6ABQ

Crystal structure of transcription factor from Listeria monocytogenes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structure-based molecular characterization and regulatory mechanism of the LftR transcription factor from Listeria monocytogenes: Conformational flexibilities and a ligand-induced regulatory mechanism.

Lee, C.Kim, M.I.Park, J.Hong, M.

(2019) PLoS One 14: e0215017-e0215017

  • DOI: 10.1371/journal.pone.0215017
  • Primary Citation of Related Structures:  
    6ABQ, 6ABT

  • PubMed Abstract: 
  • Listeria monocytogenes is a foodborne pathogen that causes listeriosis and can lead to serious clinical problems, such as sepsis and meningitis, in immunocompromised patients and neonates. Due to a growing number of antibiotic-resistant L. monocytogenes strains, listeriosis can steadily become refractory to antibiotic treatment ...

    Listeria monocytogenes is a foodborne pathogen that causes listeriosis and can lead to serious clinical problems, such as sepsis and meningitis, in immunocompromised patients and neonates. Due to a growing number of antibiotic-resistant L. monocytogenes strains, listeriosis can steadily become refractory to antibiotic treatment. To develop novel therapeutics against listeriosis, the drug resistance mechanism of L. monocytogenes needs to be determined. The transcription factor LftR from L. monocytogenes regulates the expression of a putative multidrug resistance transporter, LieAB, and belongs to the PadR-2 subfamily of the PadR family. Despite the functional significance of LftR, our molecular understanding of the transcriptional regulatory mechanism for LftR and even for the PadR-2 subfamily is highly limited. Here, we report the crystal structure of LftR, which forms a dimer and protrudes two winged helix-turn-helix motifs for DNA recognition. Structure-based mutational and comparative analyses showed that LftR interacts with operator DNA through a LftR-specific mode as well as a common mechanism used by the PadR family. Moreover, the LftR dimer harbors one intersubunit cavity in the center of the dimeric structure as a putative ligand-binding site. Finally, conformational flexibilities in the LftR dimer and in the cavity suggest that a ligand-induced regulatory mechanism would be used by the LftR transcription factor.


    Organizational Affiliation

    Division of Biological Science and Technology, Yonsei University, Wonju, Republic of Korea.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PadR family transcriptional regulatorB [auth A], A [auth B]114Listeria monocytogenesMutation(s): 0 
Gene Names: 
C7K50_07245CDR86_13565LmNIHS28_00834A6X98_02720A8L61_05580A8N58_02410A8N61_05245A9809_14535AAT74_01290AAU37_12855AB072_02880AB078_02020AB444_03425AB497_03540ABX06_14720ACG32_05400ACL84_04980ACT27_01785ACY06_02020AF066_01335AF108_09515AF133_01275AF143_05245AF286_04440AF305_12145AF314_02720AFS87_02815AFT97_07090AFX07_04945AFX17_01755AFX92_02520AFY08_04000AFY14_04005AK01_14225AK890_11065AMC15_01495AMC55_12010AOA88_02750AOE65_12725AOX90_07690AOX97_02490APD94_05305APE37_04760APE56_04960ARG07_02745ARG15_04835ARG48_02650ARG51_10070ARG88_04955ARH33_02490ARH85_02885ARJ20_09300ARL26_02025ARM02_05210ARP10_01325ARP98_08320ARS03_02760ARS65_02625ART25_00450ARU04_01310ARW58_01060ARW97_02625ARX85_08785ARX92_08395ARY17_02750ARY76_05150ARZ39_10760ARZ93_01335B1N06_12015B1N38_02030B1N39_09265B1N40_07010B1N45_11675B1N70_12880B1O10_13570B1O25_01290B1O28_00455B4X79_02835B4X80_02740B4X87_02825B4X92_02650B4Y34_05235B4Y36_05235B4Y40_02595B4Y47_10650B4Y49_04910B4Y57_05235B5H26_14225B5H46_14440BAB01_02570BBW72_02810BG064_03780BHW82_04850CCZ59_00150CK12_02410D1B71_12270D3521_03215D3B94_02840D6296_04740D9979_07450D9T24_01355DRA50_03045DU018_11245E0I39_10520E1006_10475E1017_12025E1054_07665E1A78_14970E1P77_01865E1T18_00440E1T71_00440E1V60_08180E1W03_07115E1W91_01310E1X40_13865E1Z01_05165E1Z38_09185E1Z66_05205E2C65_02385E3Y96_02430E3Z05_03885E7984_04755EAK17_01885EDI43_12065EF615_12320EGY33_12390EHM95_05485EIM30_06100EIO89_14605EP78_01860EP84_10135EPI21_04765EPI27_02840ES08_02755EVX67_01290EXZ73_13110EYW53_04940F0039_05010F0A38_12830F1F60_09135F3343_09835F3R75_01880F6515_09360FA835_10300FDP75_15695FDP88_01870FJL32_08395FJL36_10500FJU19_10360FL790_13275FLQ91_02115FLQ96_09220FLR03_14105FLR04_12690FM764_02585FMU94_04990FMZ78_10900FMZ80_10870FNX26_15275FORC68_0748FOZ78_02400FR205_11835FR217_11955FVI78_13130FZM62_13815G0Q62_000396G3O21_000877GIF79_06665GJW26_07320GNZ33_14035GON90_08710GRG85_10060GSE74_01255GUL94_02365GWY21_13150GX75_01560IO96_00455JE57_02530JI93_02810JL27_05240KV60_04875KW30_07515LH97_02645NI68_02575NI89_02565NY20_09295Q793_05250Q797_11370Q921_01925Q989_12095QJ36_06595SH25_11180SH48_14575TX60_14420TX70_00150X789_02490XN64_02595XN83_02785XU47_02020Y174_02575Y239_11165ZY91_02530

UniProt
Find proteins for L8DXR9 (Listeria monocytogenes)
Explore L8DXR9 
Go to UniProtKB:  L8DXR9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL (Subject of Investigation/LOI)
Query on CL

Download Ideal Coordinates CCD File 
C [auth B], D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.955α = 90
b = 73.955β = 90
c = 66.313γ = 120
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-07-23 
  • Released Date: 2019-06-05 
  • Deposition Author(s): Lee, C., Hong, M.

Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic Of2018R1A2B6001619
National Research Foundation (Korea)Korea, Republic Of2015R1D1A1A0105757

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-05
    Type: Initial release