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Olszak T, Shneider MM, Latka A, Maciejewska B, Browning C, Sycheva LV, Comer JE, Danis-Wlodarczyk K, Senchenkova SN, Shashkov AS, Gula G, Arabski M, Wasik S, Miroshnikov KA, Lavigne R, Leiman PG, Knirel YA, Drulis-Kawa Z
The O-specific polysaccharide lyase from the phage LKA1 tailspike reduces Pseudomonas virulence
Scientific Reports 7(1) (2017)
16302
|
-4)-b-D-ManpNAc3NAmA-(1-4)-b-D-ManpNAc3NAcA-(1-3)-a-D-FucpNAc-(1- |
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Pseudomonas aeruginosa O5 (170005)
(Ancestor NCBI TaxID 287,
species name lookup)
Taxonomic group: bacteria / Proteobacteria
(Phylum: Proteobacteria)
Associated disease: infection due to Pseudomonas aeruginosa [ICD11:
XN5L6 
]
Publication DOI: 10.1038/s41598-017-16411-4Journal NLM ID: 101563288Publisher: London: Nature Publishing Group
Correspondence: Zuzanna Drulis-Kawa <zuzanna.drulis-kawa
uwr.edu.pl>
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Institute of Genetics and Microbiology, University of Wroclaw, Wroclaw, 51-148, Poland, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia, University of Texas Medical Branch, Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, Galveston, TX, 77555-0647, USA, Vertex Pharmaceuticals (Europe) Ltd, Abingdon, Oxfordshire, OX14 4RW, UK, Affinivax Inc., Cambridge, MA, USA, Laboratory of Gene Technology, KU Leuven, Leuven, 3001, Belgium, Department of Biochemistry and Genetics, Institute of Biology, The Jan Kochanowski University in Kielce, Kielce, 25-406, Poland, Department of Molecular Physics, Institute of Physics, The Jan Kochanowski University in Kielce, Kielce, 25-406, Poland
Pseudomonas phage LKA1 of the subfamily Autographivirinae encodes a tailspike protein (LKA1gp49) which binds and cleaves B-band LPS (O-specific antigen, OSA) of Pseudomonas aeruginosa PAO1. The crystal structure of LKA1gp49 catalytic domain consists of a beta-helix, an insertion domain and a C-terminal discoidin-like domain. The putative substrate binding and processing site is located on the face of the beta-helix whereas the C-terminal domain is likely involved in carbohydrates binding. NMR spectroscopy and mass spectrometry analyses of degraded LPS (OSA) fragments show an O5 serotype-specific polysaccharide lyase specificity. LKA1gp49 reduces virulence in an in vivo Galleria mellonella infection model and sensitizes P. aeruginosa to serum complement activity. This enzyme causes biofilm degradation and does not affect the activity of ciprofloxacin and gentamicin. This is the first comprehensive report on LPS-degrading lyase derived from a Pseudomonas phage. Biological properties reveal a potential towards its applications in antimicrobial design and as a microbiological or biotechnological tool.
genetic, X-ray, O-specific polysaccharide, Enzymes, lyase, bacteriophage, Pseudomonas phage
Structure type: polymer chemical repeating unit
Location inside paper: fig.3, OPS I
Trivial name: B band polysaccharide, B-band polysaccharide
Compound class: O-polysaccharide, O-antigen
Methods: 13C NMR, 1H NMR, NMR-2D, X-ray, SDS-PAGE, sugar analysis, mild acid hydrolysis, biological assays, genetic methods, GPC, enzyme assay, cloning, crystallization, phage degradation, HR ESI-MS
3D data: 3D data
Related record ID(s): 12192, 12193
NCBI Taxonomy refs (TaxIDs): 287Reference(s) to other database(s): GlycomeDB:
33661
Show glycosyltransferases
There is only one chemically distinct structure:
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Olszak T, Shneider MM, Latka A, Maciejewska B, Browning C, Sycheva LV, Comer JE, Danis-Wlodarczyk K, Senchenkova SN, Shashkov AS, Gula G, Arabski M, Wasik S, Miroshnikov KA, Lavigne R, Leiman PG, Knirel YA, Drulis-Kawa Z
The O-specific polysaccharide lyase from the phage LKA1 tailspike reduces Pseudomonas virulence
Scientific Reports 7(1) (2017)
16302
|
a-L-Sugp2Ac3Ac-(1-3)-a-D-FucpNAc-(1-4)-Subst
Sug = 2,3-diamino-2,3,4-trideoxy-L-erythro-hex-4,5-enuronic acid = SMILES N{3}[C@H]1C=C(C(O)=O)O{1}[C@@H](O){2}[C@H]1N;
Subst = Am,1-cyclo-D-ManaN3NAmA = SMILES O[C@@H]1C(NC(C)=O)[C@H]({4}[C@H](O)[C@@H](C(O)=O)O)N[C@H](N1)C |
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Pseudomonas aeruginosa O5 170005
(Ancestor NCBI TaxID 287,
species name lookup)
Taxonomic group: bacteria / Proteobacteria
(Phylum: Proteobacteria)
Associated disease: infection due to Pseudomonas aeruginosa [ICD11:
XN5L6 ]
The structure was elucidated in this paperPublication DOI: 10.1038/s41598-017-16411-4Journal NLM ID: 101563288Publisher: London: Nature Publishing Group
Correspondence: Zuzanna Drulis-Kawa <zuzanna.drulis-kawa
uwr.edu.pl>
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Institute of Genetics and Microbiology, University of Wroclaw, Wroclaw, 51-148, Poland, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia, University of Texas Medical Branch, Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, Galveston, TX, 77555-0647, USA, Vertex Pharmaceuticals (Europe) Ltd, Abingdon, Oxfordshire, OX14 4RW, UK, Affinivax Inc., Cambridge, MA, USA, Laboratory of Gene Technology, KU Leuven, Leuven, 3001, Belgium, Department of Biochemistry and Genetics, Institute of Biology, The Jan Kochanowski University in Kielce, Kielce, 25-406, Poland, Department of Molecular Physics, Institute of Physics, The Jan Kochanowski University in Kielce, Kielce, 25-406, Poland
Pseudomonas phage LKA1 of the subfamily Autographivirinae encodes a tailspike protein (LKA1gp49) which binds and cleaves B-band LPS (O-specific antigen, OSA) of Pseudomonas aeruginosa PAO1. The crystal structure of LKA1gp49 catalytic domain consists of a beta-helix, an insertion domain and a C-terminal discoidin-like domain. The putative substrate binding and processing site is located on the face of the beta-helix whereas the C-terminal domain is likely involved in carbohydrates binding. NMR spectroscopy and mass spectrometry analyses of degraded LPS (OSA) fragments show an O5 serotype-specific polysaccharide lyase specificity. LKA1gp49 reduces virulence in an in vivo Galleria mellonella infection model and sensitizes P. aeruginosa to serum complement activity. This enzyme causes biofilm degradation and does not affect the activity of ciprofloxacin and gentamicin. This is the first comprehensive report on LPS-degrading lyase derived from a Pseudomonas phage. Biological properties reveal a potential towards its applications in antimicrobial design and as a microbiological or biotechnological tool.
genetic, X-ray, O-specific polysaccharide, Enzymes, lyase, bacteriophage, Pseudomonas phage
Structure type: oligomer
Location inside paper: fig.3, oligosaccharide 1, table S2
Compound class: O-polysaccharide, O-antigen
Methods: 13C NMR, 1H NMR, NMR-2D, X-ray, SDS-PAGE, sugar analysis, mild acid hydrolysis, biological assays, genetic methods, GPC, enzyme assay, cloning, crystallization, phage degradation, HR ESI-MS
Comments, role: major product 1 was obtained by phage degradation of the OPS
3D data: 3D data
Related record ID(s): 11945, 12193
NCBI Taxonomy refs (TaxIDs): 287
Show glycosyltransferases
NMR conditions: in D2O at 303 K
[as TSV]
13C NMR data:
Linkage Residue C1 C2 C3 C4 C5 C6
4,3,2 Ac 175.0-175.3 23.1-23.5
4,3,3 Ac 175.0-175.3 23.1-23.5
4,3 aLSugp 98.1 48.7 42.4 107.0 145.3 169.7
4,2 Ac 175.0-175.3 23.1-23.5
4 aDFucpN 100.7 49.6 74.8 71.7 68.2 16.5
Subst 71.4 45.7 52.5 76.6 77.0 177.5
1H NMR data:
Linkage Residue H1 H2 H3 H4 H5 H6
4,3,2 Ac - 1.99-2.04
4,3,3 Ac - 1.99-2.04
4,3 aLSugp 5.41 4.36 4.69 5.92 - -
4,2 Ac - 1.99-2.04
4 aDFucpN 4.81 4.28 4.16 3.68 4.23 1.19
Subst 5.04 4.22 3.78 4.06 4.52 -
1H/13C HSQC data:
Linkage Residue C1/H1 C2/H2 C3/H3 C4/H4 C5/H5 C6/H6
4,3,2 Ac 23.1-23.5/1.99-2.04
4,3,3 Ac 23.1-23.5/1.99-2.04
4,3 aLSugp 98.1/5.41 48.7/4.36 42.4/4.69 107.0/5.92
4,2 Ac 23.1-23.5/1.99-2.04
4 aDFucpN 100.7/4.81 49.6/4.28 74.8/4.16 71.7/3.68 68.2/4.23 16.5/1.19
Subst 71.4/5.04 45.7/4.22 52.5/3.78 76.6/4.06 77.0/4.52
1H NMR data:
| Linkage | Residue | H1 | H2 | H3 | H4 | H5 | H6 |
|---|
| 4,3,2 | Ac |
| 1.99
2.04 | |
| 4,3,3 | Ac |
| 1.99
2.04 | |
| 4,3 | aLSugp | 5.41 | 4.36 | 4.69 | 5.92 |
|
|
| 4,2 | Ac |
| 1.99
2.04 | |
| 4 | aDFucpN | 4.81 | 4.28 | 4.16 | 3.68 | 4.23 | 1.19 |
| | Subst | 5.04 | 4.22 | 3.78 | 4.06 | 4.52 |
|
|
13C NMR data:
| Linkage | Residue | C1 | C2 | C3 | C4 | C5 | C6 |
|---|
| 4,3,2 | Ac | 175.0
175.3 | 23.1
23.5 | |
| 4,3,3 | Ac | 175.0
175.3 | 23.1
23.5 | |
| 4,3 | aLSugp | 98.1 | 48.7 | 42.4 | 107.0 | 145.3 | 169.7 |
| 4,2 | Ac | 175.0
175.3 | 23.1
23.5 | |
| 4 | aDFucpN | 100.7 | 49.6 | 74.8 | 71.7 | 68.2 | 16.5 |
| | Subst | 71.4 | 45.7 | 52.5 | 76.6 | 77.0 | 177.5 |
|
There is only one chemically distinct structure:
Expand this record
Collapse this record
Olszak T, Shneider MM, Latka A, Maciejewska B, Browning C, Sycheva LV, Comer JE, Danis-Wlodarczyk K, Senchenkova SN, Shashkov AS, Gula G, Arabski M, Wasik S, Miroshnikov KA, Lavigne R, Leiman PG, Knirel YA, Drulis-Kawa Z
The O-specific polysaccharide lyase from the phage LKA1 tailspike reduces Pseudomonas virulence
Scientific Reports 7(1) (2017)
16302
|
a-L-Sugp2Ac3Ac-(1-3)-a-D-FucpNAc-(1-4)-b-D-ManpNAc3NAmA-(1-4)-b-D-ManpNAc3NAcA-(1-3)-a-D-FucpNAc-(1-4)-Subst
Sug = 2,3-diamino-2,3,4-trideoxy-L-erythro-hex-4,5-enuronic acid = SMILES N{3}[C@H]1C=C(C(O)=O)O{1}[C@@H](O){2}[C@H]1N;
Subst = Am,1-cyclo-D-ManaN3NAmA = SMILES O[C@@H]1C(NC(C)=O)[C@H]({4}[C@H](O)[C@@H](C(O)=O)O)N[C@H](N1)C |
Show graphically |
Pseudomonas aeruginosa O5 170005
(Ancestor NCBI TaxID 287,
species name lookup)
Taxonomic group: bacteria / Proteobacteria
(Phylum: Proteobacteria)
Associated disease: infection due to Pseudomonas aeruginosa [ICD11:
XN5L6 ]
The structure was elucidated in this paperPublication DOI: 10.1038/s41598-017-16411-4Journal NLM ID: 101563288Publisher: London: Nature Publishing Group
Correspondence: Zuzanna Drulis-Kawa <zuzanna.drulis-kawa
uwr.edu.pl>
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Institute of Genetics and Microbiology, University of Wroclaw, Wroclaw, 51-148, Poland, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia, University of Texas Medical Branch, Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, Galveston, TX, 77555-0647, USA, Vertex Pharmaceuticals (Europe) Ltd, Abingdon, Oxfordshire, OX14 4RW, UK, Affinivax Inc., Cambridge, MA, USA, Laboratory of Gene Technology, KU Leuven, Leuven, 3001, Belgium, Department of Biochemistry and Genetics, Institute of Biology, The Jan Kochanowski University in Kielce, Kielce, 25-406, Poland, Department of Molecular Physics, Institute of Physics, The Jan Kochanowski University in Kielce, Kielce, 25-406, Poland
Pseudomonas phage LKA1 of the subfamily Autographivirinae encodes a tailspike protein (LKA1gp49) which binds and cleaves B-band LPS (O-specific antigen, OSA) of Pseudomonas aeruginosa PAO1. The crystal structure of LKA1gp49 catalytic domain consists of a beta-helix, an insertion domain and a C-terminal discoidin-like domain. The putative substrate binding and processing site is located on the face of the beta-helix whereas the C-terminal domain is likely involved in carbohydrates binding. NMR spectroscopy and mass spectrometry analyses of degraded LPS (OSA) fragments show an O5 serotype-specific polysaccharide lyase specificity. LKA1gp49 reduces virulence in an in vivo Galleria mellonella infection model and sensitizes P. aeruginosa to serum complement activity. This enzyme causes biofilm degradation and does not affect the activity of ciprofloxacin and gentamicin. This is the first comprehensive report on LPS-degrading lyase derived from a Pseudomonas phage. Biological properties reveal a potential towards its applications in antimicrobial design and as a microbiological or biotechnological tool.
genetic, X-ray, O-specific polysaccharide, Enzymes, lyase, bacteriophage, Pseudomonas phage
Structure type: oligomer
Location inside paper: fig.3, oligosaccharide 2
Compound class: O-polysaccharide, O-antigen
Methods: 13C NMR, 1H NMR, NMR-2D, X-ray, SDS-PAGE, sugar analysis, mild acid hydrolysis, biological assays, genetic methods, GPC, enzyme assay, cloning, crystallization, phage degradation, HR ESI-MS
Comments, role: minor product 2 was obtained by phage degradation of the OPS
3D data: 3D data
Related record ID(s): 11945, 12192
NCBI Taxonomy refs (TaxIDs): 287
Show glycosyltransferases
There is only one chemically distinct structure:
Expand this record
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