9DM7 | pdb_00009dm7

mannosyltransferase PimE in complex with Fab_E6


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.02 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Mechanistic studies of mycobacterial glycolipid biosynthesis by the mannosyltransferase PimE.

Liu, Y.Brown, C.M.Borges, N.Nobre, R.N.Erramilli, S.Belcher Dufrisne, M.Kloss, B.Giacometti, S.Esteves, A.M.Timoteo, C.G.Tokarz, P.Cater, R.J.Lowary, T.L.Morita, Y.S.Kossiakoff, A.A.Santos, H.Stansfeld, P.J.Nygaard, R.Mancia, F.

(2025) Nat Commun 16: 3974-3974

  • DOI: https://doi.org/10.1038/s41467-025-57843-1
  • Primary Citation of Related Structures:  
    9DLF, 9DLH, 9DM5, 9DM7, 9MJB

  • PubMed Abstract: 

    Tuberculosis (TB), a leading cause of death among infectious diseases globally, is caused by Mycobacterium tuberculosis (Mtb). The pathogenicity of Mtb is largely attributed to its complex cell envelope, which includes a class of glycolipids called phosphatidyl-myo-inositol mannosides (PIMs). These glycolipids maintain the integrity of the cell envelope, regulate permeability, and mediate host-pathogen interactions. PIMs comprise a phosphatidyl-myo-inositol core decorated with one to six mannose residues and up to four acyl chains. The mannosyltransferase PimE catalyzes the transfer of the fifth PIM mannose residue from a polyprenyl phosphate-mannose (PPM) donor. This step contributes to the proper assembly and function of the mycobacterial cell envelope; however, the structural basis for substrate recognition and the catalytic mechanism of PimE remain poorly understood. Here, we present the cryo-electron microscopy (cryo-EM) structures of PimE from Mycobacterium abscessus in its apo and product-bound form. The structures reveal a distinctive binding cavity that accommodates both donor and acceptor substrates/products. Key residues involved in substrate coordination and catalysis were identified and validated via in vitro assays and in vivo complementation, while molecular dynamics simulations delineated access pathways and binding dynamics. Our integrated approach provides comprehensive insights into PimE function and informs potential strategies for anti-TB therapeutics.


  • Organizational Affiliation
    • Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mannosyltransferase415Mycobacteroides abscessusMutation(s): 0 
Gene Names: D2E76_03800
UniProt
Find proteins for A0ABD7HTP3 (Mycobacteroides abscessus)
Explore A0ABD7HTP3 
Go to UniProtKB:  A0ABD7HTP3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ABD7HTP3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab_E6 heavy chainB [auth H]126Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab_E6 light chainC [auth L]107Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.02 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2025-06-25 
  • Deposition Author(s): Liu, Y.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-25
    Type: Initial release