Bioinformatics & Structural BiologyBioinformatics & Structural BiologyBioinformatics & Structural BiologyBioinformatics & Structural Biology

M93360008生技所 研一 劉怡萱

M93360008生技所 研一 劉怡萱

Crystal Structure of PriB, a Component ofCrystal Structure of PriB, a Component ofthe Escherichia coli Replication Restart the Escherichia coli Replication Restart PrimosomePrimosome

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

PDB Code : 1txy

Classification : DNA binding protein Exp. Method : X-ray Diffraction Structure : Primosomal replication protein N Chain : a, b. Engineered: yesSource : Escherichia coli. Bacteria. Gene: prib, b4201. Expressed in: escherichia coli.Resolution : 2.0 ÀR-factor : 0.260 (Statistical factor)R-free : 0.285 (Statistical factor)Authors : J.L.Keck,M.Lopper,J.M.HoltonDate : 06-Jul-04

Polymer Chains : A, BResidues ;Atoms : 208,1515

The PDB Structure summary of PriB

Structural similarityof 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.

E. coli PriB, revealing a dimer that consists of a single structural domain formed by two oligonucleotide/oligosaccharide binding (OB) folds.

The analysis on the crystal structure of PriB

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 WorkFurther 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 EndThe End

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