Structural and Biochemical Characterization Reveals LysGH15 as an Unprecedented “EF-Hand-Like” Calcium-Binding Phage Lysin
The staphylococcal phage lysin LysGH15 demonstrates great potential against methicillin-resistant Staphylococcus aureus (MRSA). Here, we report that the lytic activity of LysGH15 and its CHAP domain is dependent on calcium ions. To elucidate the molecular mechanism, we determined the structures of three individual LysGH15 domains using X-ray crystallography or nuclear magnetic resonance (NMR). The crystal structure unexpectedly reveals an “EF-hand-like” calcium-binding site near the Cys-His-Glu-Asn quartet active site groove in the LysGH15 CHAP domain. Furthermore, the calcium ion plays an important role as a switch that modulates the lytic activity of the CHAP domain. Additionally, structure-guided mutagenesis also confirms that both E282 and the zinc ion play an important role in maintaining the lytic activity of the LysGH15 amidase-2 domain. Moreover, the NMR structure and titration-guided mutagenesis identify residues in the LysGH15 SH3b domain that are involved in the interactions with the substrate. The structure of LysGH15 is the first determined lysin structure from a staphylococcal phage, and these results represent a pivotal step forward in understanding this type of lysin.
Vyšlo v časopise:
Structural and Biochemical Characterization Reveals LysGH15 as an Unprecedented “EF-Hand-Like” Calcium-Binding Phage Lysin. PLoS Pathog 10(5): e32767. doi:10.1371/journal.ppat.1004109
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.ppat.1004109
Souhrn
The staphylococcal phage lysin LysGH15 demonstrates great potential against methicillin-resistant Staphylococcus aureus (MRSA). Here, we report that the lytic activity of LysGH15 and its CHAP domain is dependent on calcium ions. To elucidate the molecular mechanism, we determined the structures of three individual LysGH15 domains using X-ray crystallography or nuclear magnetic resonance (NMR). The crystal structure unexpectedly reveals an “EF-hand-like” calcium-binding site near the Cys-His-Glu-Asn quartet active site groove in the LysGH15 CHAP domain. Furthermore, the calcium ion plays an important role as a switch that modulates the lytic activity of the CHAP domain. Additionally, structure-guided mutagenesis also confirms that both E282 and the zinc ion play an important role in maintaining the lytic activity of the LysGH15 amidase-2 domain. Moreover, the NMR structure and titration-guided mutagenesis identify residues in the LysGH15 SH3b domain that are involved in the interactions with the substrate. The structure of LysGH15 is the first determined lysin structure from a staphylococcal phage, and these results represent a pivotal step forward in understanding this type of lysin.
Zdroje
1. ZollS, PatzoldB, SchlagM, GotzF, KalbacherH, et al. (2010) Structural basis of cell wall cleavage by a staphylococcal autolysin. PLoS Pathog 6: e1000807.
2. SeyboldU, KourbatovaEV, JohnsonJG, HalvosaSJ, WangYF, et al. (2006) Emergence of community-associated methicillin-resistant Staphylococcus aureus USA300 genotype as a major cause of health care-associated blood stream infections. Clin Infect Dis 42: 647–656.
3. DeLeoFR, OttoM (2008) An antidote for Staphylococcus aureus pneumonia? J Exp Med 205: 271–274.
4. MillerLG, Perdreau-RemingtonF, RiegG, MehdiS, PerlrothJ, et al. (2005) Necrotizing fasciitis caused by community-associated methicillin-resistant Staphylococcus aureus in Los Angeles. N Engl J Med 352: 1445–1453.
5. BrumfittW, Hamilton-MillerJ (1989) Methicillin-resistant Staphylococcus aureus. N Engl J Med 320: 1188–1196.
6. EnrightMC (2003) The evolution of a resistant pathogen–the case of MRSA. Curr Opin Pharmacol 3: 474–479.
7. HermosoJA, GarciaJL, GarciaP (2007) Taking aim on bacterial pathogens: from phage therapy to enzybiotics. Curr Opin Microbiol 10: 461–472.
8. FischettiVA (2011) Exploiting what phage have evolved to control gram-positive pathogens. Bacteriophage 1: 188–194.
9. LoefflerJM, NelsonD, FischettiVA (2001) Rapid killing of Streptococcus pneumoniae with a bacteriophage cell wall hydrolase. Science 294: 2170–2172.
10. BorysowskiJ, Weber-DabrowskaB, GorskiA (2006) Bacteriophage endolysins as a novel class of antibacterial agents. Exp Biol Med (Maywood) 231: 366–377.
11. GuJ, XuW, LeiL, HuangJ, FengX, et al. (2011) LysGH15, a novel bacteriophage lysin, protects a murine bacteremia model efficiently against lethal methicillin-resistant Staphylococcus aureus infection. J Clin Microbiol 49: 111–117.
12. GuJ, ZuoJ, LeiL, ZhaoH, SunC, et al. (2011) LysGH15 reduces the inflammation caused by lethal methicillin-resistant Staphylococcus aureus infection in mice. Bioeng Bugs 2: 96–99.
13. GuJ, LiuX, YangM, LiY, SunC, et al. (2013) Genomic characterization of lytic Staphylococcus aureus phage GH15: providing new clues to intron shift in phages. J Gen Virol 94: 906–915.
14. GuJ, LuR, LiuX, HanW, LeiL, et al. (2011) LysGH15B, the SH3b domain of staphylococcal phage endolysin LysGH15, retains high affinity to staphylococci. Curr Microbiol 63: 538–542.
15. SassP, BierbaumG (2007) Lytic activity of recombinant bacteriophage phi11 and phi12 endolysins on whole cells and biofilms of Staphylococcus aureus. Appl Environ Microbiol 73: 347–352.
16. O'FlahertyS, CoffeyA, MeaneyW, FitzgeraldGF, RossRP (2005) The recombinant phage lysin LysK has a broad spectrum of lytic activity against clinically relevant staphylococci, including methicillin-resistant Staphylococcus aureus. J Bacteriol 187: 7161–7164.
17. CabanesD, DehouxP, DussurgetO, FrangeulL, CossartP (2002) Surface proteins and the pathogenic potential of Listeria monocytogenes. Trends Microbiol 10: 238–245.
18. RossiP, AraminiJM, XiaoR, ChenCX, NwosuC, et al. (2009) Structural elucidation of the Cys-His-Glu-Asn proteolytic relay in the secreted CHAP domain enzyme from the human pathogen Staphylococcus saprophyticus. Proteins 74: 515–519.
19. McGuffinLJ, BrysonK, JonesDT (2000) The PSIPRED protein structure prediction server. Bioinformatics 16: 404–405.
20. HolmL, RosenstromP (2010) Dali server: conservation mapping in 3D. Nucleic Acids Res 38: W545–549.
21. McGowanS, BuckleAM, MitchellMS, HoopesJT, GallagherDT, et al. (2012) X-ray crystal structure of the streptococcal specific phage lysin PlyC. Proc Natl Acad Sci U S A 109: 12752–12757.
22. GoldenbergO, ErezE, NimrodG, Ben-TalN (2009) The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures. Nucleic Acids Res 37: D323–327.
23. LowLY, YangC, PeregoM, OstermanA, LiddingtonRC (2005) Structure and lytic activity of a Bacillus anthracis prophage endolysin. J Biol Chem 280: 35433–35439.
24. LuJZ, FujiwaraT, KomatsuzawaH, SugaiM, SakonJ (2006) Cell wall-targeting domain of glycylglycine endopeptidase distinguishes among peptidoglycan cross-bridges. J Biol Chem 281: 549–558.
25. HirakawaH, AkitaH, FujiwaraT, SugaiM, KuharaS (2009) Structural insight into the binding mode between the targeting domain of ALE-1 (92AA) and pentaglycine of peptidoglycan. Protein Eng Des Sel 22: 385–391.
26. ZhouY, YangW, KirbergerM, LeeHW, AyalasomayajulaG, et al. (2006) Prediction of EF-hand calcium-binding proteins and analysis of bacterial EF-hand proteins. Proteins 65: 643–655.
27. FentonM, RossRP, McAuliffeO, O'MahonyJ, CoffeyA (2011) Characterization of the staphylococcal bacteriophage lysin CHAP(K). J Appl Microbiol 111: 1025–1035.
28. DonovanDM, LardeoM, Foster-FreyJ (2006) Lysis of staphylococcal mastitis pathogens by bacteriophage phi11 endolysin. FEMS Microbiol Lett 265: 133–139.
29. PritchardDG, DongS, BakerJR, EnglerJA (2004) The bifunctional peptidoglycan lysin of Streptococcus agalactiae bacteriophage B30. Microbiology 150: 2079–2087.
30. CeliaLK, NelsonD, KerrDE (2008) Characterization of a bacteriophage lysin (Ply700) from Streptococcus uberis. Vet Microbiol 130: 107–117.
31. PetosaC, CollierRJ, KlimpelKR, LepplaSH, LiddingtonRC (1997) Crystal structure of the anthrax toxin protective antigen. Nature 385: 833–838.
32. LytleBL, VolkmanBF, WestlerWM, HeckmanMP, WuJHD (2001) Solution structure of a type I dockerin domain, a novel prokaryotic, extracellular calcium-binding domain. J Mol Biol 307: 745–753.
33. EijsinkVG, MatthewsBW, VriendG (2011) The role of calcium ions in the stability and instability of a thermolysin-like protease. Protein Sci 20: 1346–1355.
34. PaiCH, ChiangBY, KoTP, ChouCC, ChongCM, et al. (2006) Dual binding sites for translocation catalysis by Escherichia coli glutathionylspermidine synthetase. EMBO J 25: 5970–5982.
35. DonovanDM, Foster-FreyJ (2008) LambdaSa2 prophage endolysin requires Cpl-7-binding domains and amidase-5 domain for antimicrobial lysis of streptococci. FEMS Microbiol Lett 287: 22–33.
36. PritchardDG, DongS, KirkMC, CarteeRT, BakerJR (2007) LambdaSa1 and LambdaSa2 prophage lysins of Streptococcus agalactiae. Appl Environ Microbiol 73: 7150–7154.
37. BeckerSC, DongS, BakerJR, Foster-FreyJ, PritchardDG, et al. (2009) LysK CHAP endopeptidase domain is required for lysis of live staphylococcal cells. FEMS Microbiol Lett 294: 52–60.
38. HorganM, O'FlynnG, GarryJ, CooneyJ, CoffeyA, et al. (2009) Phage lysin LysK can be truncated to its CHAP domain and retain lytic activity against live antibiotic-resistant staphylococci. Appl Environ Microbiol 75: 872–874.
39. KerffF, PetrellaS, MercierF, SauvageE, HermanR, et al. (2010) Specific structural features of the N-acetylmuramoyl-L-alanine amidase AmiD from Escherichia coli and mechanistic implications for enzymes of this family. J Mol Biol 397: 249–259.
40. McLaughlinS, WangJ, GambhirA, MurrayD (2002) PIP(2) and proteins: interactions, organization, and information flow. Annu Rev Biophys Biomol Struct 31: 151–175.
41. LiangW, OuyangS, ShawN, JoachimiakA, ZhangR, et al. (2011) Conversion of D-ribulose 5-phosphate to D-xylulose 5-phosphate: new insights from structural and biochemical studies on human RPE. FASEB J 25: 497–504.
42. OtwinowskiZ, MinorW (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods in Enzymology 276: 307–326.
43. RuH, ZhaoL, DingW, JiaoL, ShawN, et al. (2012) S-SAD phasing study of death receptor 6 and its solution conformation revealed by SAXS. Acta Crystallogr D Biol Crystallogr 68: 521–530.
44. LiuZJ, LinD, TempelW, PraissmanJL, RoseJP, et al. (2005) Parameter-space screening: a powerful tool for high-throughput crystal structure determination. Acta Crystallogr D Biol Crystallogr 61: 520–527.
45. HendricksonWA (1991) Determination of macromolecular structures from anomalous diffraction of synchrotron radiation. Science 254: 51–58.
46. AdamsPD, AfoninePV, BunkocziG, ChenVB, DavisIW, et al. (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 66: 213–221.
47. EmsleyP, LohkampB, ScottWG, CowtanK (2010) Features and development of Coot. Acta Crystallogr D Biol Crystallogr 66: 486–501.
48. MurshudovGN, VaginAA, DodsonEJ (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 53: 240–255.
49. GongW, ZhouT, MoJ, PerrettS, WangJ, et al. (2012) Structural insight into recognition of methylated histone tails by retinoblastoma-binding protein 1. J Biol Chem 287: 8531–8540.
50. DelaglioF, GrzesiekS, VuisterGW, ZhuG, PfeiferJ, et al. (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6: 277–293.
51. JohnsonBA (2004) Using NMRView to visualize and analyze the NMR spectra of macromolecules. Methods Mol Biol 278: 313–352.
52. MarkleyJL, BaxA, ArataY, HilbersCW, KapteinR, et al. (1998) Recommendations for the presentation of NMR structures of proteins and nucleic acids - (IUPAC Recommendations 1998). Pure Appl Chem 70: 117–142.
53. HerrmannT, GuntertP, WuthrichK (2002) Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Mol Biol 319: 209–227.
54. BrungerAT, AdamsPD, CloreGM, DeLanoWL, GrosP, et al. (1998) Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 54: 905–921.
55. DugganBM, LeggeGB, DysonHJ, WrightPE (2001) SANE (Structure Assisted NOE Evaluation): an automated model-based approach for NOE assignment. J Biomol NMR 19: 321–329.
56. ShenY, BaxA (2013) Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks. J Biomol NMR 56: 227–241.
57. NederveenAJ, DoreleijersJF, VrankenW, MillerZ, SpronkCA, et al. (2005) RECOORD: a recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank. Proteins 59: 662–672.
58. KoradiR, BilleterM, WuthrichK (1996) MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graph 14: 51–55, 29–32.
59. LaskowskiRA, RullmannnJA, MacArthurMW, KapteinR, ThorntonJM (1996) AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR 8: 477–486.
60. OuyangS, SongX, WangY, RuH, ShawN, et al. (2012) Structural analysis of the STING adaptor protein reveals a hydrophobic dimer interface and mode of cyclic di-GMP binding. Immunity 36: 1073–1086.
61. BaytakS, ZereenF, ArslanZ (2011) Preconcentration of trace elements from water samples on a minicolumn of yeast (Yamadazyma spartinae) immobilized TiO2 nanoparticles for determination by ICP-AES. Talanta 84: 319–323.
62. WangL, YangX, LiS, WangZ, LiuY, et al. (2014) Structural and mechanistic insights into MICU1 regulation of mitochondrial calcium uptake. EMBO J 33: 594–604 (DOI: 10.1002/embj.201386523)
63. ZhaoL, HuaT, CrowleyC, RuH, NiX, et al. (2014) Structural analysis of asparaginyl endopeptidase reveals the activation mechanism and a reversible intermediate maturation stage. Cell Res 24: 344–358.
64. LavinderJJ, HariSB, SullivanBJ, MaglieryTJ (2009) High-throughput thermal scanning: a general, rapid dye-binding thermal shift screen for protein engineering. J Am Chem Soc 131: 3794–3795.
65. FyfePK, OzaSL, FairlambAH, HunterWN (2008) Leishmania trypanothione synthetase-amidase structure reveals a basis for regulation of conflicting synthetic and hydrolytic activities. J Biol Chem 283: 17672–17680.
66. LowLY, YangC, PeregoM, OstermanA, LiddingtonR (2011) Role of net charge on catalytic domain and influence of cell wall binding domain on bactericidal activity, specificity, and host range of phage lysins. J Biol Chem 286: 34391–34403.
67. Delano W (2002) PyMOL. New York, NY: Schrodinger, Inc. Available: http://www.pymol.org.
Štítky
Hygiena a epidemiológia Infekčné lekárstvo LaboratóriumČlánok vyšiel v časopise
PLOS Pathogens
2014 Číslo 5
- Parazitičtí červi v terapii Crohnovy choroby a dalších zánětlivých autoimunitních onemocnění
- Očkování proti virové hemoragické horečce Ebola experimentální vakcínou rVSVDG-ZEBOV-GP
- Koronavirus hýbe světem: Víte jak se chránit a jak postupovat v případě podezření?
Najčítanejšie v tomto čísle
- Venus Kinase Receptors Control Reproduction in the Platyhelminth Parasite
- Dual-Site Phosphorylation of the Control of Virulence Regulator Impacts Group A Streptococcal Global Gene Expression and Pathogenesis
- Severe Acute Respiratory Syndrome Coronavirus Envelope Protein Ion Channel Activity Promotes Virus Fitness and Pathogenesis
- High-Efficiency Targeted Editing of Large Viral Genomes by RNA-Guided Nucleases