bioinformatics structural biology
Skip this Video
Download Presentation
Bioinformatics & Structural Biology

Loading in 2 Seconds...

play fullscreen
1 / 10

Bioinformatics & Structural Biology - PowerPoint PPT Presentation

  • Uploaded on

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

I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
Download Presentation

PowerPoint Slideshow about 'Bioinformatics & Structural Biology' - oakley

An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.

- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript
bioinformatics structural biology

Bioinformatics & Structural Biology


生技所 研一 劉怡萱

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
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

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


  • 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


  • Give some different ideas
the end

The End

Thank for your attention