9NYK

Cryo-EM structure of the glycosyltransferase GtrB in the pre-intermediate state

Summary for 9NYK

• Entry DOI: 10.2210/pdb9nyk/pdb
• Related: 9NYC 9NYD 9NYE 9NYF
• EMDB information: 49935
• Descriptor: Glycosyltransferase sll0501, URIDINE-5'-DIPHOSPHATE-GLUCOSE, [(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, ... (4 entities in total)
• Functional Keywords: glycosyltransferase, polyisoprenyl, membrane protein
• Biological source: Synechocystis sp. PCC 6803 substr. Kazusa
• Total number of polymer chains: 4
• Total formula weight: 163029.28

Authors

Morgan, R.T.,Motta, S.,Gil-Iturbe, E.,di Muccio, G.,Bhattacharjee, B.,Romagnoli, A.,Anwar, M.T.,Mishra, B.,Ashraf, K.,Bang, I.,di Marino, D.,Lowary, T.L.,Quick, M.,Petrou, V.I.,Stowell, M.H.B.,Nygaard, R.,Mancia, F. (deposition date: 2025-03-27, release date: 2025-12-17, Last modification date: 2025-12-24)

Primary citation

Morgan, R.T.,Motta, S.,Gil-Iturbe, E.,Bhattacharjee, B.,Anwar, M.T.,Di Muccio, G.,Romagnoli, A.,Mishra, B.,Ashraf, K.U.,Bang, I.,Di Marino, D.,Lowary, T.L.,Quick, M.,Petrou, V.I.,Stowell, M.H.B.,Nygaard, R.,Mancia, F.
Mechanistic snapshots of lipid-linked sugar transfer.
Nat Commun, 16:11044-11044, 2025

PubMed Abstract: 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.

PubMed: 41353435
DOI: 10.1038/s41467-025-66769-7

Experimental method

ELECTRON MICROSCOPY (2.98 Å)