Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Mechanistic studies of mycobacterial glycolipid biosynthesis by the mannosyltransferase PimE.
Journal, issue, pages	Nat Commun, Vol. 16, Issue 1, Page 3974, Year 2025
Publish date	Apr 29, 2025
Authors	Yaqi Liu / Chelsea M Brown / Nuno Borges / Rodrigo N Nobre / Satchal Erramilli / Meagan Belcher Dufrisne / Brian Kloss / Sabrina Giacometti / Ana M Esteves / Cristina G Timóteo / Piotr Tokarz / Rosemary J Cater / Todd L Lowary / Yasu S Morita / Anthony A Kossiakoff / Helena Santos / Phillip J Stansfeld / Rie Nygaard / Filippo Mancia /
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 ...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.
External links	Nat Commun / PubMed:40301322 / PubMed Central
Methods	EM (single particle)
Resolution	2.85 - 3.46 Å
Structure data	46976 9dlf EMDB-46976, PDB-9dlf: Arabinosyltransferase AftB in complex with Fab_B3 Method: EM (single particle) / Resolution: 2.85 Å 46978 9dlh EMDB-46978, PDB-9dlh: donor substrate analog-bound AftB Method: EM (single particle) / Resolution: 3.4 Å 46998 9dm5 9mjb EMDB-46998, PDB-9dm5: Product-Bound mannosyltransferase PimE PDB-9mjb: Product-Bound mannosyltransferase PimE in complex with Fab Method: EM (single particle) / Resolution: 3.46 Å 46999 9dm7 EMDB-46999, PDB-9dm7: mannosyltransferase PimE in complex with Fab_E6 Method: EM (single particle) / Resolution: 3.02 Å
Chemicals	ChemComp-6OU: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate / phospholipidYM PDB-1a7x: FKBP12-FK1012 COMPLEX PDB-1a8b: RAT ANNEXIN V COMPLEXED WITH GLYCEROPHOSPHOETHANOLAMINE ChemComp-DSL*: MONO-TRANS, OCTA-CIS DECAPRENYL-PHOSPHATE
Source	mycolicibacterium chubuense (bacteria) homo sapiens (human) mycobacteroides abscessus (bacteria)
Keywords	MEMBRANE PROTEIN / Arabinosyltransferase / mannosyltransferase / Product-bound Mannosyltransferase PimE in complex with Fab