Architecture of Pseudomonas aeruginosa glutamyl-tRNA synthetase defines a subfamily of dimeric class Ib aminoacyl-tRNA synthetases
Edited by Paul Schimmel, Scripps Research Florida, Jupiter, FL; received March 6, 2025; accepted April 1, 2025
Significance
Pseudomonas aeruginosa is a common cause of hospital-related infections and a formidable health threat due to its evolving antibiotic resistance. PaGluRS is homologous to other bacterial GluRSs in its domain architecture, but has evolved a distinct fold in its anticodon binding domain that introduces two interchain transfer ribonucleic acid (tRNA) binding sites through an unanticipated dimeric subunit arrangement. The structure is used to predict other members of the α2-type class Ib AaRS family, including GluRSs from pathogenic organisms such as Acinetobacter baumannii, Moraxella catarrhalis, and Chlamydia trachomatis, making the novel architecture an attractive molecular target.
Abstract
The aminoacyl-tRNA synthetases (AaRSs) are an ancient family of structurally diverse enzymes that are divided into two major classes. The functionalities of most AaRSs are inextricably linked to their oligomeric states. While GluRSs were previously classified as monomers, the current investigation reveals that the form expressed in Pseudomonas aeruginosa is a rotationally pseudosymmetrical homodimer featuring intersubunit tRNA binding sites. Both subunits display a highly bent, “pipe strap” conformation, with the anticodon binding domain directed toward the active site. The tRNA binding sites are similar in shape to those of the monomeric GluRSs, but are formed through an approximately 180-degree rotation of the anticodon binding domains and dimerization via the anticodon and D-arm binding domains. As a result, each anticodon binding domain is poised to recognize the anticodon loop of a tRNA bound to the adjacent protomer. Additionally, the anticodon binding domain has an α-helical C-terminal extension containing a conserved lysine-rich consensus motif positioned near the predicted location of the acceptor arm, suggesting dual functions in tRNA recognition. The unique architecture of PaGluRS broadens the structural diversity of the GluRS family, and member synthetases of all bacterial AaRS subclasses have now been identified that exhibit oligomerization.
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Data, Materials, and Software Availability
Three-dimensional coordinates of PaGluRS are available at the PDB (https://www.rcsb.org/) under accession codes 5TGT (119) and 8VC5 (120). Accompanying SAXS data can be retrieved from Simple Scattering (https://simplescattering.com/) under accession code XSBHEVPH (121).
Acknowledgments
I.K.W. and J.W. were supported through the Hatch program of the National Institute of Food and Agriculture. This project has been funded in whole or in part with Federal funds from the National Institute of Allergy and Infectious Diseases (NIAID), NIH, Department of Health and Human Services, under Contract No. 75N93022C00036 from September 1, 2022. Seattle Structural Genomics Center for Infectious Disease was funded under NIAID Contracts No. HHSN272201700059C from September 1, 2017, through August 31, 2022; HHSN272201200025C from September 1, 2012, through August 31, 2017; and HHSN272200700057C from September 28, 2007, through September 27, 2012. The multiangle light scattering and small-angle X-ray scattering work was conducted at the ALS, a national user facility operated by Lawrence Berkeley National Laboratory on behalf of the U.S. Department of Energy (DOE), Office of Basic Energy Sciences, Office of Biological and Environmental Research, and Advanced Scientific Computing Research through the Integrated Diffraction Analysis Technologies program and the Biopreparedness Research Virtual Environment (BRaVE) Taskforce 5 (DOE-BRAVET5), under contract number DE-AC02-O5CH11231. Additional support comes from the NIH project ALS-ENABLE (P30 GM124169) and a High-End Instrumentation Grant S10OD018483.
Author contributions
M.K.F., T.E.E., P.J.M., and B.L.S. designed research; M.K.F., S. Seibold, A.E.D., S. Subramanian, I.Q.P., D.M.D., D.D.L., A.B.A., R.C., S.N.H., J.M.B., K.P.B., and S.L. performed research; J.M.B., I.K.W., and J.W. contributed new reagents/analytic tools; M.K.F., S.J.M., J.M.B., A.C.S., S.E.T., and S.L. analyzed data; P.J.M. procured funding; and M.K.F., A.E.D., S. Subramanian, S.L., and B.L.S. wrote the paper.
Competing interests
The authors declare no competing interest.
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Three-dimensional coordinates of PaGluRS are available at the PDB (https://www.rcsb.org/) under accession codes 5TGT (119) and 8VC5 (120). Accompanying SAXS data can be retrieved from Simple Scattering (https://simplescattering.com/) under accession code XSBHEVPH (121).
Submission history
Received: March 6, 2025
Accepted: April 1, 2025
Published online: May 9, 2025
Published in issue: May 13, 2025
Keywords
Acknowledgments
I.K.W. and J.W. were supported through the Hatch program of the National Institute of Food and Agriculture. This project has been funded in whole or in part with Federal funds from the National Institute of Allergy and Infectious Diseases (NIAID), NIH, Department of Health and Human Services, under Contract No. 75N93022C00036 from September 1, 2022. Seattle Structural Genomics Center for Infectious Disease was funded under NIAID Contracts No. HHSN272201700059C from September 1, 2017, through August 31, 2022; HHSN272201200025C from September 1, 2012, through August 31, 2017; and HHSN272200700057C from September 28, 2007, through September 27, 2012. The multiangle light scattering and small-angle X-ray scattering work was conducted at the ALS, a national user facility operated by Lawrence Berkeley National Laboratory on behalf of the U.S. Department of Energy (DOE), Office of Basic Energy Sciences, Office of Biological and Environmental Research, and Advanced Scientific Computing Research through the Integrated Diffraction Analysis Technologies program and the Biopreparedness Research Virtual Environment (BRaVE) Taskforce 5 (DOE-BRAVET5), under contract number DE-AC02-O5CH11231. Additional support comes from the NIH project ALS-ENABLE (P30 GM124169) and a High-End Instrumentation Grant S10OD018483.
Author contributions
M.K.F., T.E.E., P.J.M., and B.L.S. designed research; M.K.F., S. Seibold, A.E.D., S. Subramanian, I.Q.P., D.M.D., D.D.L., A.B.A., R.C., S.N.H., J.M.B., K.P.B., and S.L. performed research; J.M.B., I.K.W., and J.W. contributed new reagents/analytic tools; M.K.F., S.J.M., J.M.B., A.C.S., S.E.T., and S.L. analyzed data; P.J.M. procured funding; and M.K.F., A.E.D., S. Subramanian, S.L., and B.L.S. wrote the paper.
Competing interests
The authors declare no competing interest.
Notes
This article is a PNAS Direct Submission.
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Cite this article
Architecture of Pseudomonas aeruginosa glutamyl-tRNA synthetase defines a subfamily of dimeric class Ib aminoacyl-tRNA synthetases, Proc. Natl. Acad. Sci. U.S.A.
122 (19) e2504757122,
https://doi.org/10.1073/pnas.2504757122
(2025).
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