The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
Dissecting the molecular basis underlying mycobacterial cell-wall hydrolysis by the catalytic domains of D29 LysA and DS6A LysA phage endolysins
Open accessPreprint — published as 10.1016/j.ijbiomac.2025.148896 · Paper page
Abstract
Mycobacteria encompass a broad range of microorganisms that cause infections with a significant impact on human health, resulting in millions of deaths each year. From tuberculosis and leprosy, caused by Mycobacterium tuberculosis and Mycobacterium leprae , respectively, to infections caused by emerging/opportunistic pathogens such as Mycobacterium abscessus . The battle to combat this health burden is further challenged by limitations in the treatments currently available and the rise of antimicrobial resistance. This underscores the need for new therapeutic strategies to combat these infections. Mycobacteriophage LysA endolysins are complex, multi-domain peptidoglycan hydrolases with reported antimicrobial relevance and the potential to treat mycobacterial infections. However, despite the therapeutic prospects of LysAs, our understanding of their mechanism of action remains limited. This study provides a comprehensive structural-functional analysis of the catalytic domains of two LysA endolysins encoded by the bacteriophages D29 and DS6A , which are known to infect pathogenic mycobacteria, including M. tuberculosis . As part of this work, we have characterized the four catalytic domains present in both endolysins ( D29 N4/ D29 GH19 and DS6A GH19/ DS6A Ami2B) both alone and in complex with PG analogues. To achieve this, we combined protein engineering, X-ray crystallography, small-angle X-ray scattering, and in silico tools. To our knowledge, this has led to the first experimental structures reported for mycobacteriophage endolysins, which reveals key aspects of peptidoglycan binding and hydrolysis by D29 LysA and DS6A LysA lysins, as well as other homologous LysAs, including the hydrolase domains similar to those examined here. Altogether, this represents a significant step forward in understanding how mycobacterial cell-wall hydrolysis occurs by this important class of endolysins and opens the door to their future use in therapeutic applications as enzybiotics. Information that will allow the rational design of a la carte enzymes with optimized lytic properties against mycobacterial pathogens.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
Research works printed but not linked: 64
- 10.1107/S0907444909052925 · DOI · Paper page
- 10.1101/cshperspect.a019794 · DOI
- Anantharaman V & Aravind L (2003) Evolutionary history, structural features and biochemical diversity of the NlpC/P60 superfamily of enzymes · DOI · Paper page
- Bartlett HP , Dawson CC , Glickman CM , Osborn DW , Evans CR , Garcia BJ , Frost LC , Cummings JE , Whittel N , Slayden RA , et al (2024) Targeting intracellular nontuberculous mycobacteria and M. tuberculosis with a bactericidal enzymatic cocktail. Microbiol Spectr 12 · DOI
- 10.1016/j.tcsw.2020.100044 · DOI
- 10.1016/j.jmb.2011.08.014 · DOI
- 10.1016/j.ijmm.2014.12.018 · DOI
- 10.1074/jbc.M114.557306 · DOI
- Catalão MJ , Filipe SR & Pimentel M (2019) Revisiting antituberculosis therapeutic strategies that target the peptidoglycan structure and synthesis. Front Microbiol 10 · DOI
- 10.1107/S0907444909042073 · DOI · Paper page
- 10.1107/S1600577520009960 · DOI
- 10.1007/978-981-13-7709-9_11 · DOI
- 10.1107/S0907444910007493 · DOI · Paper page
- Eniyan K , Sinha A , Ahmad S & Bajpai U (2020) Functional characterization of the endolysins derived from mycobacteriophage PDRPxv. World J Microbiol Biotechnol 36 · DOI
- 10.1107/S0907444913000061 · DOI
- Evans R , O’Neill M , Pritzel A , Antropova N , Senior A , Green T , Žídek A , Bates R , Blackwell S , Yim J , et al (2022) Protein complex prediction with AlphaFold-Multimer. bioRxiv: 2021.10.04.463034 · DOI · Paper page
- Froman S ;, Drake W , Will E & Bogen FAPHA (1954) Bacteriophage Active Against Virulent Mycobacterium tuberculosis 1. Isolation and Activity · DOI
- 10.1111/mmi.15295 · DOI
- 10.1016/j.chembiol.2022.11.001 · DOI
- Haddad Kashani H , Schmelcher M , Sabzalipoor H , Seyed Hosseini E & Moniri R (2018) Recombinant endolysins as potential therapeutics against antibiotic-resistant staphylococcus aureus: Current status of research and novel delivery strategies. Clin Microbiol Rev 31 · DOI
- 10.1111/j.1742-4658.2006.05487.x · DOI
- Holm L , Laiho A , Törönen P & Salgado M (2023) DALI shines a light on remote homologs: One hundred discoveries. Protein Science 32 · DOI
- 10.1016/0014-5793(96)00174-3 · DOI
- 10.1038/S41579-020-0331-1 · DOI · Paper page
- 10.1099/mic.0.000831 · DOI
- 10.1002/1873-3468.12848 · DOI
- 10.1107/S0907444909047337 · DOI · Paper page
- 10.1016/j.jmb.2009.12.038 · DOI
- 10.1128/IAI.71.11.6199-6204.2003 · DOI
- 2020, Mercury 4.0: from visualization to analysis, design and prediction, urn:issn:1600-5767, 53, 226
- 10.1021/ja405464b · DOI
- 10.1107/S0021889807021206 · DOI · Paper page
- Meroueh SO , Bencze KZ , Hesek D , Lee M , Fisher JF , Stemmler TL & Mobashery S (2006) Three-dimensional structure of the bacterial cell wall peptidoglycan PNAS · DOI
- Nelson D , Loomis L & Fischetti VA (2001) Prevention and elimination of upper respiratory colonization of mice by group A streptococci by using a bacteriophage lytic enzyme · DOI
- 10.1016/J.JBC.2023.104801 · DOI
- 10.1111/mmi.12555 · DOI
- 10.1371/journal.pone.0034052 · DOI
- 10.1074/jbc.M411006200 · DOI
- Saadhali SA , Hassan S , Elizabeth Hanna L , Devi Ranganathan U & Kumar V (2016) Homology modeling, substrate docking, and molecular simulation studies of mycobacteriophage Che12 lysin A. J Mol Model · DOI
- 10.1111/mmi.13435 · DOI
- 10.1093/nar/gkw389 · DOI
- 10.1038/nature01026 · DOI
- 10.1111/mmi.14636 · DOI
- 10.1038/msb.2011.75 · DOI
- 10.1107/S1399004714013674 · DOI
- Urdániz E , Martín M , Payaslián F , Defelipe LA , Dodes M , Martinez M , Alzari PM , Cabrera G , Martí MA & Piuri M (2022) Gp29 LysA of mycobacteriophage TM4 can hydrolyze peptidoglycan through an N-acetyl-muramoyl-L-alanine amidase activity. Biochim Biophys Acta Proteins Proteom 1870 · DOI
- 10.1002/prot.10465 · DOI
- 10.1111/j.1574-6976.2007.00094.x · DOI
- 10.1128/JB.186.18.5978-5987.2004 · DOI
- 10.1164/arrd.1960.82.6.781 · DOI
- 2010, Structure of the γ-d-glutamyl-l-diamino acid endopeptidase YkfC from Bacillus cereus in complex with l-Ala-γ-d-Glu: insights into substrate recognition by NlpC/P60 cysteine peptidases, urn:issn:1744-3091, 66, 1354
- Yang F , Labani-Motlagh A , Bohorquez JA , Moreira JD , Ansari D , Patel S , Spagnolo F , Florence J , Vankayalapati A , Sakai T , et al (2024) Bacteriophage therapy for the treatment of Mycobacterium tuberculosis infections in humanized mice. Commun Biol 7 · DOI
- 10.1016/j.jmb.2011.08.014 · DOI
- 10.1111/mmi.14636 · DOI
- 10.1111/mmi.15295 · DOI
- 10.1111/j.1742-4658.2006.05487.x · DOI
- 10.1111/mmi.12555 · DOI
- 10.1099/mic.0.000831 · DOI
- 10.1016/j.bbapap.2021.140745 · DOI
- 10.1128/mBio.01120-13 · DOI
- 10.1038/s41598-018-25355-2 · DOI
- 10.1002/pro.3528 · DOI
- 10.1038/nature12070 · DOI · Paper page
- 10.1107/S2059798317011597 · DOI
Metadata
- Authors
- Ceballos-Zúñiga, F., Gálvez-Larrosa, L., Muñoz, I. G., Infantes, L., & Pérez-Dorado, I.
- Affiliations
- Consejo Superior de Investigaciones Científicas (ES)
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Blas Cabrera, Spanish Research Council, Serrano 119, 28006 Madrid, Spain
- Spanish National Cancer Research Centre (ES)
- Venue
- International Journal of Biological Macromolecules
- Publisher
- openRxiv
- Published
- 2025-01-24
- Volume
- 334
- Issue
- Pt 1
- Pages
- 148896-148896
- ISSN
- 0141-8130 (ISSN-L)
- OpenAlex
- W4416009356
- Cited by
- 4
- References
- 1
- Citations by year
- 2026: 4
- FWCI
- 2.13
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- International Journal of Biological Macromolecules (publishedVersion, cc-by-nc)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (acceptedVersion, other-oa)
- Funders
- Diamond Light Source
- Comunidad de Madrid (2019-T1/BMD-14774)
- European Commission
- European Synchrotron Radiation Facility
- Consejo Superior de Investigaciones Científicas (202380E208, MMT24-IQF-01, 2024ICT153)
- Topics
- Life Sciences › Immunology and Microbiology › Virology › Bacteriophages and microbial interactions
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Health Sciences › Medicine › Infectious Diseases › Tuberculosis Research and Epidemiology
- Keywords
- peptidoglycan hydrolase, catalytic domain, substrate binding site, peptidoglycan recognition, conformational change, phage therapy, tuberculosis, antimicrobial resistance, mycobacteria
- MeSH terms
- Cell Wall, Hydrolysis, Models, Molecular, Mycobacteriophages, Mycobacterium, Endopeptidases, Peptidoglycan, Viral Proteins, Crystallography, X-Ray, Catalytic Domain
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 ›
Are you an author, or do you see a problem with this page? Request a review
