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- PDB-9nye: Cryo-EM structure of the glycosyltransferase GtrB in the apo stat... -

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Basic information

Entry
Database: PDB / ID: 9nye
TitleCryo-EM structure of the glycosyltransferase GtrB in the apo state (octamer volume)
ComponentsGlycosyltransferase sll0501
KeywordsMEMBRANE PROTEIN / glycosyltransferase / polyisoprenyl
Function / homologyTransferases; Glycosyltransferases / : / Glycosyltransferase 2-like / Glycosyl transferase family 2 / glycosyltransferase activity / Nucleotide-diphospho-sugar transferases / plasma membrane / Uncharacterized glycosyltransferase sll0501
Function and homology information
Biological speciesSynechocystis sp. PCC 6803 substr. Kazusa (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsMorgan, R.T. / Motta, S. / Gil-Iturbe, E. / di Muccio, G. / Bhattacharjee, B. / Romagnoli, A. / Anwar, M.T. / Mishra, B. / Ashraf, K. / Bang, I. ...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.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM132120 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS120496 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM123228 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R00GM123228 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM150831 United States
CitationJournal: Nat Commun / Year: 2025
Title: Mechanistic snapshots of lipid-linked sugar transfer.
Authors: Ryan 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 ...Authors: Ryan 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 /
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 ...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.
History
DepositionMar 27, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyltransferase sll0501
B: Glycosyltransferase sll0501
C: Glycosyltransferase sll0501
D: Glycosyltransferase sll0501
E: Glycosyltransferase sll0501
F: Glycosyltransferase sll0501
G: Glycosyltransferase sll0501
H: Glycosyltransferase sll0501


Theoretical massNumber of molelcules
Total (without water)318,9768
Polymers318,9768
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Glycosyltransferase sll0501


Mass: 39872.016 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Gene: sll0501
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q55487, Transferases; Glycosyltransferases
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Apo-GtrB / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.293346 MDa / Experimental value: NO
Source (natural)Organism: Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1500 nm / Calibrated defocus max: 2500 nm
Image recordingAverage exposure time: 4 sec. / Electron dose: 70.91 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3757

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 152605 / Symmetry type: POINT
RefinementHighest resolution: 2.79 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00320016
ELECTRON MICROSCOPYf_angle_d0.57927176
ELECTRON MICROSCOPYf_dihedral_angle_d4.8672680
ELECTRON MICROSCOPYf_chiral_restr0.0443128
ELECTRON MICROSCOPYf_plane_restr0.0063384

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