6BTC

SCCmec type IV LP1413 - nucleic acids binding protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17741 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystal Structure of an Unusual Single-Stranded DNA-Binding Protein Encoded by Staphylococcal Cassette Chromosome Elements.

Mir-Sanchis, I.Pigli, Y.Z.Rice, P.A.

(2018) Structure 26: 1144

  • DOI: 10.1016/j.str.2018.05.016

  • PubMed Abstract: 
  • Methicillin-resistant Staphylococcus aureus is a global public health threat. Methicillin resistance is carried on mobile genetic elements belonging to the staphylococcal cassette chromosome (SCC) family. The molecular mechanisms that SCC elements ex ...

    Methicillin-resistant Staphylococcus aureus is a global public health threat. Methicillin resistance is carried on mobile genetic elements belonging to the staphylococcal cassette chromosome (SCC) family. The molecular mechanisms that SCC elements exploit for stable maintenance and for horizontal transfer are poorly understood. Previously, we identified several conserved SCC genes with putative functions in DNA replication, including lp1413, which we found encodes a single-stranded DNA (ssDNA)-binding protein. We report here the 2.18 Å crystal structure of LP1413, which shows that it adopts a winged helix-turn-helix fold rather than the OB-fold normally seen in replication-related ssDNA-binding proteins. However, conserved residues form a hydrophobic pocket not normally found in winged helix-turn-helix domains. LP1413 also has a conserved but disordered C-terminal tail. As deletion of the tail does not significantly affect cooperative binding to ssDNA, we propose that it mediates interactions with other proteins. LP1413 could play several different roles in vivo.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The University of Chicago, 929 E. 57(th) St., Chicago, IL 60637, USA.,Department of Biochemistry and Molecular Biology, The University of Chicago, 929 E. 57(th) St., Chicago, IL 60637, USA. Electronic address: price@uchicago.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LP1413 - SCCmec type IV-encoded DNA binding protein
A, B
96Staphylococcus aureusMutation(s): 0 
Find proteins for Q0WXP5 (Staphylococcus aureus)
Go to UniProtKB:  Q0WXP5
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17741 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.220 
  • Space Group: P 61 2 2
  • Diffraction Data DOI: 
    10.15785/SBGRID/531 SBGrid
Unit Cell:
Length (Å)Angle (°)
a = 97.033α = 90.00
b = 97.033β = 90.00
c = 127.794γ = 120.00
Software Package:
Software NamePurpose
HKL-3000data scaling
PHENIXphasing
PHENIXrefinement
REFMACrefinement
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01 GM121655

Revision History 

  • Version 1.0: 2018-07-25
    Type: Initial release
  • Version 1.1: 2018-08-01
    Type: Data collection, Database references
  • Version 1.2: 2018-08-22
    Type: Data collection, Database references
  • Version 1.3: 2019-02-20
    Type: Author supporting evidence, Data collection
  • Version 1.4: 2019-07-17
    Type: Data collection, Refinement description