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Structure paper

TitleMechanistic snapshots of lipid-linked sugar transfer.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 11044, Year 2025
Publish dateDec 6, 2025
AuthorsRyan T Morgan / Stefano Motta / Eva Gil-Iturbe / Biddut Bhattacharjee / Mohammad T Anwar / Giovanni Di Muccio / Alice Romagnoli / Bedangshu Mishra / Khuram U Ashraf / Injin Bang / Daniele Di Marino / Todd L Lowary / Matthias Quick / Vasileios I Petrou / Michael H B Stowell / Rie Nygaard / Filippo Mancia /
PubMed AbstractEnzymes undergo dynamic conformational changes during catalysis, yet conventional high-resolution structural methods typically capture only the most stable states. Here, we address this gap using ...Enzymes undergo dynamic conformational changes during catalysis, yet conventional high-resolution structural methods typically capture only the most stable states. Here, we address this gap using rapid UV photolysis of a chemically caged substrate with cryogenic time-resolved electron microscopy (cryo-TREM). We elucidate the catalytic mechanism of GtrB, a membrane-bound glycosyltransferase that transfers glucose from UDP-glucose to the lipid carrier undecaprenyl phosphate. We visualized how GtrB, which has an active site ~15 Å from the membrane, transitions during the catalytic cycle to move each substrate in proximity for catalysis. From a single dataset, we resolved distinct conformational states: the initial substrate-bound state, a catalytically poised intermediate, and the product-bound state. Through molecular dynamics simulations and biochemical analyses, we identify coordinated movements within the active site that drive catalysis. These findings provide a molecular framework for understanding how glycosyltransferases function and highlight a broadly applicable strategy for capturing dynamic enzymatic states in native-like environments.
External linksNat Commun / PubMed:41353435 / PubMed Central
MethodsEM (single particle)
Resolution2.54 - 3.19 Å
Structure data

49930

9nyc

EMDB-49930, PDB-9nyc:
Cryo-EM structure of the glycosyltransferase GtrB in the substrate-bound state
Method: EM (single particle) / Resolution: 2.54 Å

49931

9nyd

EMDB-49931, PDB-9nyd:
Cryo-EM structure of the glycosyltransferase GtrB in the pre-catalysis and product-bound state
Method: EM (single particle) / Resolution: 2.85 Å

49932

9nye

EMDB-49932, PDB-9nye:
Cryo-EM structure of the glycosyltransferase GtrB in the apo state (octamer volume)
Method: EM (single particle) / Resolution: 2.79 Å

49933

9nyf

EMDB-49933, PDB-9nyf:
Cryo-EM structure of the glycosyltransferase GtrB (tetramer volume)
Method: EM (single particle) / Resolution: 3.19 Å

49935

9nyk

EMDB-49935, PDB-9nyk:
Cryo-EM structure of the glycosyltransferase GtrB in the pre-intermediate state
Method: EM (single particle) / Resolution: 2.98 Å

Chemicals

ChemComp-UPG:
URIDINE-5'-DIPHOSPHATE-GLUCOSE

ChemComp-5TR:
[(2~{E},6~{E},10~{E},14~{E},18~{Z},22~{E},26~{Z},30~{E},34~{E},38~{E})-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,14,18,22,26,30,34,38,42-undecaenyl] dihydrogen phosphate

ChemComp-MG:
Unknown entry

ChemComp-UDP:
URIDINE-5'-DIPHOSPHATE / UDP*YM

PDB-1b94:
RESTRICTION ENDONUCLEASE ECORV WITH CALCIUM

Source
  • synechocystis sp. pcc 6803 substr. kazusa (bacteria)
KeywordsMEMBRANE PROTEIN / glycosyltransferase / polyisoprenyl

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