6ECI

Structure of the FAD binding protein MSMEG_5243 from Mycobacterium smegmatis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

FAD-sequestering proteins protect mycobacteria against hypoxic and oxidative stress.

Harold, L.K.Antoney, J.Ahmed, F.H.Hards, K.Carr, P.D.Rapson, T.Greening, C.Jackson, C.J.Cook, G.M.

(2019) J Biol Chem 294: 2903-2912

  • DOI: https://doi.org/10.1074/jbc.RA118.006237
  • Primary Citation of Related Structures:  
    6ECI

  • PubMed Abstract: 

    The ability to persist in the absence of growth triggered by low oxygen levels is a critical process for the survival of mycobacterial species in many environmental niches. MSMEG_5243 ( fsq ), a gene of unknown function in Mycobacterium smegmatis , is up-regulated in response to hypoxia and regulated by DosRDosS/DosT, an oxygen- and redox-sensing two-component system that is highly conserved in mycobacteria. In this communication, we demonstrate that MSMEG_5243 is a f lavin- seq uestering protein and henceforth refer to it as Fsq. Using an array of biochemical and structural analyses, we show that Fsq is a member of the diverse superfamily of flavin- and deazaflavin-dependent oxidoreductases (FDORs) and is widely distributed in mycobacterial species. We created a markerless deletion mutant of fsq and demonstrate that fsq is required for cell survival during hypoxia. Using fsq deletion and overexpression, we found that fsq enhances cellular resistance to hydrogen peroxide treatment. The X-ray crystal structure of Fsq, solved to 2.7 Å, revealed a homodimeric organization with FAD bound noncovalently. The Fsq structure also uncovered no potential substrate-binding cavities, as the FAD is fully enclosed, and electrochemical studies indicated that the Fsq:FAD complex is relatively inert and does not share common properties with electron-transfer proteins. Taken together, our results suggest that Fsq reduces the formation of reactive oxygen species (ROS) by sequestering free FAD during recovery from hypoxia, thereby protecting the cofactor from undergoing autoxidation to produce ROS. This finding represents a new paradigm in mycobacterial adaptation to hypoxia.


  • Organizational Affiliation

    From the Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
132Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: MSMEI_5105
UniProt
Find proteins for I7GF07 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore I7GF07 
Go to UniProtKB:  I7GF07
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI7GF07
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth G]
CA [auth H]
DA [auth I]
EA [auth L]
AA [auth E],
BA [auth G],
CA [auth H],
DA [auth I],
EA [auth L],
FA [auth N],
GA [auth N],
HA [auth O],
IA [auth Q],
JA [auth Q],
KA [auth S],
LA [auth S],
U [auth A],
W [auth B],
X [auth C],
Y [auth D],
Z [auth E]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
V [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.268α = 90
b = 186.039β = 90
c = 195.388γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)Australia--

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-26
    Type: Initial release
  • Version 1.1: 2019-01-16
    Changes: Data collection, Database references
  • Version 1.2: 2019-03-06
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Refinement description