4Y0L

Mycobacterial membrane protein MmpL11D2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The Structure and Interactions of Periplasmic Domains of Crucial MmpL Membrane Proteins from Mycobacterium tuberculosis.

Chim, N.Torres, R.Liu, Y.Capri, J.Batot, G.Whitelegge, J.P.Goulding, C.W.

(2015) Chem.Biol. 22: 1098-1107

  • DOI: 10.1016/j.chembiol.2015.07.013

  • PubMed Abstract: 
  • Mycobacterium tuberculosis mycobacterial membrane protein large (MmpL) proteins are important in substrate transport across the inner membrane. Here, we show that MmpL proteins are classified into two phylogenetic clusters, where MmpL cluster II cont ...

    Mycobacterium tuberculosis mycobacterial membrane protein large (MmpL) proteins are important in substrate transport across the inner membrane. Here, we show that MmpL proteins are classified into two phylogenetic clusters, where MmpL cluster II contains three soluble domains (D1, D2, and D3) and has two full-length members, MmpL3 and MmpL11. Significantly, MmpL3 is currently the most druggable M. tuberculosis target. We have solved the 2.4-Å MmpL11-D2 crystal structure, revealing structural homology to periplasmic porter subdomains of RND (multidrug) transporters. The resulting predicted cluster II MmpL membrane topology has D1 and D2 residing, and possibly interacting, within the periplasm. Crosslinking and biolayer interferometry experiments confirm that cluster II D1 and D2 bind with weak affinities, and guided D1-D2 heterodimeric model assemblies. The predicted full-length MmpL3 and MmpL11 structural models reveal key substrate binding and transport residues, and may serve as templates to set the stage for in silico anti-tuberculosis drug development.


    Organizational Affiliation

    Department of Molecular Biology and Biochemistry, UCI, Irvine, CA 92697, USA.,The Pasarow Mass Spectrometry Laboratory, NPI-Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA 90024, USA.,Department of Molecular Biology and Biochemistry, UCI, Irvine, CA 92697, USA; Department of Pharmaceutical Sciences, UCI, Irvine, CA 92697, USA. Electronic address: celia.goulding@uci.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative membrane protein mmpL11
A
88Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: mmpL11
Find proteins for P9WJT9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WJT9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download SDF File 
Download CCD File 
A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.208 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 65.600α = 90.00
b = 91.730β = 90.00
c = 32.850γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
iMOSFLMdata reduction
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-08-12
    Type: Initial release
  • Version 1.1: 2015-09-02
    Type: Database references, Other