Structure of the Essential Peptidoglycan Amidotransferase MurT/GatD Complex from Streptococcus Pneumoniae

Overview

Journal Nat Commun

Specialty Biology

Date 2018 Aug 11

PMID 30093673

Citations 17

Authors

Cecile Morlot

Daniel Straume

Katharina Peters

Olav A Hegnar

Nolwenn Simon

Anne-Marie Villard

Carlos Contreras-Martel

Francisco Leisico

Eefjan Breukink

Christine Gravier-Pelletier

Laurent Le Corre

Waldemar Vollmer

Nicolas Pietrancosta

Leiv Sigve Havarstein

Andre Zapun

Affiliations

Soon will be listed here.

Abstract

The universality of peptidoglycan in bacteria underlies the broad spectrum of many successful antibiotics. However, in our times of widespread resistance, the diversity of peptidoglycan modifications offers a variety of new antibacterials targets. In some Gram-positive species such as Streptococcus pneumoniae, Staphylococcus aureus, or Mycobacterium tuberculosis, the second residue of the peptidoglycan precursor, D-glutamate, is amidated into iso-D-glutamine by the essential amidotransferase MurT/GatD complex. Here, we present the structure of this complex at 3.0 Å resolution. MurT has central and C-terminal domains similar to Mur ligases with a cysteine-rich insertion, which probably binds zinc, contributing to the interface with GatD. The mechanism of amidation by MurT is likely similar to the condensation catalyzed by Mur ligases. GatD is a glutaminase providing ammonia that is likely channeled to the MurT active site through a cavity network. The structure and assay presented here constitute a knowledge base for future drug development studies.

Citing Articles

Insights into Peptidoglycan-Targeting Radiotracers for Imaging Bacterial Infections: Updates, Challenges, and Future Perspectives.

Koatale P, Welling M, Ndlovu H, Kgatle M, Mdanda S, Mdlophane A ACS Infect Dis. 2024; 10(2):270-286.

PMID: 38290525 PMC: 10862554. DOI: 10.1021/acsinfecdis.3c00443.

Amidation of glutamate residues in mycobacterial peptidoglycan is essential for cell wall cross-linking.

Shaku M, Ocius K, Apostolos A, Pires M, VanNieuwenhze M, Dhar N Front Cell Infect Microbiol. 2023; 13:1205829.

PMID: 37692163 PMC: 10484409. DOI: 10.3389/fcimb.2023.1205829.

Amino Acid Starvation-Induced Glutamine Accumulation Enhances Pneumococcal Survival.

Zhang C, Liu Y, An H, Wang X, Xu L, Deng H mSphere. 2023; 8(3):e0062522.

PMID: 37017541 PMC: 10286718. DOI: 10.1128/msphere.00625-22.

CRISPRi-mediated characterization of novel anti-tuberculosis targets: Mycobacterial peptidoglycan modifications promote beta-lactam resistance and intracellular survival.

Silveiro C, Marques M, Olivenca F, Pires D, Mortinho D, Nunes A Front Cell Infect Microbiol. 2023; 13:1089911.

PMID: 37009497 PMC: 10050696. DOI: 10.3389/fcimb.2023.1089911.

Hijacking the Peptidoglycan Recycling Pathway of Escherichia coli to Produce Muropeptides.

Rousseau A, Michaud J, Pradeau S, Armand S, Cottaz S, Richard E Chemistry. 2022; 29(6):e202202991.

PMID: 36256497 PMC: 10107939. DOI: 10.1002/chem.202202991.

References

Higuchi R, Krummel B, Saiki R . A general method of in vitro preparation and specific mutagenesis of DNA fragments: study of protein and DNA interactions. Nucleic Acids Res. 1988; 16(15):7351-67. PMC: 338413. DOI: 10.1093/nar/16.15.7351. View

Bouhss A, Blanot D, van Heijenoort J, Parquet C . Invariant amino acids in the Mur peptide synthetases of bacterial peptidoglycan synthesis and their modification by site-directed mutagenesis in the UDP-MurNAc:L-alanine ligase from Escherichia coli. Biochemistry. 1997; 36(39):11556-63. DOI: 10.1021/bi970797f. View

Siewert G, Strominger J . Biosynthesis of the peptidoglycan of bacterial cell walls. XI. Formation of the isoglutamine amide group in the cell walls of Staphylococcus aureus. J Biol Chem. 1968; 243(4):783-90. View

Ruane K, Lloyd A, Fulop V, Dowson C, Barreteau H, Boniface A . Specificity determinants for lysine incorporation in Staphylococcus aureus peptidoglycan as revealed by the structure of a MurE enzyme ternary complex. J Biol Chem. 2013; 288(46):33439-48. PMC: 3829189. DOI: 10.1074/jbc.M113.508135. View

Leisico F, Vieira D, Figueiredo T, Silva M, Cabrita E, Sobral R . First insights of peptidoglycan amidation in Gram-positive bacteria - the high-resolution crystal structure of Staphylococcus aureus glutamine amidotransferase GatD. Sci Rep. 2018; 8(1):5313. PMC: 5871853. DOI: 10.1038/s41598-018-22986-3. View

Kuzmic P . Program DYNAFIT for the analysis of enzyme kinetic data: application to HIV proteinase. Anal Biochem. 1996; 237(2):260-73. DOI: 10.1006/abio.1996.0238. View

Figueiredo T, Sobral R, Ludovice A, Almeida J, Bui N, Vollmer W . Identification of genetic determinants and enzymes involved with the amidation of glutamic acid residues in the peptidoglycan of Staphylococcus aureus. PLoS Pathog. 2012; 8(1):e1002508. PMC: 3267633. DOI: 10.1371/journal.ppat.1002508. View

Xu H, Trawick J, Haselbeck R, Forsyth R, Yamamoto R, Archer R . Staphylococcus aureus TargetArray: comprehensive differential essential gene expression as a mechanistic tool to profile antibacterials. Antimicrob Agents Chemother. 2010; 54(9):3659-70. PMC: 2934999. DOI: 10.1128/AAC.00308-10. View

Munch D, Roemer T, Lee S, Engeser M, Sahl H, Schneider T . Identification and in vitro analysis of the GatD/MurT enzyme-complex catalyzing lipid II amidation in Staphylococcus aureus. PLoS Pathog. 2012; 8(1):e1002509. PMC: 3266927. DOI: 10.1371/journal.ppat.1002509. View

10.

Cha S, An Y, Jeong C, Yu J, Chung K . ATP-binding mode including a carbamoylated lysine and two Mg(2+) ions, and substrate-binding mode in Acinetobacter baumannii MurF. Biochem Biophys Res Commun. 2014; 450(2):1045-50. DOI: 10.1016/j.bbrc.2014.06.108. View

11.

Emanuele Jr J, Jin H, Yanchunas Jr J, Villafranca J . Evaluation of the kinetic mechanism of Escherichia coli uridine diphosphate-N-acetylmuramate:L-alanine ligase. Biochemistry. 1997; 36(23):7264-71. DOI: 10.1021/bi970266r. View

12.

Murshudov G, Skubak P, Lebedev A, Pannu N, Steiner R, Nicholls R . REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 2011; 67(Pt 4):355-67. PMC: 3069751. DOI: 10.1107/S0907444911001314. View

13.

Figueiredo T, Ludovice A, Sobral R . Contribution of peptidoglycan amidation to beta-lactam and lysozyme resistance in different genetic lineages of Staphylococcus aureus. Microb Drug Resist. 2014; 20(3):238-49. PMC: 4050451. DOI: 10.1089/mdr.2014.0042. View

14.

Wu G, Robertson D, Brooks 3rd C, Vieth M . Detailed analysis of grid-based molecular docking: A case study of CDOCKER-A CHARMm-based MD docking algorithm. J Comput Chem. 2003; 24(13):1549-62. DOI: 10.1002/jcc.10306. View

15.

Sink R, Kotnik M, Zega A, Barreteau H, Gobec S, Blanot D . Crystallographic Study of Peptidoglycan Biosynthesis Enzyme MurD: Domain Movement Revisited. PLoS One. 2016; 11(3):e0152075. PMC: 4816537. DOI: 10.1371/journal.pone.0152075. View

16.

Sheldrick G . Experimental phasing with SHELXC/D/E: combining chain tracing with density modification. Acta Crystallogr D Biol Crystallogr. 2010; 66(Pt 4):479-85. PMC: 2852312. DOI: 10.1107/S0907444909038360. View

17.

Berg K, Biornstad T, Straume D, Havarstein L . Peptide-regulated gene depletion system developed for use in Streptococcus pneumoniae. J Bacteriol. 2011; 193(19):5207-15. PMC: 3187432. DOI: 10.1128/JB.05170-11. View

18.

Barreteau H, Kovac A, Boniface A, Sova M, Gobec S, Blanot D . Cytoplasmic steps of peptidoglycan biosynthesis. FEMS Microbiol Rev. 2008; 32(2):168-207. DOI: 10.1111/j.1574-6976.2008.00104.x. View

19.

Thanassi J, Dougherty T, Dougherty B, Pucci M . Identification of 113 conserved essential genes using a high-throughput gene disruption system in Streptococcus pneumoniae. Nucleic Acids Res. 2002; 30(14):3152-62. PMC: 135739. DOI: 10.1093/nar/gkf418. View

20.

Davis K, Akinbi H, Standish A, Weiser J . Resistance to mucosal lysozyme compensates for the fitness deficit of peptidoglycan modifications by Streptococcus pneumoniae. PLoS Pathog. 2008; 4(12):e1000241. PMC: 2587705. DOI: 10.1371/journal.ppat.1000241. View