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Research Article

Structural and Functional Insights into Peptidoglycan Access for the Lytic Amidase LytA of Streptococcus pneumoniae

Peter Mellroth, Tatyana Sandalova, Alexey Kikhney, Francisco Vilaplana, Dusan Hesek, Mijoon Lee, Shahriar Mobashery, Staffan Normark, Dmitri Svergun, Birgitta Henriques-Normark, Adnane Achour
Rino Rappuoli, Editor
Peter Mellroth
aDepartment of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
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Tatyana Sandalova
bScience for Life Laboratory, Center for Infectious Medicine (CIM), Department of Medicine, Karolinska University Hospital Huddinge, Karolinska Institutet, Stockholm, Sweden
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Alexey Kikhney
cEuropean Molecular Biology Laboratory (EMBL), Hamburg Outstation, Hamburg, Germany
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Francisco Vilaplana
dDivision of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, Sweden
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Dusan Hesek
eDepartments of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
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Mijoon Lee
eDepartments of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
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Shahriar Mobashery
eDepartments of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
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Staffan Normark
aDepartment of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
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Dmitri Svergun
cEuropean Molecular Biology Laboratory (EMBL), Hamburg Outstation, Hamburg, Germany
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Birgitta Henriques-Normark
aDepartment of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
fDepartment of Laboratory Medicine, Division of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
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Adnane Achour
bScience for Life Laboratory, Center for Infectious Medicine (CIM), Department of Medicine, Karolinska University Hospital Huddinge, Karolinska Institutet, Stockholm, Sweden
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Rino Rappuoli
Novartis Vaccines and Diagnostics
Roles: Editor
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DOI: 10.1128/mBio.01120-13
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  • FIG 1 
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    FIG 1 

    The catalytic N-terminal amidase domain of LytA contains a Y-shaped substrate-binding crevice. (A) The overall three-dimensional structure of LytAAMI is presented in two perpendicular views. The catalytic Zn2+ ion is displayed as a pink sphere. The cysteine residues, both mutated to alanine, are also pink. α-Helices, β-sheets, and loops are colored purple, yellow, and green, respectively. (B) Interactions between the octahedrally coordinated Zn2+ ion and residues His26, His133, Asp149, and three water molecules within the active site are indicated by dashed purple lines. Catalytic residues, Zn2+ ligands, and residues coordinating water molecules are green, purple, and white, respectively. Two hydrogen bonds formed between cis-Pro150 and residues His133 and Glu134, both located on helix α4, are dashed gray lines. Hydrogen bonds formed between Zn2+-bound water molecules and LytAAMI residues are dashed green lines.

  • FIG 2 
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    FIG 2 

    A muropeptide fragment comprising a pentasaccharide motif fits snugly within the Y-shaped substrate-binding crevice of LytAAMI. (A) Surface of LytAAMI, with the Y-shaped substrate-binding crevice colored in green and the three contiguous subregions α, β, and γ indicated. The catalytic Zn2+ ion is displayed as a pink sphere, and the locations of key substrate-interacting residues are marked. (B) A molecular model of a PG fragment consisting of five sugars (MurNAc-GlcNAc-MurNAc-GlcNAc-MurNAc, with a stem peptide linked to the central MurNAc) was placed within the substrate-binding crevices of LytAAMI. The position of the substrate fragment M5P within the active site was first obtained by superposing the crystal structure of LytAAMI on PGRP-Iα in complex with M5P (Protein Data Bank [PDB] accession number 2APH). Sugar chains and peptide stems were thereafter added to both ends of M5P in order to create the M(GM5P) GM fragment. The surface is colored according to electrostatic potentials; purple represents acidic and red basic residues. (C) The PG motif M(GM5P) GM fits snugly into the binding crevice of AmiE, taking the same conformation as in the molecular model of LytA. (D) The surface representation of the crystal structure of AmpD in complex with the reaction product reveals significant differences in the structural shapes and the electrostatic potentials of the substrate-binding crevice.

  • FIG 3 
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    FIG 3 

    A motif corresponding to the tetrasaccharide muropeptide substrate (di-GM5P) is cleaved by LytA. (A) Incubation of the GM5P substrate with LytA or inactive LytA-H133A does not result in any product peak, as demonstrated by the HPAEC-PAD analysis. The chromatogram for GM5P incubated in buffer alone is provided for comparison. The masses of the substrate peak were determined using MALDI-TOF MS (right panels). Calculated masses and a cartoon of the corresponding substrate are shown (lower panels). (B) Incubation of the tetra-saccharide substrate di-GM5P (peak 1) with either wt-LytA or LytAMI resulted in the production of two new peaks (2 and 3), as determined by HPAEC-PAD. In contrast, no peaks appeared following incubation with inactive LytA-H133A. The profile of di-GM5P incubated with buffer alone is also provided as a reference. The masses of the substrate and of each product peak were determined using MALDI-TOF MS (right panels). Calculated masses of the substrate (di-GM5P) and products (GMGM5P and 5P) and corresponding cartoons are shown (lower panels).

  • FIG 4 
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    FIG 4 

    The C-terminal domain of phage LytA contains six choline-binding sites. (A) Two perpendicular views of the crystal structure of p-LytACBD, comprising residues 173 to 318. The numbering of the β-strands, starting with number 8, reflects their positions in the full-length LytA (numbers 1 to 7 in the amidase domain). The β-hairpin formed by β8 and β9 constitute the last-step, solenoid-shaped choline-binding domain, which faces the amidase domain on its N-terminal side. (B) The classical choline-binding site, localized between residues Trp178 and Tyr185, was not occupied by a choline molecule in the crystal, most likely due to a crystal packing artifact. However, a clear electron density for choline was present in the second nonclassical choline-binding site formed by residues Trp186, Tyr194, and Tyr214. The 1σ electron density in the 2Fo-Fc omit map is displayed in blue. (C) The dimer of p-LytACBD, generated along the crystallographic 2-fold axis, indicates the possibility for simultaneous binding of 12 choline molecules. Orange boxes represent consensus choline binding sites that were not occupied by cholines in the crystal structure.

  • FIG 5 
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    FIG 5 

    The full-length LytA dimer adopts a rigid V-shaped scaffold with the two amidase domains in the trans configuration. (A) SAXS data demonstrate that the wild type and bacteriophage LytA are similar in shape and that both form dimers in solution in the presence of choline (curves 1 and 2, respectively). Without choline, the same molecule is monomeric in solution (curve 3). The CBD of wt-LytA forms a dimer in solution, in line with results from the crystal structure (curve 4). The logarithm of the scattering intensity is displayed versus momentum transfer (s = 4π sinθ/λ), where 2θ is the scattering angle and λ (the X-ray scattering wavelength) is 1.5 Å. The data for different samples were offset vertically for clarity (dots, experimental data; smooth curves, scattering computed from the models). a.u., arbitrary units. (B) Ab initio model of the wt-LytA dimer (gray spheres) superimposed with the best rigid-body model using the crystal structures of LytAAMI and p-LytACBD (ribbons). (C) Three perpendicular views of the rigid-body model of the full-length LytA dimer reveal the trans configurations of the amidase domains. Surfaces are colored according to surface charge representation.

Tables

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  • TABLE 1 

    Data collection and refinement statistics

    ParameterResult(s) forc:
    LytAAMILytAAMIp-LytACBD
    PDB code4IVV4IWT
    Data collection statistics
        Wavelength (Å)0.9791.28 (Zn peak)0.976
        Resolution (Å) (range)43.7–1.05 (1.11–1.05)43.7–1.5 (1.58–1.5)40.5–2.6 (2.74–2.6)
        Space groupP32P32P21
        Cell dimensions for a, b, c (Å)50.4, 50.4, 72.650.4, 50.4, 72.540.58, 113.4, 40.64
        α, β, γ (°)90.0, 90.0, 120.090.0, 90.0, 120.090.0, 94.9, 90.0
    No. of reflectionsa
        Observed253,820 (36,305)325,209 (44,377)29,567 (3,739)
        Unique95,581 (14,111)10,591 (4)10,591 (1,495)
        <I/s(I)>7.3 (1.7)30.0 (17.7)7.4 (1.8)
        Completeness (%)99 (100)99.9 (99.9)93.9 (90.1)
        Rmerge (%)6.8 (53.2)5.7 (9.7)14.0 (61.5)
        Solvent content in the crystal (%)535352
        B-factor from Wilson plot (Å2)812.848.5
        Anomalous completeness (%)99.7 (99.9)
        DelAnom correlation between half-sets0.23 (0.3)
        Midslope of anomalous normal probability1.554
    Refinement statisticsb
        Rcryst (%)14.9721.16
        Rfree (%)16.2428.2
        No. of atoms
            Total1,6402,509
            Protein1,4272,478
            Solvent25540
        No. of ligands210
    Avg B-factor values
        Protein main chains (Å2)10.530.7
        Protein side chains (Å2)12.331.7
        Zn/choline (Å2)1050
        Solvent (Å2)31.225
        RMSD from ideal geometry
            Bond length (Å)0.0060.01
            Bond angle (°)1.171.25
        Ramachandran plot
            % of residues in preferred regions98.794.4
            % of residues in disallowed regions00
    • ↵a Values in parentheses correspond to the highest-resolution shell.

    • ↵b Five percent of reflections were used for monitoring the refinement.

    • ↵c The two colums for LytAAMI represent data sets collected at different X-ray wavelengths. Both sets were required for solving the structure.

  • TABLE 2 

    Activities of LytA point mutants in the turbidity lysis assay

    Mutation(s)ActivityaFunction or positionb
    None (wt-LytA)*****
    H24A−Buried
    H26A−Zinc ligand
    H54A−Buried
    E87A−Catalytic
    H133A−Zinc ligand
    D149A−Zinc ligand
    S33Q*β-Region
    Y41A/R*β-Region
    K131A*Buried
    H147A/K*Catalytic
    N30L/Q***β-Region
    R44E/Q***β-Region
    W72A***γ-Region
    G75A***γ-Region
    N79A***γ-Region
    V148E/K***α-Region
    G29A****α-Region
    S33A****β-Region
    C60R****Peripheral
    S91A****Peripheral
    K45R*****Branch point
    F52A/V*****β-Region
    C60A/E*****Peripheral
    C60A + C136A*****Peripheral + buried
    C136A*****Buried
    T137A*****Peripheral
    N142A*****Peripheral
    H144A*****γ-Region
    S145A*****Branch point
    H166A*****Peripheral
    • ↵a The relative enzymatic activities of LytA protein variants are given in the following intervals: *****, 100 to 80%; ****, 79 to 60%; ***, 59 to 40%; **, 39 to 20%; *, 19 to 5%; −, 4 to 0%.

    • ↵b Buried residues are part of the hydrophobic core, and peripheral residues are surface-exposed residues outside the binding crevice. Zinc ligand and catalytic residues form the catalytic center. Branch point residues and α-, β-, and γ-regions represent subregions of the binding crevice.

Supplemental Material

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  • FIG S1

    Sequence alignment of LytA, prophage p-LytA, and AmiE. The sequences of LytA, prophage p-LytA, and Staphylococcus epidermidis AmiE (PDB 3LAT) were aligned using CLUSTAL W. Red boxes indicate residues conserved among the three autolysins. Residues which are not conserved between LytA and p-LytA are shown in green frames. The secondary structures derived from the crystal structures of the LytAAMI and LytACBD domains are depicted in black and blue, respectively. Red stars indicate key catalytic residues. α, β, and γ indicate residues lining each respective subregion within the binding crevice, and × indicates the noncatalytic residues located at the branch point. Aromatic residues involved in choline binding are indicated by blue squares. Download Figure S1, TIF file, 12.9 MB.

    Copyright © 2014 Mellroth et al.

    This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.

  • FIG S2

    Comparative circular-dichroism analysis demonstrates that mutation of both cysteine residues to alanine does not alter the overall fold of LytA. The far-UV circular-dichroism spectra of singly and doubly mutated LytA and wt-LytA show that the proteins have similar folds. Download Figure S2, TIF file, 4.6 MB.

    Copyright © 2014 Mellroth et al.

    This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.

  • FIG S3

    Key LytA residues for substrate binding and catalysis line the entire Y-shaped binding crevice. Site-directed mutagenesis combined with functional studies allowed us to map key catalytic residues, residues with intermediary importance, and residues that do not affect catalysis, colored in pink, yellow, and green, respectively. All the residues that are important for catalysis are localized within the entire length of the Y-shaped binding crevice. Download Figure S3, TIF file, 3.1 MB.

    Copyright © 2014 Mellroth et al.

    This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.

  • TABLE S1

    Structural superimposition of active-site residues of LytA and its five closest structural homologs. Table S1, DOCX file, 0.1 MB.

    Copyright © 2014 Mellroth et al.

    This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.

  • FIG S5

    Microscale thermophoresis binding dynamics suggest that multiple point interactions are essential for efficient muropeptide binding to LytA. LytA-H133A (0.5 µM) was incubated with serial dilutions (ranging from 1 mM to 30 nM) of di-GM5P (A), GM5P (B), and M5P (C). The insets display raw thermophoresis data recorded at 23°C using a light-emitting diode (LED) at 50% and an infrared laser at 60%. Data points represent results from a typical Master Software Tools (MST) experiment, and the curve fitting the experiment was obtained using the MST analysis software. Download Figure S5, TIF file, 6 MB.

    Copyright © 2014 Mellroth et al.

    This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.

  • TABLE S2

    SAXS data collection and analysis parameters. Table S2, DOCX file, 0.1 MB.

    Copyright © 2014 Mellroth et al.

    This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.

  • FIG S6

    SAXS models of the LytA dimer suggest rigid CBDs and flexible LytAAMI head groups. (A) Experimental SAXS data from wt-LytA fitted with an ensemble of models selected by EOM from the initial pool of 10,000 models with random orientations of the N termini. (B) The initial pool of 10,000 models with random orientations of the N termini has a broad distribution of Rg values (blue bars). The Rg distribution of the ensemble selected by EOM is narrower; however, it indicates a certain flexibility of the N-terminal domains (red bars). (C) The 10 best models of the full-length LytA dimer obtained from EOM analysis (χ = 1.8) indicate a certain level of lateral flexibility of the LytAAMI domains, while the LytACBD dimer is rigid. Download Figure S6, TIF file, 9.7 MB.

    Copyright © 2014 Mellroth et al.

    This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.

  • TEXT S1

    Supplemental materials and methods and supplemental references. Data collection, processing and structural determination of the amidase domain of LytA and of the choline-binding domain of prophage LytA. Ab initio shape determination and molecular modeling, circular-dichroism analysis results, microscale thermophoresis, and references. Download Text S1, PDF file, 0.1 MB.

    Copyright © 2014 Mellroth et al.

    This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.

  • FIG S4

    The monosaccharide (M5P) substrate is not cleaved by LytA. (a) Incubation of the M5P substrate with either LytA or LytA-H133 does not result in any product peak, as demonstrated by HPAEC-PAD analysis. The chromatogram for the substrate alone is also provided for comparison. MALDI-TOF MS analysis confirmed that no cleavage products were formed for the substrate following incubation with either LytA or LytA-H133. The mass-to-charge clusters correspond to both substrates with different Na substitutions. (b) The chemical composition of the M5P substrate is drawn. Download Figure S4, TIF file, 11 MB.

    Copyright © 2014 Mellroth et al.

    This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.

Additional Files

  • Figures
  • Tables
  • Supplemental Material
  • Supplementary Data

    Supplementary Data

    Files in this Data Supplement:

    • Text s1, PDF - Text s1, PDF
    • Figure sf01, TIF - Figure sf01, TIF
    • Figure sf02, TIF - Figure sf02, TIF
    • Figure sf03, TIF - Figure sf03, TIF
    • Figure sf04, TIF - Figure sf04, TIF
    • Figure sf05, TIF - Figure sf05, TIF
    • Figure sf06, TIF - Figure sf06, TIF
    • Table st1, DOCX - Table st1, DOCX
    • Table st2, DOCX - Table st2, DOCX
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Structural and Functional Insights into Peptidoglycan Access for the Lytic Amidase LytA of Streptococcus pneumoniae
Peter Mellroth, Tatyana Sandalova, Alexey Kikhney, Francisco Vilaplana, Dusan Hesek, Mijoon Lee, Shahriar Mobashery, Staffan Normark, Dmitri Svergun, Birgitta Henriques-Normark, Adnane Achour
mBio Feb 2014, 5 (1) e01120-13; DOI: 10.1128/mBio.01120-13

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Structural and Functional Insights into Peptidoglycan Access for the Lytic Amidase LytA of Streptococcus pneumoniae
Peter Mellroth, Tatyana Sandalova, Alexey Kikhney, Francisco Vilaplana, Dusan Hesek, Mijoon Lee, Shahriar Mobashery, Staffan Normark, Dmitri Svergun, Birgitta Henriques-Normark, Adnane Achour
mBio Feb 2014, 5 (1) e01120-13; DOI: 10.1128/mBio.01120-13
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