4PQK

C-Terminal domain of DNA binding protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.241 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Mechanism of staphylococcal multiresistance plasmid replication origin assembly by the RepA protein.

Schumacher, M.A.Tonthat, N.K.Kwong, S.M.Chinnam, N.B.Liu, M.A.Skurray, R.A.Firth, N.

(2014) Proc Natl Acad Sci U S A 111: 9121-9126

  • DOI: 10.1073/pnas.1406065111
  • Primary Citation of Related Structures:  
    5KBJ, 4PQK, 4PQL, 4PT7, 4PTA

  • PubMed Abstract: 
  • The staphylococcal multiresistance plasmids are key contributors to the alarming rise in bacterial multidrug resistance. A conserved replication initiator, RepA, encoded on these plasmids is essential for their propagation. RepA proteins consist of flexibly linked N-terminal (NTD) and C-terminal (CTD) domains ...

    The staphylococcal multiresistance plasmids are key contributors to the alarming rise in bacterial multidrug resistance. A conserved replication initiator, RepA, encoded on these plasmids is essential for their propagation. RepA proteins consist of flexibly linked N-terminal (NTD) and C-terminal (CTD) domains. Despite their essential role in replication, the molecular basis for RepA function is unknown. Here we describe a complete structural and functional dissection of RepA proteins. Unexpectedly, both the RepA NTD and CTD show similarity to the corresponding domains of the bacterial primosome protein, DnaD. Although the RepA and DnaD NTD both contain winged helix-turn-helices, the DnaD NTD self-assembles into large scaffolds whereas the tetrameric RepA NTD binds DNA iterons using a newly described DNA binding mode. Strikingly, structural and atomic force microscopy data reveal that the NTD tetramer mediates DNA bridging, suggesting a molecular mechanism for origin handcuffing. Finally, data show that the RepA CTD interacts with the host DnaG primase, which binds the replicative helicase. Thus, these combined data reveal the molecular mechanism by which RepA mediates the specific replicon assembly of staphylococcal multiresistant plasmids.


    Organizational Affiliation

    School of Biological Sciences, University of Sydney, Sydney, NSW 2006, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Maltose ABC transporter periplasmic protein, Truncated replication protein RepAA, B, C, D487Escherichia coli str. K-12 substr. MC4100Staphylococcus aureus
This entity is chimeric
Mutation(s): 0 
Gene Names: malEBN896_3748
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Find proteins for B1B3N6 (Staphylococcus aureus)
Explore B1B3N6 
Go to UniProtKB:  B1B3N6
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranoseE, F, G, H3 N/A Oligosaccharides Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900009
Query on PRD_900009
E, F, G, Halpha-maltotrioseOligosaccharide /  Nutrient

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.241 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.22α = 107.67
b = 93.668β = 108.3
c = 100.806γ = 84.93
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-18
    Type: Initial release
  • Version 1.1: 2014-07-23
    Changes: Database references
  • Version 1.2: 2017-08-09
    Changes: Source and taxonomy
  • Version 1.3: 2017-11-22
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary