Bioinformatics structural biology
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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,*

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Bioinformatics & Structural Biology

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Bioinformatics structural biology

Bioinformatics & Structural Biology

M93360008

生技所 研一 劉怡萱


Bioinformatics structural biology

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


Bioinformatics structural biology

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


Bioinformatics structural biology

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.


Bioinformatics structural biology

  • 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.


Bioinformatics structural biology

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


Bioinformatics structural biology

  • 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.


Bioinformatics structural biology

  • 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).


Bioinformatics structural biology

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


The end

The End

Thank for your attention


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