4L9N

Crystal structure of MepR A103V mutant from multidrug resistant S. aureus clinical isolate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The molecular mechanisms of allosteric mutations impairing MepR repressor function in multidrug-resistant strains of Staphylococcus aureus.

Birukou, I.Tonthat, N.K.Seo, S.M.Schindler, B.D.Kaatz, G.W.Brennan, R.G.

(2013) mBio 4: e00528-e00513

  • DOI: 10.1128/mBio.00528-13
  • Primary Citation of Related Structures:  
    4LD5, 4L9T, 4L9V, 4L9J, 4L9N

  • PubMed Abstract: 
  • Overexpression of the Staphylococcus aureus multidrug efflux pump MepA confers resistance to a wide variety of antimicrobials. mepA expression is controlled by MarR family member MepR, which represses mepA and autorepresses its own production. Mutations in mepR are a primary cause of mepA overexpression in clinical isolates of multidrug-resistant S ...

    Overexpression of the Staphylococcus aureus multidrug efflux pump MepA confers resistance to a wide variety of antimicrobials. mepA expression is controlled by MarR family member MepR, which represses mepA and autorepresses its own production. Mutations in mepR are a primary cause of mepA overexpression in clinical isolates of multidrug-resistant S. aureus. Here, we report crystal structures of three multidrug-resistant MepR variants, which contain the single-amino-acid substitution A103V, F27L, or Q18P, and wild-type MepR in its DNA-bound conformation. Although each mutation impairs MepR function by decreasing its DNA binding affinity, none is located in the DNA binding domain. Rather, all are found in the linker region connecting the dimerization and DNA binding domains. Specifically, the A103V substitution impinges on F27, which resolves potential steric clashes via displacement of the DNA binding winged-helix-turn-helix motifs that lead to a 27-fold reduction in DNA binding affinity. The F27L substitution forces F104 into an alternative rotamer, which kinks helix 5, thereby interfering with the positioning of the DNA binding domains and decreasing mepR operator affinity by 35-fold. The Q18P mutation affects the MepR structure and function most significantly by either creating kinks in the middle of helix 1 or completely unfolding its C terminus. In addition, helix 5 of Q18P is either bent or completely dissected into two smaller helices. Consequently, DNA binding is diminished by 2,000-fold. Our structural studies reveal heretofore-unobserved allosteric mechanisms that affect repressor function of a MarR family member and result in multidrug-resistant Staphylococcus aureus.


    Organizational Affiliation

    Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MepRA, B145Staphylococcus aureusMutation(s): 1 
Gene Names: 
mepRBN1321_80052BTN44_11220DD547_00321DDL17_12505DQV20_04900DQV53_02015E3A28_07080E3K14_01680E4U00_07045EP54_02880EQ90_08705ERS072840_01506FA040_06450FVP29_16075G0V24_02365G0X12_07640G0X27_10000G0Y02_02300G0Z08_02615G6W67_03610G6W97_10850G6X24_05290G6X31_13635G6X35_08530G6Y10_02445G6Y24_06545G6Y28_10025G6Y30_16190GF545_04600GIX97_11475GO677_07370GO706_13580GO746_06035GO788_13690GO793_15615GO803_06190GO810_09515GO821_13400GO894_01000GO915_02925GO941_13505GO942_09445HMPREF2819_05630M1K003_0421NCTC10654_00435NCTC10702_00659NCTC10988_00500NCTC5664_00388NCTC7878_00347NCTC9944_00351RK64_02240SAMEA1029528_01243SAMEA1029547_00434SAMEA1029553_01009SAMEA1469856_01570SAMEA1469884_01591SAMEA1531680_00045SAMEA1531701_01842SAMEA1964876_01770SAMEA1965205_01695SAMEA1966505_01676SAMEA1969349_01757SAMEA1969845_00148SAMEA1971706_00716SAMEA1972827_00318SAMEA2076212_00102SAMEA2076218_00102SAMEA2076220_01289SAMEA2076226_00840SAMEA2076463_01493SAMEA2076464_01433SAMEA2076470_01651SAMEA2076472_01499SAMEA2076478_01267SAMEA2076480_01490SAMEA2076481_01200SAMEA2076743_00651SAMEA2076745_00154SAMEA2076746_01069SAMEA2076747_01445SAMEA2076749_01836SAMEA2076751_01567SAMEA2076752_00451SAMEA2076755_01339SAMEA2076756_01397SAMEA2076758_01316SAMEA2076759_01398SAMEA2076761_01127SAMEA2076762_00322SAMEA2076763_01145SAMEA2076764_00314SAMEA2076765_01029SAMEA2077023_00314SAMEA2077025_01665SAMEA2077027_01657SAMEA2077029_01599SAMEA2077031_01780SAMEA2077034_00977SAMEA2077035_01038SAMEA2077039_00451SAMEA2077040_01300SAMEA2077041_00312SAMEA2077044_01717SAMEA2077045_01227SAMEA2077046_01587SAMEA2077293_01330SAMEA2077294_01245SAMEA2077295_01533SAMEA2077297_01608SAMEA2077300_00789SAMEA2077301_01531SAMEA2077302_01140SAMEA2077303_01612SAMEA2077307_01560SAMEA2077832_00959SAMEA2078252_01456SAMEA2078256_01518SAMEA2078307_01370SAMEA2078308_01488SAMEA2078553_01410SAMEA2078558_01038SAMEA2078560_01265SAMEA2078569_01498SAMEA2078570_01765SAMEA2078572_01479SAMEA2078824_01508SAMEA2078837_01152SAMEA2079048_01645SAMEA2079051_01347SAMEA2079277_01516SAMEA2079291_01438SAMEA2079503_01291SAMEA2079507_00212SAMEA2079512_00843SAMEA2079517_00964SAMEA2079724_00621SAMEA2079727_01296SAMEA2079728_00319SAMEA2079732_00148SAMEA2079742_00103SAMEA2079946_00319SAMEA2079949_00319SAMEA2079951_00869SAMEA2079952_00148SAMEA2079957_00148SAMEA2079958_00148SAMEA2079960_01348SAMEA2079961_01122SAMEA2079968_00103SAMEA2080329_00434SAMEA2080330_00434SAMEA2080334_00319SAMEA2080433_00148SAMEA2080812_01602SAMEA2080898_01469SAMEA2080900_01748SAMEA2080904_01627SAMEA2080913_01657SAMEA2081043_01093SAMEA2081053_01670SAMEA2081054_01575SAMEA2081055_01716SAMEA2081060_01547SAMEA2081211_01443SAMEA2081213_01544SAMEA2081218_00714SAMEA2081341_00671SAMEA2081342_00102SAMEA2081349_00103SAMEA2081359_00857SAMEA2081362_00340SAMEA2081468_00949SAMEA2081474_01040SAMEA2081475_00417SAMEA2081476_01194SAMEA2081479_01126SAMEA2081480_00664SAMEA2081560_01492SAMEA2081561_01694SAMEA2081564_01320SAMEA2081567_00743SAMEA2081568_01317SAMEA2081569_01453SAMEA2081570_01319SAMEA2081571_01346SAMEA2081572_01621SAMEA2081573_01635SAMEA2081575_00451SAMEA2081577_01029SAMEA2081578_01491SAMEA2081579_01617SAMEA2081581_01584SAMEA2081582_01828SAMEA2081673_00102SAMEA2081674_00102SAMEA958766_00341SAMEA958770_00807SAMEA958772_00476SAMEA958778_00711SAMEA958779_00294SAMEA958785_00429SAMEA958793_00444SAMEA958798_01549SAMEA958804_01327SAMEA958810_01678SAMEA958836_01100SAMEA958838_00758SAMEA958845_00151SAMEA958846_00103SAMEA958848_01334SAMEA958855_01005SAMEA958858_00724SAMEA958870_01265SAMEA958906_02324SAMEA958924_00721SAMEA958925_00739SAMEA958951_01852SAMEA958953_00475SAMEA958961_01190SAMEA958979_00148SAMEA958987_01171SAMEA958995_01260SAST44_03215SAST45_04190

Find proteins for Q5Y812 (Staphylococcus aureus)
Explore Q5Y812 
Go to UniProtKB:  Q5Y812
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.793α = 90
b = 95.125β = 90
c = 105.614γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-11
    Type: Initial release
  • Version 1.1: 2013-10-30
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description