1
|
Gp29 LysA of mycobacteriophage TM4 can hydrolyze peptidoglycan through an N-acetyl-muramoyl-L-alanine amidase activity. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140745. [PMID: 34906734 DOI: 10.1016/j.bbapap.2021.140745] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 01/09/2023]
Abstract
Bacteriophage endolysins are crucial for progeny release at the end of the lytic cycle. Mycobacteriophage's genomes carry a lysin A essential gene, whose product cleaves the peptidoglycan (PG) layer and a lysin B, coding for an esterase, that cleaves the linkage between the mycolic acids and the arabinogalactan-PG complex. Lysin A mycobacteriophage proteins are highly modular and in gp29 (LysA) of phage TM4 three distinctive domains were identified. By bioinformatics analysis the central module was previously found to be similar to an amidase-2 domain family with an N-acetylmuramoyl -L-alanine amidase activity. We demonstrated experimentally that purified LysA is able to lyse a suspension of Micrococcus lysodeikticus and can promote cell lysis when expressed in E. coli and Mycobacterium smegmatis. After incubation of LysA with MDP (Muramyl dipeptide, N-acetyl-muramyl-L-alanyl-D-isoglutamine) we detected the presence of N-acetylmuramic acid (NAcMur) and L-Ala- D- isoGlutamine (L-Ala-D-isoGln) corroborating the proposed muramidase activity of this enzyme. This protein was stabilized at acidic pH in the presence of Zn consistent with the increase of the enzymatic activity under these conditions. By homology modeling, we predicted that the Zn ion is coordinated by His 226, His 335, and Asp 347 and we also identified the amino acid Glu 290 as the catalytic residue. LysA activity was completely abolished in derived mutants on these key residues, suggesting that the PG hydrolysis solely relies on the central domain of the protein.
Collapse
|
2
|
Woodward RL, Castleman MM, Meloche CE, Karpen ME, Carlson CG, Yobi WH, Jepsen JC, Lewis BW, Zarnosky BN, Cook PD. X-ray crystallographic structure of BshB, the zinc-dependent deacetylase involved in bacillithiol biosynthesis. Protein Sci 2019; 29:1035-1039. [PMID: 31867856 DOI: 10.1002/pro.3808] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/16/2019] [Accepted: 12/17/2019] [Indexed: 11/05/2022]
Abstract
Many gram-positive bacteria produce bacillithiol to aid in the maintenance of redox homeostasis and degradation of toxic compounds, including the antibiotic fosfomycin. Bacillithiol is produced via a three-enzyme pathway that includes the action of the zinc-dependent deacetylase BshB. Previous studies identified conserved aspartate and histidine residues within the active site that are involved in metal binding and catalysis, but the enzymatic mechanism is not fully understood. Here we report two X-ray crystallographic structures of BshB from Bacillus subtilis that provide insight into the BshB catalytic mechanism.
Collapse
Affiliation(s)
- Robert L Woodward
- Department of Chemistry and Biochemistry, University of Mount Union, Alliance, Ohio
| | | | - Chelsea E Meloche
- Department of Chemistry, Grand Valley State University, Allendale, Michigan
| | - Mary E Karpen
- Department of Chemistry, Grand Valley State University, Allendale, Michigan
| | - Clare G Carlson
- Department of Chemistry, Grand Valley State University, Allendale, Michigan
| | - William H Yobi
- Department of Chemistry and Biochemistry, University of Mount Union, Alliance, Ohio
| | - Jacqueline C Jepsen
- Department of Chemistry and Biochemistry, University of Mount Union, Alliance, Ohio
| | - Benjamin W Lewis
- Department of Chemistry and Biochemistry, University of Mount Union, Alliance, Ohio
| | - Brooke N Zarnosky
- Department of Chemistry and Biochemistry, University of Mount Union, Alliance, Ohio
| | - Paul D Cook
- Department of Chemistry, Grand Valley State University, Allendale, Michigan
| |
Collapse
|
3
|
Blanco Capurro JI, Hopkins CW, Pierdominici Sottile G, González Lebrero MC, Roitberg AE, Marti MA. Theoretical Insights into the Reaction and Inhibition Mechanism of Metal-Independent Retaining Glycosyltransferase Responsible for Mycothiol Biosynthesis. J Phys Chem B 2017; 121:471-478. [PMID: 27935720 DOI: 10.1021/acs.jpcb.6b10130] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Understanding enzymatic reactions with atomic resolution has proven in recent years to be of tremendous interest for biochemical research, and thus, the use of QM/MM methods for the study of reaction mechanisms is experiencing a continuous growth. Glycosyltransferases (GTs) catalyze the formation of glycosidic bonds, and are important for many biotechnological purposes, including drug targeting. Their reaction product may result with only one of the two possible stereochemical outcomes for the reacting anomeric center, and therefore, they are classified as either inverting or retaining GTs. While the inverting GT reaction mechanism has been widely studied, the retaining GT mechanism has always been controversial and several questions remain open to this day. In this work, we take advantage of our recent GPU implementation of a pure QM(DFT-PBE)/MM approach to explore the reaction and inhibition mechanism of MshA, a key retaining GT responsible for the first step of mycothiol biosynthesis, a low weight thiol compound found in pathogens like Mycobacterium tuberculosis that is essential for its survival under oxidative stress conditions. Our results show that the reaction proceeds via a front-side SNi-like concerted reaction mechanism (DNAN in IUPAC nomenclature) and has a 17.5 kcal/mol free energy barrier, which is in remarkable agreement with experimental data. Detailed analysis shows that the key reaction step is the diphosphate leaving group dissociation, leading to an oxocarbenium-ion-like transition state. In contrast, fluorinated substrate analogues increase the reaction barrier significantly, rendering the enzyme effectively inactive. Detailed analysis of the electronic structure along the reaction suggests that this particular inhibition mechanism is associated with fluorine's high electronegative nature, which hinders phosphate release and proper stabilization of the transition state.
Collapse
Affiliation(s)
- Juan I Blanco Capurro
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria , Intendente Guiraldes 2160, C1428EGA, Ciudad Autónoma de Buenos Aires, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad Universitaria , Intendente Guiraldes 2160, C1428EGA, Ciudad Autónoma de Buenos Aires, Argentina
| | - Chad W Hopkins
- Department of Physics, University of Florida , Gainesville, Florida 32611, United States
| | - Gustavo Pierdominici Sottile
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes , Sáenz Peña 352, Bernal B1876BXD, Argentina
| | - Mariano C González Lebrero
- Departamento de Quimica Inorgánica, Anlı́tica y Quı́mica Fı́sica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria , Intendente Guiraldes 2160, C1428EGA, Ciudad Autónoma de Buenos Aires, Argentina.,Insituto de Quimica Inorgánica, Materiales Ambiente y Energı́a (INQUIMAE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria , Intendente Guiraldes 2160, C1428EGA, Ciudad Autónoma de Buenos Aires, Argentina
| | - Adrian E Roitberg
- Department of Chemistry, University of Florida , Gainesville, Florida 32611, United States
| | - Marcelo A Marti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria , Intendente Guiraldes 2160, C1428EGA, Ciudad Autónoma de Buenos Aires, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad Universitaria , Intendente Guiraldes 2160, C1428EGA, Ciudad Autónoma de Buenos Aires, Argentina
| |
Collapse
|