bioinformatics & structural biology
DESCRIPTION
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,* - PowerPoint PPT PresentationTRANSCRIPT
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
Thank for your attentionThank for your attention