5EY9

Structure of FadD32 from Mycobacterium marinum complexed to AMPC12

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 

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This is version 1.2 of the entry. See complete history. 


Literature

Insight into Structure-Function Relationships and Inhibition of the Fatty Acyl-AMP Ligase (FadD32) Orthologs from Mycobacteria.

Guillet, V., Galandrin, S., Maveyraud, L., Ladeveze, S., Mariaule, V., Bon, C., Eynard, N., Daffe, M., Marrakchi, H., Mourey, L.

(2016) J Biol Chem 291: 7973-7989

  • DOI: 10.1074/jbc.M115.712612
  • Primary Citation of Related Structures:  
    5EY8, 5EY9

  • PubMed Abstract: 

    • Mycolic acids are essential components of the mycobacterial cell envelope, and their biosynthetic pathway is one of the targets of first-line antituberculous drugs. This pathway contains a number of potential targets, including some that have been identified only recently and have yet to be explored ...

    Mycolic acids are essential components of the mycobacterial cell envelope, and their biosynthetic pathway is one of the targets of first-line antituberculous drugs. This pathway contains a number of potential targets, including some that have been identified only recently and have yet to be explored. One such target, FadD32, is required for activation of the long meromycolic chain and is essential for mycobacterial growth. We report here an in-depth biochemical, biophysical, and structural characterization of four FadD32 orthologs, including the very homologous enzymes fromMycobacterium tuberculosisandMycobacterium marinum Determination of the structures of two complexes with alkyl adenylate inhibitors has provided direct information, with unprecedented detail, about the active site of the enzyme and the associated hydrophobic tunnel, shedding new light on structure-function relationships and inhibition mechanisms by alkyl adenylates and diarylated coumarins. This work should pave the way for the rational design of inhibitors of FadD32, a highly promising drug target.

    Organizational Affiliation: 

    From the Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse, France lionel.mourey@ipbs.fr.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Long-chain-fatty-acid--AMP ligase FadD32A, B629Mycobacterium marinumMutation(s): 0 
Gene Names: fadD32, MMAR_5365
EC: 6.2.1 (PDB Primary Data), 6.2.1.20 (UniProt)
UniProt
Find proteins for B2HMK0 (Mycobacterium marinum (strain ATCC BAA-535 / M))
Explore B2HMK0 
Go to UniProtKB:  B2HMK0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2HMK0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5SV
Query on 5SV
Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]		[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl icosyl hydrogen phosphate
C30 H54 N5 O7 P
JFYKNVSLLXBVHG-BQOYKFDPSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A],
I [auth B],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
I [auth B],
J [auth B],
K [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
5SV Binding MOAD:  5EY9 Kd: 3870 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.79α = 90
b = 100.15β = 90
c = 212.32γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
BALBESphasing
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European CommunityNew Medicines for Tuberculosis (grant LSHP-CT-2005-018923)

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-16
    Type: Initial release
  • Version 1.1: 2016-03-23
    Changes: Database references
  • Version 1.2: 2016-04-20
    Changes: Database references