Access Preprint From Server
April 1st, 2025
Version: 1
Hamilton College
biochemistry
biorxiv

Direct Amide Bond Formation By A Spore Peptidoglycan Biosynthetic Enzyme

Hopkins, M. E.•Yasinov, Z.•Fakler, M. J.•Wilde, G. E.•Wetmore, K. G.•Welsh, M. A.

The cortex layer of the peptidoglycan cell wall surrounding bacterial spores contains a modified sugar, muramic-{delta}-lactam, that is essential for spore germination. Genetic evidence has linked the conserved enzyme SwsB to the muramic-{delta}-lactam biosynthetic pathway. SwsB belongs to a large family of metal-dependent deacetylases, but its function is unclear because a putative catalytic residue is mutated. We have used native cortex peptidoglycan substrates to show that SwsB acts not as a deacetylase but as a monofunctional muramic-{delta}-lactam cyclase, the first enzyme reported with this activity. SwsB is remarkable in that it catalyzes lactam synthesis by direct intramolecular condensation of a carboxylate and primary amine with no apparent requirement for chemical energy input. SwsB will accept a minimal peptidoglycan substrate and, surprisingly, does not require a metal ion cofactor for cyclase activity. Our results suggest an in vivo role for SwsB and lay the foundation for mechanistic and structural studies of an unusual enzyme.

Similar Papers

biorxiv
Mon Apr 07 2025
AQuaRef: Machine learning accelerated quantum refinement of protein structures
Cryo-EM and X-ray crystallography provide crucial experimental data for obtaining atomic-detail models of biomacromolecules. Refining these models relies on library-based stereochemical restraints, which, in addition to being limited to known chemical entities, do not include meaningful noncovalent interactions relying solely on nonbonded repulsions. Quantum mechanical (QM) calculations could alle...
Zubatyuk, R.
•
Biczysko, M.
•
Ranasinghe, K.
•
Moriarty, N. W.
...•
Afonine, P. V.
biorxiv
Sun Apr 06 2025
Attenuative effect of Grifola frondosa (maitake mushroom) on severe DSS-induced colitis in vitamin D-deficient mice
Scope: Vitamin D deficiency, which has been a global health issue for decades, is involved in gut health and diseases. We examined the health benefits of Grifola frondosa (maitake mushroom), a potent dietary source of fungal vitamin D (D2), on DSS-induced colitis in vitamin D-deficient mice. Methods and results: C57BL/6J mice were fed a control diet, vitamin D3-deficient diet (DD), maitake-fortifi...
Nishikawa, M.
•
Miyagi, R.
•
Kugimiya, Y.
•
Chudan, S.
...•
Ikushiro, S.
biorxiv
Sun Apr 06 2025
THA_1941 from Thermosipho africanus: A Thermostable β-1,3-Glucan Phosphorylase for Efficient β-1,3-Glucan Synthesis
{beta}-1,3-Glucan phosphorylases capable of utilizing glucose as a priming substrate are key biocatalysts for the synthesis of functional {beta}-1,3-glucan. In this study, we identified THA_1941 from Thermosipho africanus (Ta{beta}GP) as a GH161 {beta}-1,3-glucan phosphorylase exhibiting robust synthetic activity towards glucose, as confirmed by 13C nuclear magnetic resonance, liquid chromatograph...
Mao, G.
•
Yu, J.
•
Lin, J.
•
Song, M.
...•
Song, A.
biorxiv
Sun Apr 06 2025
The Pseudomonas aeruginosa Membrane Histidine Kinase BqsS/CarS Directly Senses Environmental Ferrous Iron (Fe2+)
Canonical prokaryotic two-component signal transduction systems (TCSs) are widely utilized by bacteria to respond to their environment and are typically composed of a transmembrane sensor His kinase (HK) and a cytosolic DNA-binding response regulator (RR) that work together to respond to environmental stimuli. An important TCS that regulates the expression of genes involved in biofilm formation an...
Paredes, A.
•
Iheacho, C.
•
Chacon, K. N.
•
Smith, A. T.
biorxiv
Sat Apr 05 2025
Linoleic acid metabolite, 13-S-hydroxyoctadecadienoic acid, suppresses cancer cell growth by inhibiting mTOR
Mechanistic target of rapamycin (mTOR) is a key protein kinase that integrates various internal and external signals to control biological events including cell growth. Whereas substantial efforts were made to elucidate protein subunits interacting with mTOR, endogenous metabolite-mTOR interactions remain largely unknown. Using affinity protein purification and mass spectrometry, we identified dir...
Park, S. J.
•
Kwon, H.
•
Yang, A. Y.
•
Lee, B.
...•
Kim, S.
biorxiv
Sat Apr 05 2025
Comparison of Urinary Proteome Modifications Between Methamphetamine-Abstinent Rehabilitation Patients for Over Three Months and Healthy Individuals
Methamphetamine addiction is characterized by complex mechanisms and a high relapse rate, posing a serious public health threat. In this study, urinary proteome modifications of rehabilitation patients who had abstained from methamphetamine for over three months and those of healthy individuals were analyzed and compared. A total of 984 differentially modified peptides were identified, 362 of whic...
Chen, Y.
•
Shen, Z.
•
Liang, J.
•
Deng, Y.
•
Gao, Y.
biorxiv
Sat Apr 05 2025
Human endogenous retrovirus K (HERV-K) envelope structures in pre- and post-fusion by Cryo-EM
The HERV-K envelope glycoprotein (Env) is aberrantly expressed in diseases including cancers and autoimmune disorders and is targeted by antibodies. The lack of structural information has hindered functional and immune recognition studies. We solved structures of the HERV-K Env in both pre- and post-fusion states with novel monoclonal antibodies using cryo-EM. The pre-fusion Env assembles as a tri...
Shek, J.
•
Sun, C.
•
Wilson, E. M.
•
Moadab, F.
...•
Ollmann Saphire, E.
biorxiv
Fri Apr 04 2025
Complex carbohydrates catabolism capacity of bladder microbiota inhabiting healthy and overactive female bladders
Overactive bladder syndrome (OAB) is a poorly understood symptom complex that affects 40% of females over the age of 40, with clinical features including urinary urgency and incontinence. In addition to inflammation, oxidative stress, nerve damage and reduced blood flow, alterations in the urinary microbiome (urobiome), specifically in bladder bacterial diversity, have been reported to be associat...
Gourdine, J.-P.
•
Pacentine, I. V.
•
Barstad, A.
•
Dahl, E. M.
...•
Karstens, L.
biorxiv
Fri Apr 04 2025
A transfer RNA methyltransferase with an unusual domain composition catalyzes 2'-O-methylation at position 6 in tRNA.
Thermococcus kodakarensis tRNATrp contains 2\'-O-methylcytidine at position 6 (Cm6). However, the tRNA methyltransferase responsible for the modification has not been identified. Using comparative genomics we predicted TK1257 as a candidate for the modification. Biochemical and mass spectrometry studies of purified recombinant TK1257 gene product show it to possess a tRNA methyltransferase activit...
Matsuda, T.
•
Yamagami, R.
•
Ihara, A.
•
Suzuki, T.
...•
Hori, H.
biorxiv
Fri Apr 04 2025
Biochemical characterization of cyanobacterial HtpG from Synechococcus elongatus PCC 7942
The 90 kDa Heat Shock Protein (Hsp90) is an essential and highly conserved molecular chaperone that supports the folding and maturation of a diverse array of client proteins across prokaryotic and eukaryotic organisms. In bacteria, HtpG, the Hsp90 homolog, plays a central role in stress response and protein homeostasis, particularly under high-temperature and other stress conditions. Despite exten...
Jiang, L.
•
Boyenle, I.
•
Delaeter, N.
•
Liu, Y.