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Kenyon JJ, Senchenkova SN, Shashkov AS, Shneider MM, Popova AV, Knirel YA, Hall RM
K17 capsular polysaccharide produced by Acinetobacter baumannii isolate G7 contains an amide of 2-acetamido-2-deoxy-D-galacturonic acid with D-alanine
International Journal of Biological Macromolecules 144 (2020)
857-862
|
D-Ala-(2-6)-a-D-GalpNAcA-(1-4)-a-D-GalpNAcA-(1-3)-b-D-QuipNAc4NAc |
Show graphically |
Acinetobacter baumannii K17 G7
(Ancestor NCBI TaxID 470,
species name lookup)
Taxonomic group: bacteria / Proteobacteria
(Phylum: Proteobacteria)
Associated disease: infection due to Acinetobacter baumannii [ICD11:
XN8LS 
]
The structure was elucidated in this paperNCBI PubMed ID: 31715229Publication DOI: 10.1016/j.ijbiomac.2019.09.163Journal NLM ID: 7909578Publisher: Butterworth-Heinemann
Correspondence: johanna.kenyon
qut.edu.au
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, M. M. Shemyakin & Y. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia, State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia, School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia, Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, Smolensk, Russia
The K17 capsular polysaccharide (CPS) produced by Acinetobacter baumannii G7, which carries the KL17 configuration at the capsule biosynthesis locus, was isolated and studied by chemical methods along with one- and two-dimensional 1H and 13C NMR spectroscopy. Selective cleavage of the glycosidic linkage of a 2,4-diacetamido-2,4,6-trideoxy-D-glucose (D-QuiNAc4NAc) residue by (i) trifluoroacetic acid solvolysis or (ii) alkaline β-elimination (NaOH-NaBH4) of the 4-linked D-alanine amide of a 2-acetamido-2-deoxy-D-galacturonic acid residue (d-GalNAcA6DAla) yielded trisaccharides that were isolated by Fractogel TSK HW-40 gel-permeation chromatography and identified by using NMR spectroscopy and high-resolution electrospray ionization mass spectrometry. The following structure was established for the trisaccharide repeat (K unit) of the CPS: →4)-α-D-GalpNAcA6DAla-(1→4)-α-D-GalpNAcA-(1→3)-β-D-QuipNAc4NAc-(1→. The presence of the itrA1 gene coding for the initial glycosylphosphotransferase in the KL17 gene cluster established the first sugar of the K unit as D-QuipNAc4NAc. KL17 includes genes for three transferases that had been annotated previously as glycosyltransferases (Gtrs). As only two Gtrs are required for the K17 structure and one D-GalpNAcA residue is modified by a D-alanine amide, these assignments were re-assessed. One transferase was found to belong to the ATPgrasp_TupA protein family that includes D-alanine-D-alanine ligases, and thus was renamed Alt1 (alanine transferase). Alt1 represents a novel family that amidate the carboxyl group of D-GalpNAcA or D-GalpA.
capsular polysaccharide, Acinetobacter baumannii, D-alanine, K locus, KL17
Structure type: oligomer ; 750.2682 [M-H]-
C
29H
45N
5O
18Location inside paper: Fig.4, OS1, table 1
Compound class: CPS
Contained glycoepitopes: IEDB_142345
Methods: 13C NMR, NMR-2D, GLC, chemical methods, NMR-1D, GPC, bioinformatic analysis, solvolysis with anhydrous CF3CO2H, HR-ESI-MS1H NMR
Comments, role: OS1 was obtained by solvolysis CPS with anhydrous CF3CO2H; NMR data for aDQuipNAc4NAc 1H: 5.10 4.01 3.99 3.77 3.95 1.13; 13C: 92.2 54.4 74.9 58.3-58.5 68.0 18.0.
Related record ID(s): 4190, 32130
NCBI Taxonomy refs (TaxIDs): 470
Show glycosyltransferases
NMR conditions: in D2O at 303 K
[as TSV]
13C NMR data:
Linkage Residue C1 C2 C3 C4 C5 C6
3,4,6 xDAla? 178.4 50.4 18.2
3,4,2 Ac 175.1-176.1 23.2-23.8
3,4 aDGalpNA 98.6-98.9 50.4 67.9 79.7-79.8 72.5 174.4
3,2 Ac 175.1-176.1 23.2-23.8
3 aDGalpNA 100.2 50.8 68.8 70.3 73.0 171.8
2 Ac 175.1-176.1 23.2-23.8
4 Ac 175.1-176.1 23.2-23.8
bDQuipN4N 95.9 57.4 77.0 58.3-58.5 72.6 18.0
1H NMR data:
Linkage Residue H1 H2 H3 H4 H5 H6
3,4,6 xDAla? - 4.37 1.39
3,4,2 Ac - 1.93-2.08
3,4 aDGalpNA 5.08 4.22 4.01 4.30 4.77 -
3,2 Ac - 1.93-2.08
3 aDGalpNA 5.09 4.16 3.88 4.38 4.19 -
2 Ac - 1.93-2.08
4 Ac - 1.93-2.08
bDQuipN4N 4.70 3.72 3.81 3.77 3.52 1.16
1H/13C HSQC data:
Linkage Residue C1/H1 C2/H2 C3/H3 C4/H4 C5/H5 C6/H6
3,4,6 xDAla? 50.4/4.37 18.2/1.39
3,4,2 Ac 23.2-23.8/1.93-2.08
3,4 aDGalpNA 98.6-98.9/5.08 50.4/4.22 67.9/4.01 79.7-79.8/4.30 72.5/4.77
3,2 Ac 23.2-23.8/1.93-2.08
3 aDGalpNA 100.2/5.09 50.8/4.16 68.8/3.88 70.3/4.38 73.0/4.19
2 Ac 23.2-23.8/1.93-2.08
4 Ac 23.2-23.8/1.93-2.08
bDQuipN4N 95.9/4.70 57.4/3.72 77.0/3.81 58.3-58.5/3.77 72.6/3.52 18.0/1.16
1H NMR data:
| Linkage | Residue | H1 | H2 | H3 | H4 | H5 | H6 |
|---|
| 3,4,6 | xDAla? |
| 4.37 | 1.39 | |
| 3,4,2 | Ac |
| 1.93
2.08 | |
| 3,4 | aDGalpNA | 5.08 | 4.22 | 4.01 | 4.30 | 4.77 |
|
| 3,2 | Ac |
| 1.93
2.08 | |
| 3 | aDGalpNA | 5.09 | 4.16 | 3.88 | 4.38 | 4.19 |
|
| 2 | Ac |
| 1.93
2.08 | |
| 4 | Ac |
| 1.93
2.08 | |
| | bDQuipN4N | 4.70 | 3.72 | 3.81 | 3.77 | 3.52 | 1.16 |
|
13C NMR data:
| Linkage | Residue | C1 | C2 | C3 | C4 | C5 | C6 |
|---|
| 3,4,6 | xDAla? | 178.4 | 50.4 | 18.2 | |
| 3,4,2 | Ac | 175.1
176.1 | 23.2
23.8 | |
| 3,4 | aDGalpNA | 98.6
98.9 | 50.4 | 67.9 | 79.7
79.8 | 72.5 | 174.4 |
| 3,2 | Ac | 175.1
176.1 | 23.2
23.8 | |
| 3 | aDGalpNA | 100.2 | 50.8 | 68.8 | 70.3 | 73.0 | 171.8 |
| 2 | Ac | 175.1
176.1 | 23.2
23.8 | |
| 4 | Ac | 175.1
176.1 | 23.2
23.8 | |
| | bDQuipN4N | 95.9 | 57.4 | 77.0 | 58.3
58.5 | 72.6 | 18.0 |
|
There is only one chemically distinct structure:
Expand this record
Collapse this record
Kenyon JJ, Senchenkova SN, Shashkov AS, Shneider MM, Popova AV, Knirel YA, Hall RM
K17 capsular polysaccharide produced by Acinetobacter baumannii isolate G7 contains an amide of 2-acetamido-2-deoxy-D-galacturonic acid with D-alanine
International Journal of Biological Macromolecules 144 (2020)
857-862
|
D-Ala-(2-6)-b-L-4dthrHexp4enNAcA-(1-4)-a-D-GalpNAcA-(1-3)-D-QuiNAc4NAc-ol |
Show graphically |
Acinetobacter baumannii K17 G7
(Ancestor NCBI TaxID 470,
species name lookup)
Taxonomic group: bacteria / Proteobacteria
(Phylum: Proteobacteria)
Associated disease: infection due to Acinetobacter baumannii [ICD11:
XN8LS ]
The structure was elucidated in this paperNCBI PubMed ID: 31715229Publication DOI: 10.1016/j.ijbiomac.2019.09.163Journal NLM ID: 7909578Publisher: Butterworth-Heinemann
Correspondence: johanna.kenyon
qut.edu.au
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, M. M. Shemyakin & Y. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia, State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia, School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia, Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, Smolensk, Russia
The K17 capsular polysaccharide (CPS) produced by Acinetobacter baumannii G7, which carries the KL17 configuration at the capsule biosynthesis locus, was isolated and studied by chemical methods along with one- and two-dimensional 1H and 13C NMR spectroscopy. Selective cleavage of the glycosidic linkage of a 2,4-diacetamido-2,4,6-trideoxy-D-glucose (D-QuiNAc4NAc) residue by (i) trifluoroacetic acid solvolysis or (ii) alkaline β-elimination (NaOH-NaBH4) of the 4-linked D-alanine amide of a 2-acetamido-2-deoxy-D-galacturonic acid residue (d-GalNAcA6DAla) yielded trisaccharides that were isolated by Fractogel TSK HW-40 gel-permeation chromatography and identified by using NMR spectroscopy and high-resolution electrospray ionization mass spectrometry. The following structure was established for the trisaccharide repeat (K unit) of the CPS: →4)-α-D-GalpNAcA6DAla-(1→4)-α-D-GalpNAcA-(1→3)-β-D-QuipNAc4NAc-(1→. The presence of the itrA1 gene coding for the initial glycosylphosphotransferase in the KL17 gene cluster established the first sugar of the K unit as D-QuipNAc4NAc. KL17 includes genes for three transferases that had been annotated previously as glycosyltransferases (Gtrs). As only two Gtrs are required for the K17 structure and one D-GalpNAcA residue is modified by a D-alanine amide, these assignments were re-assessed. One transferase was found to belong to the ATPgrasp_TupA protein family that includes D-alanine-D-alanine ligases, and thus was renamed Alt1 (alanine transferase). Alt1 represents a novel family that amidate the carboxyl group of D-GalpNAcA or D-GalpA.
capsular polysaccharide, Acinetobacter baumannii, D-alanine, K locus, KL17
Structure type: oligomer ; 734.2732 [M-H]-
C
29H
45N
5O
17Location inside paper: Fig.4, OS2, table 1
Compound class: CPS
Methods: 13C NMR, NMR-2D, GLC, chemical methods, NMR-1D, GPC, bioinformatic analysis, solvolysis with anhydrous CF3CO2H, HR-ESI-MS1H NMR
Comments, role: OS2 was obtained by treated CPS with 0.1 M NaOH in the presence of NaBH4.
Related record ID(s): 4189, 32130
NCBI Taxonomy refs (TaxIDs): 470
Show glycosyltransferases
NMR conditions: in D2O at 303 K
[as TSV]
13C NMR data:
Linkage Residue C1 C2 C3 C4 C5 C6
3,4,6 xDAla? 177.6 50.4 17.5
3,4,2 Ac 175.1-176.1 23.2-23.8
3,4 bL4dthrHexp4enNA 100.3 53.3 64.7 110.7 143.3 169.6
3,2 Ac 175.1-176.1 23.2-23.8
3 aDGalpNA 100.0 50.8 67.0 79.3 72.3 175.0
2 Ac 175.1-176.1 23.2-23.8
4 Ac 175.1-176.1 23.2-23.8
xDQuiN4N-ol 61.8 55.1 77.0 57.1 67.1 20.6
1H NMR data:
Linkage Residue H1 H2 H3 H4 H5 H6
3,4,6 xDAla? - 4.39 1.44
3,4,2 Ac - 1.93-2.08
3,4 bL4dthrHexp4enNA 5.28 4.08 4.52 4.94 - -
3,2 Ac - 1.93-2.08
3 aDGalpNA 5.20 4.10 4.09 4.58 4.40 -
2 Ac - 1.93-2.08
4 Ac - 1.93-2.08
xDQuiN4N-ol 3.48-3.62 4.00 4.28 3.86 3.64 1.16
1H/13C HSQC data:
Linkage Residue C1/H1 C2/H2 C3/H3 C4/H4 C5/H5 C6/H6
3,4,6 xDAla? 50.4/4.39 17.5/1.44
3,4,2 Ac 23.2-23.8/1.93-2.08
3,4 bL4dthrHexp4enNA 100.3/5.28 53.3/4.08 64.7/4.52 110.7/4.94
3,2 Ac 23.2-23.8/1.93-2.08
3 aDGalpNA 100.0/5.20 50.8/4.10 67.0/4.09 79.3/4.58 72.3/4.40
2 Ac 23.2-23.8/1.93-2.08
4 Ac 23.2-23.8/1.93-2.08
xDQuiN4N-ol 61.8/3.48-3.62 55.1/4.00 77.0/4.28 57.1/3.86 67.1/3.64 20.6/1.16
1H NMR data:
| Linkage | Residue | H1 | H2 | H3 | H4 | H5 | H6 |
|---|
| 3,4,6 | xDAla? |
| 4.39 | 1.44 | |
| 3,4,2 | Ac |
| 1.93
2.08 | |
| 3,4 | bL4dthrHexp4enNA | 5.28 | 4.08 | 4.52 | 4.94 |
|
|
| 3,2 | Ac |
| 1.93
2.08 | |
| 3 | aDGalpNA | 5.20 | 4.10 | 4.09 | 4.58 | 4.40 |
|
| 2 | Ac |
| 1.93
2.08 | |
| 4 | Ac |
| 1.93
2.08 | |
| | xDQuiN4N-ol | 3.48
3.62 | 4.00 | 4.28 | 3.86 | 3.64 | 1.16 |
|
13C NMR data:
| Linkage | Residue | C1 | C2 | C3 | C4 | C5 | C6 |
|---|
| 3,4,6 | xDAla? | 177.6 | 50.4 | 17.5 | |
| 3,4,2 | Ac | 175.1
176.1 | 23.2
23.8 | |
| 3,4 | bL4dthrHexp4enNA | 100.3 | 53.3 | 64.7 | 110.7 | 143.3 | 169.6 |
| 3,2 | Ac | 175.1
176.1 | 23.2
23.8 | |
| 3 | aDGalpNA | 100.0 | 50.8 | 67.0 | 79.3 | 72.3 | 175.0 |
| 2 | Ac | 175.1
176.1 | 23.2
23.8 | |
| 4 | Ac | 175.1
176.1 | 23.2
23.8 | |
| | xDQuiN4N-ol | 61.8 | 55.1 | 77.0 | 57.1 | 67.1 | 20.6 |
|
There is only one chemically distinct structure:
Expand this record
Collapse this record
Kenyon JJ, Senchenkova SN, Shashkov AS, Shneider MM, Popova AV, Knirel YA, Hall RM
K17 capsular polysaccharide produced by Acinetobacter baumannii isolate G7 contains an amide of 2-acetamido-2-deoxy-D-galacturonic acid with D-alanine
International Journal of Biological Macromolecules 144 (2020)
857-862
|
D-Ala-(2-6)-+
|
-4)-a-D-GalpNAcA-(1-4)-a-D-GalpNAcA-(1-3)-b-D-QuipNAc4NAc-(1- |
Show graphically |
Acinetobacter baumannii K17 G7
(Ancestor NCBI TaxID 470,
species name lookup)
Taxonomic group: bacteria / Proteobacteria
(Phylum: Proteobacteria)
Associated disease: infection due to Acinetobacter baumannii [ICD11:
XN8LS ]
The structure was elucidated in this paperNCBI PubMed ID: 31715229Publication DOI: 10.1016/j.ijbiomac.2019.09.163Journal NLM ID: 7909578Publisher: Butterworth-Heinemann
Correspondence: johanna.kenyon
qut.edu.au
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, M. M. Shemyakin & Y. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia, State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia, School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia, Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, Smolensk, Russia
The K17 capsular polysaccharide (CPS) produced by Acinetobacter baumannii G7, which carries the KL17 configuration at the capsule biosynthesis locus, was isolated and studied by chemical methods along with one- and two-dimensional 1H and 13C NMR spectroscopy. Selective cleavage of the glycosidic linkage of a 2,4-diacetamido-2,4,6-trideoxy-D-glucose (D-QuiNAc4NAc) residue by (i) trifluoroacetic acid solvolysis or (ii) alkaline β-elimination (NaOH-NaBH4) of the 4-linked D-alanine amide of a 2-acetamido-2-deoxy-D-galacturonic acid residue (d-GalNAcA6DAla) yielded trisaccharides that were isolated by Fractogel TSK HW-40 gel-permeation chromatography and identified by using NMR spectroscopy and high-resolution electrospray ionization mass spectrometry. The following structure was established for the trisaccharide repeat (K unit) of the CPS: →4)-α-D-GalpNAcA6DAla-(1→4)-α-D-GalpNAcA-(1→3)-β-D-QuipNAc4NAc-(1→. The presence of the itrA1 gene coding for the initial glycosylphosphotransferase in the KL17 gene cluster established the first sugar of the K unit as D-QuipNAc4NAc. KL17 includes genes for three transferases that had been annotated previously as glycosyltransferases (Gtrs). As only two Gtrs are required for the K17 structure and one D-GalpNAcA residue is modified by a D-alanine amide, these assignments were re-assessed. One transferase was found to belong to the ATPgrasp_TupA protein family that includes D-alanine-D-alanine ligases, and thus was renamed Alt1 (alanine transferase). Alt1 represents a novel family that amidate the carboxyl group of D-GalpNAcA or D-GalpA.
capsular polysaccharide, Acinetobacter baumannii, D-alanine, K locus, KL17
Structure type: polymer chemical repeating unit
Location inside paper: Fig.3, table 1
Compound class: O-polysaccharide, O-antigen, CPS
Contained glycoepitopes: IEDB_142345
Methods: 13C NMR, NMR-2D, GLC, chemical methods, NMR-1D, GPC, bioinformatic analysis, solvolysis with anhydrous CF3CO2H, HR-ESI-MS1H NMR
Enzymes that release or process the structure: Alt1, Gtr39, Gtr40, Wzy(K17)
Related record ID(s): 4189, 4190
NCBI Taxonomy refs (TaxIDs): 470Reference(s) to other database(s): GlycomeDB:
33545
Show glycosyltransferases
NMR conditions: in D2O at 323 K
[as TSV]
13C NMR data:
Linkage Residue C1 C2 C3 C4 C5 C6
3,4,2 Ac 175.1-176.1 23.2-23.8
3,4,6 xDAla? 178.4 50.5 19.0
3,4 aDGalpNA 100.1 51.1 69.1 77.5 72.7 170.5
3,2 Ac 175.1-176.1 23.2-23.8
3 aDGalpNA 98.6 50.5 67.9 79.7 72.5 174.4
2 Ac 175.1-176.1 23.2-23.8
4 Ac 175.1-176.1 23.2-23.8
bDQuipN4N 102.5 56.4 77.0 58.4 72.0 17.9
1H NMR data:
Linkage Residue H1 H2 H3 H4 H5 H6
3,4,2 Ac - 1.93-2.08
3,4,6 xDAla? - 4.33 1.37
3,4 aDGalpNA 5.05 4.13 4.05 4.32 4.70 -
3,2 Ac - 1.93-2.08
3 aDGalpNA 5.09 4.16 3.88 4.38 4.19 -
2 Ac - 1.93-2.08
4 Ac - 1.93-2.08
bDQuipN4N 4.65 3.68 3.85 3.66 3.34 1.07
1H/13C HSQC data:
Linkage Residue C1/H1 C2/H2 C3/H3 C4/H4 C5/H5 C6/H6
3,4,2 Ac 23.2-23.8/1.93-2.08
3,4,6 xDAla? 50.5/4.33 19.0/1.37
3,4 aDGalpNA 100.1/5.05 51.1/4.13 69.1/4.05 77.5/4.32 72.7/4.70
3,2 Ac 23.2-23.8/1.93-2.08
3 aDGalpNA 98.6/5.09 50.5/4.16 67.9/3.88 79.7/4.38 72.5/4.19
2 Ac 23.2-23.8/1.93-2.08
4 Ac 23.2-23.8/1.93-2.08
bDQuipN4N 102.5/4.65 56.4/3.68 77.0/3.85 58.4/3.66 72.0/3.34 17.9/1.07
1H NMR data:
| Linkage | Residue | H1 | H2 | H3 | H4 | H5 | H6 |
|---|
| 3,4,2 | Ac |
| 1.93
2.08 | |
| 3,4,6 | xDAla? |
| 4.33 | 1.37 | |
| 3,4 | aDGalpNA | 5.05 | 4.13 | 4.05 | 4.32 | 4.70 |
|
| 3,2 | Ac |
| 1.93
2.08 | |
| 3 | aDGalpNA | 5.09 | 4.16 | 3.88 | 4.38 | 4.19 |
|
| 2 | Ac |
| 1.93
2.08 | |
| 4 | Ac |
| 1.93
2.08 | |
| | bDQuipN4N | 4.65 | 3.68 | 3.85 | 3.66 | 3.34 | 1.07 |
|
13C NMR data:
| Linkage | Residue | C1 | C2 | C3 | C4 | C5 | C6 |
|---|
| 3,4,2 | Ac | 175.1
176.1 | 23.2
23.8 | |
| 3,4,6 | xDAla? | 178.4 | 50.5 | 19.0 | |
| 3,4 | aDGalpNA | 100.1 | 51.1 | 69.1 | 77.5 | 72.7 | 170.5 |
| 3,2 | Ac | 175.1
176.1 | 23.2
23.8 | |
| 3 | aDGalpNA | 98.6 | 50.5 | 67.9 | 79.7 | 72.5 | 174.4 |
| 2 | Ac | 175.1
176.1 | 23.2
23.8 | |
| 4 | Ac | 175.1
176.1 | 23.2
23.8 | |
| | bDQuipN4N | 102.5 | 56.4 | 77.0 | 58.4 | 72.0 | 17.9 |
|
There is only one chemically distinct structure:
Expand this record
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