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Cited by 12Protein Structure and DynamicsEnzyme Structure and FunctionBacterial Genetics and Biotechnology

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A novel fold for acyltransferase-3 (AT3) proteins provides a framework for transmembrane acyl-group transfer

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Newman, Kahlan E, Tindall, Sarah N, Mader, Sophie L, Khalid, Syma, Thomas, Gavin H, Van Der Woude, Marjan W·2023·eLife
DOI 10.7554/elife.81547PMC PMC9833829

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Abstract

Acylation of diverse carbohydrates occurs across all domains of life and can be catalysed by proteins with a membrane bound acyltransferase-3 (AT3) domain (PF01757). In bacteria, these proteins are essential in processes including symbiosis, resistance to viruses and antimicrobials, and biosynthesis of antibiotics, yet their structure and mechanism are largely unknown. In this study, evolutionary co-variance analysis was used to build a computational model of the structure of a bacterial O-antigen modifying acetyltransferase, OafB. The resulting structure exhibited a novel fold for the AT3 domain, which molecular dynamics simulations demonstrated is stable in the membrane. The AT3 domain contains 10 transmembrane helices arranged to form a large cytoplasmic cavity lined by residues known to be essential for function. Further molecular dynamics simulations support a model where the acyl-coA donor spans the membrane through accessing a pore created by movement of an important loop capping the inner cavity, enabling OafB to present the acetyl group close to the likely catalytic resides on the extracytoplasmic surface. Limited but important interactions with the fused SGNH domain in OafB are identified, and modelling suggests this domain is mobile and can both accept acyl-groups from the AT3 and then reach beyond the membrane to reach acceptor substrates. Together this new general model of AT3 function provides a framework for the development of inhibitors that could abrogate critical functions of bacterial pathogens.

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Metadata

Authors
Newman, K. E., Tindall, S. N., Mader, S. L., Khalid, S., Thomas, G. H., & Van Der Woude, M. W.
Affiliations
  • University of Southampton (GB)
  • University of York (GB)
  • University of Oxford (GB)
Corresponding author
  • Khalid, Syma
  • Thomas, Gavin H
  • Van Der Woude, Marjan W
ORCID
Venue
eLife
Publisher
eLife Sciences Publications, Ltd
Published
2023-01-11
Volume
12
ISSN
2050-084X (ISSN-L)
DOI
10.7554/elife.81547
PMC
PMC9833829
OpenAlex
W4315619292
Cited by
12
References
2
Citations by year
2026: 2 · 2025: 2 · 2024: 6 · 2023: 2
FWCI
0.82
Type
journal article
Language
en
Open access
Licence
Locations
  • eLife (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • ePrints Soton (University of Southampton) (acceptedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • Engineering and Physical Sciences Research Council (PhD Studentship Project Number: 2446840, established Career Fellowship EP/V030779/1, HECBioSim EP/R029407/1, High Performance Computing resource EP/T022205/1)
  • Biotechnology and Biological Sciences Research Council (White Rose DTP BB/M011151/1)
  • Federation of European Biochemical Societies (Long term fellowship)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
Keywords
protein fold, transmembrane helices, molecular dynamics simulation, antibiotic biosynthesis, bacterial virulence, inhibitor development
MeSH terms
Acetyltransferases, Acylation, Bacteria, Protein Structure, Secondary

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

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