7C2N

Crystal structure of mycolic acid transporter MmpL3 from Mycobacterium smegmatis complexed with SPIRO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Structural Basis for the Inhibition of Mycobacterial MmpL3 by NITD-349 and SPIRO.

Yang, X.Hu, T.Yang, X.Xu, W.Yang, H.Guddat, L.W.Zhang, B.Rao, Z.

(2020) J Mol Biol 432: 4426-4434

  • DOI: https://doi.org/10.1016/j.jmb.2020.05.019
  • Primary Citation of Related Structures:  
    7C2M, 7C2N

  • PubMed Abstract: 

    Novel antitubercular agents are urgently needed to combat the emergence of global drug resistance to human tuberculosis. Mycobacterial membrane protein Large 3 (MmpL3) is a promising drug target because its activity is essential and required for cell-wall biosynthesis. Several classes of MmpL3 inhibitors have been developed against Mycobacterium tuberculosis (Mtb) with potent anti-tuberculosis activity. These include the drug candidate SQ109, which has progressed to phase IIb/III clinical trials. Here, we have determined the crystal structures of MmpL3 in complex with NITD-349 and SPIRO. Both inhibitors bind deep in the central channel of transmembrane domain and cause conformational changes to the protein. The amide nitrogen and indole nitrogen of NITD-349 and the piperidine nitrogen of SPIRO interact and clamp Asp645. Structural analysis of the two structures reveals that these inhibitors target the proton relay pathway to block the activity of MmpL3. The findings presented here enrich our understanding of the binding modes of MmpL3 inhibitors and provide directions to enable further rational drug design targeting MmpL3.


  • Organizational Affiliation

    Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100101, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Drug exporters of the RND superfamily-like protein,Endolysin934Mycolicibacterium smegmatis MC2 155Enterobacteria phage RB59
This entity is chimeric
Mutation(s): 2 
Gene Names: mmpL3MSMEI_0243eRB59_126
EC: 3.2.1.17
Membrane Entity: Yes 
UniProt
Find proteins for A0QP27 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QP27 
Go to UniProtKB:  A0QP27
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0QP27
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L6T
Query on L6T

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A]
alpha-D-glucopyranosyl 6-O-dodecyl-alpha-D-glucopyranoside
C24 H46 O11
HIJNTEBBIQHGEK-FXPCSOOLSA-N
FG0
Query on FG0

Download Ideal Coordinates CCD File 
I [auth A]1'-(2,3-dihydro-1,4-benzodioxin-6-ylmethyl)spiro[6,7-dihydrothieno[3,2-c]pyran-4,4'-piperidine]
C20 H23 N O3 S
NCRPMBWORFWNGT-UHFFFAOYSA-N
MHA
Query on MHA

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]
(CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID
C6 H10 N2 O5
QZTKDVCDBIDYMD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.49α = 90
b = 140.386β = 90
c = 145.229γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81520108019
Chinese Academy of SciencesChina2017YFC0840300

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-02
    Type: Initial release
  • Version 1.1: 2021-06-16
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description