6JDG

Complexed crystal structure of PaSSB with ssDNA dT20 at 2.39 angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.388 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Complexed crystal structure of SSB reveals a novel single-stranded DNA binding mode (SSB)3:1: Phe60 is not crucial for defining binding paths.

Huang, Y.H.Lin, E.S.Huang, C.Y.

(2019) Biochem.Biophys.Res.Commun. 520: 353-358

  • DOI: 10.1016/j.bbrc.2019.10.036

  • PubMed Abstract: 
  • Single-stranded DNA-binding protein (SSB) is essential to cells as it participates in DNA metabolic processes, such as DNA replication, repair, and recombination. Escherichia coli SSB (EcSSB) tetramer cooperatively binds and wraps ssDNA in two major ...

    Single-stranded DNA-binding protein (SSB) is essential to cells as it participates in DNA metabolic processes, such as DNA replication, repair, and recombination. Escherichia coli SSB (EcSSB) tetramer cooperatively binds and wraps ssDNA in two major binding modes. In this study, we report the complex crystal structure of Pseudomonas aeruginosa SSB (PaSSB) with ssDNA dT20 at 2.39 Å resolution (PDB entry 6JDG) that revealed a new binding mode, namely, (SSB) 3:1 . In the (SSB) 65 mode revealed by the EcSSB-dC35 complex structure, all four subunits fully participate in the binding to ssDNA. However, only three subunits in the PaSSB tetramer can participate in wrapping ssDNA in the (SSB) 3:1 mode. The bound ssDNA in the PaSSB-ssDNA complex adopts an Ω-shaped conformation rather than a χ-shaped conformation in the (SSB) 65 mode possibly due to the disability of Phe60. Phe60 is known to play a critical role in defining DNA-binding paths and promoting the wrapping of ssDNA around SSB tetramers. However, it is not important in the (SSB) 3:1 mode. The ssDNA binding path revealed by our structural evidence suggests that ssDNA occupies half of the binding sites of the two subunits and slightly comes into contact with the ssDNA binding sites of the third subunit. Accordingly, we propose and sketch a possible wrapping mechanism of SSB via this novel ssDNA-binding mode, (SSB) 3:1 .


    Organizational Affiliation

    Department of Beauty Science, National Taichung University of Science and Technology, No.193, Sec.1, San-Min Rd., Taichung City, Taiwan.,School of Biomedical Sciences, Chung Shan Medical University, No.110, Sec.1, Chien-Kuo N. Rd., Taichung City, Taiwan; Department of Medical Research, Chung Shan Medical University Hospital, No.110, Sec.1, Chien-Kuo N. Rd., Taichung City, Taiwan. Electronic address: cyhuang@csmu.edu.tw.,School of Biomedical Sciences, Chung Shan Medical University, No.110, Sec.1, Chien-Kuo N. Rd., Taichung City, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Single-stranded DNA-binding protein
A, B, C, D
121Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 0 
Gene Names: ssb
Find proteins for P40947 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  P40947
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')E,F,G20synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.388 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.213 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 60.042α = 90.00
b = 60.042β = 90.00
c = 129.642γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
MOLREPphasing
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-12-11
    Type: Initial release