6GYZ

Crystal structure of GlmM from Staphylococcus aureus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Inhibition of the Staphylococcus aureus c-di-AMP cyclase DacA by direct interaction with the phosphoglucosamine mutase GlmM.

Tosi, T.Hoshiga, F.Millership, C.Singh, R.Eldrid, C.Patin, D.Mengin-Lecreulx, D.Thalassinos, K.Freemont, P.Grundling, A.

(2019) PLoS Pathog 15: e1007537-e1007537

  • DOI: 10.1371/journal.ppat.1007537
  • Primary Citation of Related Structures:  
    6GYY, 6GYX, 6GYZ, 6GYW

  • PubMed Abstract: 
  • c-di-AMP is an important second messenger molecule that plays a pivotal role in regulating fundamental cellular processes, including osmotic and cell wall homeostasis in many Gram-positive organisms. In the opportunistic human pathogen Staphylococcus ...

    c-di-AMP is an important second messenger molecule that plays a pivotal role in regulating fundamental cellular processes, including osmotic and cell wall homeostasis in many Gram-positive organisms. In the opportunistic human pathogen Staphylococcus aureus, c-di-AMP is produced by the membrane-anchored DacA enzyme. Inactivation of this enzyme leads to a growth arrest under standard laboratory growth conditions and a re-sensitization of methicillin-resistant S. aureus (MRSA) strains to ß-lactam antibiotics. The gene coding for DacA is part of the conserved three-gene dacA/ybbR/glmM operon that also encodes the proposed DacA regulator YbbR and the essential phosphoglucosamine mutase GlmM, which is required for the production of glucosamine-1-phosphate, an early intermediate of peptidoglycan synthesis. These three proteins are thought to form a complex in vivo and, in this manner, help to fine-tune the cellular c-di-AMP levels. To further characterize this important regulatory complex, we conducted a comprehensive structural and functional analysis of the S. aureus DacA and GlmM enzymes by determining the structures of the S. aureus GlmM enzyme and the catalytic domain of DacA. Both proteins were found to be dimers in solution as well as in the crystal structures. Further site-directed mutagenesis, structural and enzymatic studies showed that multiple DacA dimers need to interact for enzymatic activity. We also show that DacA and GlmM form a stable complex in vitro and that S. aureus GlmM, but not Escherichia coli or Pseudomonas aeruginosa GlmM, acts as a strong inhibitor of DacA function without the requirement of any additional cellular factor. Based on Small Angle X-ray Scattering (SAXS) data, a model of the complex revealed that GlmM likely inhibits DacA by masking the active site of the cyclase and preventing higher oligomer formation. Together these results provide an important mechanistic insight into how c-di-AMP production can be regulated in the cell.


    Organizational Affiliation

    Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphoglucosamine mutaseAB455Staphylococcus aureusMutation(s): 0 
Gene Names: 
glmMBTN44_13160EP54_06960EQ90_12990HMPREF3211_00023RK64_11470RK68_01815RK73_08340DD547_02193DQV53_12505FA040_09780G0V24_10060G0Z08_01370G0Z18_06585G6Y10_09070GO746_03845GO803_12340GO805_10895NCTC10654_02323NCTC10702_03404NCTC9944_02306SAMEA1029528_02077SAMEA1029547_01820SAMEA1029553_01828SAMEA1964876_02024SAMEA1965205_02011SAMEA1966505_01896SAMEA1969349_02032SAMEA1969845_02320SAMEA1971706_01876SAMEA1972827_02140SAMEA2076212_02089SAMEA2076218_02253SAMEA2076220_02241SAMEA2076226_02033SAMEA2076463_01683SAMEA2076464_01882SAMEA2076470_01858SAMEA2076472_01924SAMEA2076478_02070SAMEA2076480_01781SAMEA2076481_02040SAMEA2076743_01896SAMEA2076745_01995SAMEA2076746_01943SAMEA2076747_02006SAMEA2076749_01399SAMEA2076751_01884SAMEA2076752_01823SAMEA2076755_01778SAMEA2076756_01860SAMEA2076758_01789SAMEA2076759_01688SAMEA2076761_01333SAMEA2076762_02366SAMEA2076763_02392SAMEA2076764_02017SAMEA2076765_01830SAMEA2077023_01933SAMEA2077025_01812SAMEA2077027_01876SAMEA2077029_01917SAMEA2077031_02034SAMEA2077034_02388SAMEA2077035_01776SAMEA2077039_01857SAMEA2077040_01618SAMEA2077041_01812SAMEA2077044_02084SAMEA2077045_01696SAMEA2077046_01747SAMEA2077293_02049SAMEA2077294_01998SAMEA2077295_01880SAMEA2077297_01769SAMEA2077300_02015SAMEA2077301_01856SAMEA2077302_01798SAMEA2077303_01927SAMEA2077307_01671SAMEA2077832_01795SAMEA2078252_02127SAMEA2078256_01923SAMEA2078307_01968SAMEA2078308_01884SAMEA2078553_01874SAMEA2078558_02045SAMEA2078560_00656SAMEA2078569_02165SAMEA2078570_01971SAMEA2078572_00958SAMEA2078824_01792SAMEA2078837_01927SAMEA2079048_02216SAMEA2079051_01822SAMEA2079277_02451SAMEA2079503_01859SAMEA2079507_01900SAMEA2079724_02017SAMEA2079727_02320SAMEA2079728_00520SAMEA2079732_02241SAMEA2079742_02172SAMEA2079946_02307SAMEA2079949_02078SAMEA2079951_02184SAMEA2079952_02243SAMEA2079957_02347SAMEA2079958_02220SAMEA2079960_02175SAMEA2079961_02198SAMEA2079968_02230SAMEA2080329_02359SAMEA2080330_02311SAMEA2080334_02246SAMEA2080433_02367SAMEA2080812_02080SAMEA2080898_01780SAMEA2080900_02132SAMEA2080904_01782SAMEA2080913_01719SAMEA2081043_02075SAMEA2081053_01876SAMEA2081054_01765SAMEA2081055_01863SAMEA2081060_02280SAMEA2081211_01774SAMEA2081218_02221SAMEA2081341_02022SAMEA2081342_02132SAMEA2081349_02263SAMEA2081359_02192SAMEA2081362_02210SAMEA2081468_01830SAMEA2081474_02039SAMEA2081475_02000SAMEA2081476_01670SAMEA2081479_01741SAMEA2081480_02093SAMEA2081560_01894SAMEA2081561_01863SAMEA2081564_02098SAMEA2081567_01989SAMEA2081568_02091SAMEA2081569_01794SAMEA2081570_02098SAMEA2081571_01910SAMEA2081572_01893SAMEA2081573_01684SAMEA2081575_01808SAMEA2081577_01684SAMEA2081578_01991SAMEA2081579_02038SAMEA2081581_01633SAMEA2081582_02047SAMEA2081673_02120SAMEA2081674_02181SAMEA958766_02666SAMEA958770_00160SAMEA958772_02610SAMEA958778_02395SAMEA958779_01007SAMEA958785_01943SAMEA958793_01878SAMEA958798_00672SAMEA958804_01948SAMEA958810_02063SAMEA958836_02240SAMEA958838_02259SAMEA958846_01939SAMEA958848_01816SAMEA958855_01452SAMEA958858_01905SAMEA958870_00654SAMEA958898_02327SAMEA958906_01287SAMEA958924_02615SAMEA958925_01817SAMEA958951_00154SAMEA958953_01591SAMEA958961_00928SAMEA958979_01885SAMEA958995_02515

EC: 5.4.2.10
Find proteins for A0A0D6H967 (Staphylococcus aureus)
Explore A0A0D6H967 
Go to UniProtKB:  A0A0D6H967
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.653α = 90
b = 93.884β = 90
c = 156.308γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-01-23
    Type: Initial release
  • Version 1.1: 2019-01-30
    Changes: Data collection, Database references
  • Version 1.2: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.3: 2019-07-10
    Changes: Data collection