5ZTC

Apo structure of TetR family transcription regulator Lmo2088 of Listeria monocytogenes EGDe


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

X-ray crystal structure of putative transcription regulator lmo2088 from Listeria monocytogenes.

Samad, A.Li, Y.Zhang, C.Chen, F.Zeng, W.Fan, X.Jin, T.

(2019) Biochem Biophys Res Commun 520: 434-440

  • DOI: 10.1016/j.bbrc.2019.10.033
  • Primary Citation of Related Structures:  
    5ZTC

  • PubMed Abstract: 
  • Listeria monocytogenes is a gram-positive food borne pathogen. The lmo2088 belongs to the TetR family of transcriptional regulators from L. monocytogenes. These transcriptional factors regulate multidrug resistance transporters in L. monocytogenes. Here, we report native protein crystal structure of lmo2088 at a resolution of 1 ...

    Listeria monocytogenes is a gram-positive food borne pathogen. The lmo2088 belongs to the TetR family of transcriptional regulators from L. monocytogenes. These transcriptional factors regulate multidrug resistance transporters in L. monocytogenes. Here, we report native protein crystal structure of lmo2088 at a resolution of 1.7 Å. Lmo2088 comprises of an N-terminal DNA binding domain and a variable C-terminal effector binding domain. Furthermore, we identified specific consensus sequences selected by systematic evolution of ligands by exponential enrichment in vitro. The specific binding of lmo2088 with DNA consensus sequence was validated by electrophoretic mobility shift assay, fluorescence polarization and isothermal titration calorimetry. We speculate that the structure of lmo2088 might provide an insight into the regulatory function of lmo2088 of L. monocytogenes.


    Organizational Affiliation

    Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China; Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China; CAS Center for Excellence in Molecular Cell Science, Shanghai, China. Electronic address: jint@ustc.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lmo2088 proteinA, B204Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: lmo2088
UniProt
Find proteins for Q8Y5H4 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
Explore Q8Y5H4 
Go to UniProtKB:  Q8Y5H4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.72α = 90
b = 41.96β = 90.37
c = 71.66γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2018-05-02 
  • Released Date: 2019-06-12 
  • Deposition Author(s): Samad, A., Jin, T.

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-12
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-13
    Changes: Data collection, Database references