Structural Basis of Murein Peptide Specificity of a γ-D-Glutamyl-L-Diamino Acid Endopeptidase

Xu, Qingping; Sudek, Sebastian; McMullan, Daniel; Miller, Mitchell D.; Geierstanger, Bernhard H.; Jones, David H.; Krishna, Sanjeev; Spraggon, Glen; Bursalay, Badry; Abdubek, Polat; Acosta, Claire; Ambing, Eileen; Astakhova, Tamara; Axelrod, Herbert L.; Carlton, Dennis; Caruthers, J.M.; Chiu, Hsiu‐Ju; Clayton, Thomas; Deller, Marc C.; Duan, Lian; Elias, Ylva; Elsliger, Marc‐André; Feuerhelm, Julie; Grzechnik, Slawomir K.; Hale, Joanna; Han, Gye Won; Haugen, Justin; Jaroszewski, Lukasz; Jin, Kevin K.; Klock, Heath E.; Knuth, Mark W.; Koźbiał, Piotr; Kumar, Abhinav; Marciano, David; Morse, Andrew; Nigoghossian, Edward; Okach, Linda; Oommachen, Silvya; Paulsen, Jessica; Reyes, Ron; Rife, Christopher L.; Trout, Christina V.; Bedem, Henry van den; Weekes, Dana; White, Aprilfawn; Wolf, Guenter; Zubieta, Chloé; Hodgson, Keith O.; Wooley, John; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Wilson, Ian A.

doi:10.1016/j.str.2008.12.008

Cited by 67 publications

(101 citation statements)

References 58 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In this superfamily of papain-like enzymes, a conserved cysteine residue was predicted to be a catalytic residue on amino acid sequence alignment (2,16). Recently, the three-dimensional structures of NlpC/P60 enzymes were reported (Spr from E. coli, ABA23003 from Anabaena variabilis, and ACC79413 from Nostoc punctiforme) (3,26). In these enzymes, the conserved cysteine residues are located at a predicted active site and are structurally conserved.…”

Section: Dl-endopeptidase Activity Of Lyte or Cwlo Is Essential For mentioning

confidence: 99%

Synthetic Lethality of the lytE cwlO Genotype in Bacillus subtilis Is Caused by Lack of d , l -Endopeptidase Activity at the Lateral Cell Wall

2012

View full text Add to dashboard Cite

Bacterial peptidoglycan acts as an exoskeleton to protect the bacterial cell. Although peptidoglycan biosynthesis by penicillinbinding proteins is well studied, few studies have described peptidoglycan disassembly, which is necessary for a dynamic structure that allows cell growth. In Bacillus subtilis, more than 35 genes encoding cell wall lytic enzymes have been identified; however, only two D,L-endopeptidases (lytE and cwlO) are involved in cell proliferation. In this study, we demonstrated that the D,L-endopeptidase activity at the lateral cell wall is essential for cell proliferation. Inactivation of LytE and CwlO by point mutation of the catalytic residues caused cell growth defects. However, the forced expression of LytF or CwlS, which are paralogs of LytE, did not suppress lytE cwlO synthetic lethality. Subcellular localization studies of these D,L-endopeptidases showed LytF and CwlS at the septa and poles, CwlO at the cylindrical part of the cell, and LytE at the septa and poles as well as the cylindrical part. Furthermore, construction of N-terminal and C-terminal domain-swapped enzymes of LytE, LytF, CwlS, and CwlO revealed that localization was dependent on the N-terminal domains. Only the chimeric proteins that were enzymatically active and localized to the sidewall were able to suppress the synthetic lethality, suggesting that the lack of D,L-endopeptidase activity at the cylindrical part of the cell leads to a growth defect. The functions of LytE and CwlO in cell morphogenesis were discussed.

show abstract

Section: Dl-endopeptidase Activity Of Lyte or Cwlo Is Essential For mentioning

confidence: 99%

Synthetic Lethality of the lytE cwlO Genotype in Bacillus subtilis Is Caused by Lack of d , l -Endopeptidase Activity at the Lateral Cell Wall

2012

View full text Add to dashboard Cite

show abstract

“…Structural analyses of Spr (39), AvPCP and NpPCP endopeptidases from cyanobacteria (48), and YkfC from B. cereus (BcYkfC) (49), from the NlpC/P60 family, showed a characteristic Cys-His-His catalytic triad in the active sites of these cys- teine peptidases. In the deduced active sites of LytF, LytE, CwlS, CwlO, and PgdS (shown as red arrowheads in Fig.…”

Section: Structural and Surface Properties Of Catalytic Domains Of DLmentioning

confidence: 99%

Solution Structure of IseA, an Inhibitor Protein of dl-Endopeptidases from Bacillus subtilis, Reveals a Novel Fold with a Characteristic Inhibitory Loop

Arai

Fukui

Kobayashi

et al. 2012

Journal of Biological Chemistry

View full text Add to dashboard Cite

Background:IseA from Bacillus subtilis is an inhibitor protein against DL-endopeptidases including synthetic lethal autolysins. Results: We solved the solution structure of IseA using NMR. Titration with LytF DL-endopeptidase indicated interaction sites around the loop region. Conclusion: The IseA structure revealed a novel "hacksaw"-like fold with a characteristic inhibitory loop. Significance: The results suggest a new inhibition mechanism of IseA with a unique loop.

show abstract

“…PcsB contains a CHAP domain found in some phage and bacterial murein amidases and endopeptidases ( Fig. 1) (2,29,56,71). PcsB is a relatively abundant (ϳ5,000 monomers per cell) protein whose function is essential, although bypass suppressors can be isolated (1; unpublished data).…”

mentioning

confidence: 99%

Characterization of Mutants Deficient in the l,d -Carboxypeptidase (DacB) and WalRK (VicRK) Regulon, Involved in Peptidoglycan Maturation of Streptococcus pneumoniae Serotype 2 Strain D39

2011

View full text Add to dashboard Cite

Peptidoglycan (PG) hydrolases play critical roles in the remodeling of bacterial cell walls during division. PG hydrolases have been studied extensively in several bacillus species, such as Escherichia coli and Bacillus subtilis, but remain relatively uncharacterized in ovococcus species, such as Streptococcus pneumoniae (pneumococcus). In this work, we identified genes that encode proteins with putative PG hydrolytic domains in the genome of S. pneumoniae strain D39. Knockout mutations in these genes were constructed, and the resulting mutants were characterized in comparison with the parent strain for growth, cell morphology, PG peptide incorporation, and in some cases, PG peptide composition. In addition, we characterized deletion mutations in nonessential genes of unknown function in the WalRK Spn two-component system regulon, which also contains the essential pcsB cell division gene. Several mutants did not show overt phenotypes, which is perhaps indicative of redundancy. In contrast, two new mutants showed distinct defects in PG biosynthesis. One mutation was in a gene designated dacB (spd_0549), which we showed encodes an L,D-carboxypeptidase involved in PG maturation. Notably, dacB mutants, similar to dacA (D,D-carboxypeptidase) mutants, exhibited defects in cell shape and septation, consistent with the idea that the availability of PG peptide precursors is important for proper PG biosynthesis. Epistasis analysis indicated that DacA functions before DacB in D-Ala removal, and immunofluorescence microscopy showed that DacA and DacB are located over the entire surface of pneumococcal cells. The other mutation was in WalRK Spn regulon gene spd_0703, which encodes a putative membrane protein that may function as a type of conserved streptococcal shape, elongation, division, and sporulation (SEDS) protein.

show abstract

Structural Basis of Murein Peptide Specificity of a γ-D-Glutamyl-L-Diamino Acid Endopeptidase

Cited by 67 publications

References 58 publications

Synthetic Lethality of the lytE cwlO Genotype in Bacillus subtilis Is Caused by Lack of d , l -Endopeptidase Activity at the Lateral Cell Wall

Synthetic Lethality of the lytE cwlO Genotype in Bacillus subtilis Is Caused by Lack of d , l -Endopeptidase Activity at the Lateral Cell Wall

Solution Structure of IseA, an Inhibitor Protein of dl-Endopeptidases from Bacillus subtilis, Reveals a Novel Fold with a Characteristic Inhibitory Loop

Characterization of Mutants Deficient in the l,d -Carboxypeptidase (DacB) and WalRK (VicRK) Regulon, Involved in Peptidoglycan Maturation of Streptococcus pneumoniae Serotype 2 Strain D39

Contact Info

Product

Resources

About