chain : a, b. Engineered: yes Source: Escherichia coli. Bacteria. Gene: prib, b4201. Expressed in: escherichia coli. Resolution: 2.0 À R-factor : 0.260 (Statistical factor) R-free: 0.285 (Statistical factor) Authors: J.L.Keck,M.Lopper,J.M.Holton Date: 06-Jul-04 Polymer Chains :A, B Residues ;Atoms : 208,1515

4. The analysis on the crystal structure of PriB • E. coli PriB, revealing a dimer that consists of a single structural domain formed by two oligonucleotide/oligosaccharide binding (OB) folds. • Structural similarity • of PriB to single-stranded DNA binding proteins reveals insights into its mechanisms of DNA binding. • The structure further establishes a putative protein interaction surface that may contribute to the role of PriB in primosome assembly by facilitating interactions with PriA and DnaT. • This is the first high-resolution structure of any of the proteins involved in oriC-independent replisome loading and provides unique insight into a critical aspect of genome maintenance in E. coli.

5. Briefly, the PriB monomer structure has two pleated β-sheets capped by a small α-helix located between the third and the fourth strands to form a β-barrel The core of the -barrel is filled with hydrophobic residues.

6. The structure shows that PriB forms a homodimeric β-barrel with two oligonucleotide/oligosaccharide binding (OB) folds.

7. 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.

8. Interestingly, of the eight lysine residues of the PriB dimer, only Lys82 is positionally conserved with a lysine residue of SSB involved in contacting nucleic acid, Lys87. Located at the base of the L45 loop, PriB Lys82 appears to be in a prime position to make contacts with ssDNA (Figure 4A).

9. Further Work • To understand the parameters of Structural Biology (ex: R-factor 、R-free 、Space Group ) • To compare the paper “Crystal Structure of PriB, a Primosomal DNA Replication Protein of Escherichia coli*” in JBC 2004 with this paper (§Institute of Molecular Biology, Academia Sinica) • To analyze the basic properties of PriB by Swiss-Pdb Viewer • To observe the crystal structure of the E. coli PriB homodimer by Swiss-Pdb Viewer • To compare the crystal structure of the E. coli PriB homodimer with the hetertetramer of SSB by Swiss-Pdb Viewer • Give some different ideas

10. The End Thank for your attention