Taxonomic group: bacteria / Proteobacteria
(Phylum: Proteobacteria)
Host organism: Homo sapiens
Associated disease: infection due to Acinetobacter baumannii [ICD11:
XN8LS 
]
The structure was elucidated in this paperNCBI PubMed ID: 32571186Publication DOI: 10.1134/S0006297920050053Journal NLM ID: 0376536Publisher: Nauka/Interperiodica
Correspondence: yknirel
gmail.com
Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, 142279, Russia, Higher Chemical College of the Russian Academy of Sciences, D. I. Mendeleev University of Chemical Technology of Russia, Moscow, Russia, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia, Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, Smolensk, 214019, Russia, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Moscow Region, 141701, Russia
Aerobic gram-negative bacterium Acinetobacter baumannii has recently become one of the most relevant pathogens associated with hospital-acquired infections worldwide. A. baumannii produces a capsule around the cell, which represents a thick viscous layer of structurally variable capsular polysaccharide (CPS). The capsule protects the bacteria against unfavorable environmental factors and biological systems, including bacteriophages and host immune system. Many A. baumannii phages have structural depolymerases (tailspikes) that specifically recognize and digest bacterial CPS. In this work, we studied the interaction of tailspike proteins of four lytic depolymerase-carrying phages with A. baumannii CPS. Depolymerases of three bacteriophages (Fri1, AS12, and BS46) were identified as specific glycosidases that cleave the CPS of A. baumannii strains 28, 1432, and B05, respectively, by the hydrolytic mechanism. The gp54 depolymerase from bacteriophage AP22 was characterized as a polysaccharide lyase that cleaves the CPS of A. baumannii strain 1053 by β-elimination at hexuronic acid (ManNAcA) residues.
Acinetobacter baumannii, capsular polysaccharide, NMR spectroscopy, bacteriophage, Polysaccharide lyase, Tailspike, depolymerase, glycosidase, hexuronic acid, receptor binding protein
Structure type: oligomer ; 802.3092 [M-H]2−
Location inside paper: p.572, Fig.4, table S6, oligosaccharide 10
Compound class: CPS
Contained glycoepitopes: IEDB_135813,IEDB_137340,IEDB_141807,IEDB_151531
Methods: 13C NMR, 1H NMR, NMR-2D, DNA techniques, GPC, enzymatic digestion, HR-ESI-MS
Comments, role: major oligosaccharide 10 derived by the CPS digestion with the phage BS46 depolymerase gp47. NMR data for →3)bDGlcpNAc residue 1H: 4.62 3.81 3.66 3.52 3.46 3.74-3.89, 13C: 96.4 57.9 79.1 69.7 77.2 62.1.
Related record ID(s): 5049, 5050, 5051, 5052, 5053, 5054, 5055, 25166, 25167, 25168, 25170, 32134
NCBI Taxonomy refs (TaxIDs): 470Reference(s) to other database(s): GTC:G27114UK
Show glycosyltransferases
NMR conditions: in D2O at 293 K
[as TSV]
13C NMR data:
Linkage Residue C1 C2 C3 C4 C5 C6
3,3,3,3,3,4,2 Ac 174.6-176.1 23.2-23.7
3,3,3,3,3,4 aLFucpN 99.6 51.0 68.5-68.7 72.4 68.0 16.5
3,3,3,3,3,2 Ac 174.6-176.1 23.2-23.7
3,3,3,3,3 aDGalpNA 99.6 50.9 69.7 76.3 71.7 ?
3,3,3,3,2 Ac 174.6-176.1 23.2-23.7
3,3,3,3 aLFucpN 98.8 49.1 74.3 72.4 68.6 16.8
3,3,3,2 Ac 174.6-176.1 23.2-23.7
3,3,3 bDGlcpN 103.5 57.1 79.1 69.7 77.0 62.2
3,3,2 Ac 174.6-176.1 23.2-23.7
3,3,4,2 Ac 174.6-176.1 23.2-23.7
3,3,4 aLFucpN 97.6 50.7 68.5-68.7 72.4 67.9-68.5 16.5
3,3 aDGalpNA 99.3 49.6 78.0 74.7 72.0 ?
3,2 Ac 174.6-176.1 23.2-23.7
3 aLFucpN 98.2-98.6 50.1 73.9 72.4 67.9-68.5 16.8
2 Ac 174.6-176.1 23.2-23.7
aDGlcpN 92.3 55.5 76.4 69.7 72.8 61.9
1H NMR data:
Linkage Residue H1 H2 H3 H4 H5 H6
3,3,3,3,3,4,2 Ac - 1.89-2.04
3,3,3,3,3,4 aLFucpN 5.27 4.07 3.97 3.78 4.44 1.14-1.16
3,3,3,3,3,2 Ac - 1.89-2.04
3,3,3,3,3 aDGalpNA 5.15 4.34 4.16 4.44 4.54 -
3,3,3,3,2 Ac - 1.89-2.04
3,3,3,3 aLFucpN 4.90 4.29 4.03 3.76 3.97 1.19
3,3,3,2 Ac - 1.89-2.04
3,3,3 bDGlcpN 4.62 3.73 3.75 3.52 3.43 3.77-3.93
3,3,2 Ac - 1.89-2.04
3,3,4,2 Ac - 1.89-2.04
3,3,4 aLFucpN 5.59 4.09 3.91 3.78 4.44 1.14-1.16
3,3 aDGalpNA 5.14 4.44 4.20 4.76 4.49 -
3,2 Ac - 1.89-2.04
3 aLFucpN 4.97-5.00 4.27 4.05 3.76 3.97 1.19
2 Ac - 1.89-2.04
aDGlcpN 5.06 4.01 3.85 3.53 3.87 3.79-3.83
1H/13C HSQC data:
Linkage Residue C1/H1 C2/H2 C3/H3 C4/H4 C5/H5 C6/H6
3,3,3,3,3,4,2 Ac 23.2-23.7/1.89-2.04
3,3,3,3,3,4 aLFucpN 99.6/5.27 51.0/4.07 68.5-68.7/3.97 72.4/3.78 68.0/4.44 16.5/1.14-1.16
3,3,3,3,3,2 Ac 23.2-23.7/1.89-2.04
3,3,3,3,3 aDGalpNA 99.6/5.15 50.9/4.34 69.7/4.16 76.3/4.44 71.7/4.54
3,3,3,3,2 Ac 23.2-23.7/1.89-2.04
3,3,3,3 aLFucpN 98.8/4.90 49.1/4.29 74.3/4.03 72.4/3.76 68.6/3.97 16.8/1.19
3,3,3,2 Ac 23.2-23.7/1.89-2.04
3,3,3 bDGlcpN 103.5/4.62 57.1/3.73 79.1/3.75 69.7/3.52 77.0/3.43 62.2/3.77-3.93
3,3,2 Ac 23.2-23.7/1.89-2.04
3,3,4,2 Ac 23.2-23.7/1.89-2.04
3,3,4 aLFucpN 97.6/5.59 50.7/4.09 68.5-68.7/3.91 72.4/3.78 67.9-68.5/4.44 16.5/1.14-1.16
3,3 aDGalpNA 99.3/5.14 49.6/4.44 78.0/4.20 74.7/4.76 72.0/4.49
3,2 Ac 23.2-23.7/1.89-2.04
3 aLFucpN 98.2-98.6/4.97-5.00 50.1/4.27 73.9/4.05 72.4/3.76 67.9-68.5/3.97 16.8/1.19
2 Ac 23.2-23.7/1.89-2.04
aDGlcpN 92.3/5.06 55.5/4.01 76.4/3.85 69.7/3.53 72.8/3.87 61.9/3.79-3.83
1H NMR data:
| Linkage | Residue | H1 | H2 | H3 | H4 | H5 | H6 |
|---|
| 3,3,3,3,3,4,2 | Ac |
| 1.89
2.04 | |
| 3,3,3,3,3,4 | aLFucpN | 5.27 | 4.07 | 3.97 | 3.78 | 4.44 | 1.14
1.16 |
| 3,3,3,3,3,2 | Ac |
| 1.89
2.04 | |
| 3,3,3,3,3 | aDGalpNA | 5.15 | 4.34 | 4.16 | 4.44 | 4.54 |
|
| 3,3,3,3,2 | Ac |
| 1.89
2.04 | |
| 3,3,3,3 | aLFucpN | 4.90 | 4.29 | 4.03 | 3.76 | 3.97 | 1.19 |
| 3,3,3,2 | Ac |
| 1.89
2.04 | |
| 3,3,3 | bDGlcpN | 4.62 | 3.73 | 3.75 | 3.52 | 3.43 | 3.77
3.93 |
| 3,3,2 | Ac |
| 1.89
2.04 | |
| 3,3,4,2 | Ac |
| 1.89
2.04 | |
| 3,3,4 | aLFucpN | 5.59 | 4.09 | 3.91 | 3.78 | 4.44 | 1.14
1.16 |
| 3,3 | aDGalpNA | 5.14 | 4.44 | 4.20 | 4.76 | 4.49 |
|
| 3,2 | Ac |
| 1.89
2.04 | |
| 3 | aLFucpN | 4.97
5.00 | 4.27 | 4.05 | 3.76 | 3.97 | 1.19 |
| 2 | Ac |
| 1.89
2.04 | |
| | aDGlcpN | 5.06 | 4.01 | 3.85 | 3.53 | 3.87 | 3.79
3.83 |
|
13C NMR data:
| Linkage | Residue | C1 | C2 | C3 | C4 | C5 | C6 |
|---|
| 3,3,3,3,3,4,2 | Ac | 174.6
176.1 | 23.2
23.7 | |
| 3,3,3,3,3,4 | aLFucpN | 99.6 | 51.0 | 68.5
68.7 | 72.4 | 68.0 | 16.5 |
| 3,3,3,3,3,2 | Ac | 174.6
176.1 | 23.2
23.7 | |
| 3,3,3,3,3 | aDGalpNA | 99.6 | 50.9 | 69.7 | 76.3 | 71.7 | ? |
| 3,3,3,3,2 | Ac | 174.6
176.1 | 23.2
23.7 | |
| 3,3,3,3 | aLFucpN | 98.8 | 49.1 | 74.3 | 72.4 | 68.6 | 16.8 |
| 3,3,3,2 | Ac | 174.6
176.1 | 23.2
23.7 | |
| 3,3,3 | bDGlcpN | 103.5 | 57.1 | 79.1 | 69.7 | 77.0 | 62.2 |
| 3,3,2 | Ac | 174.6
176.1 | 23.2
23.7 | |
| 3,3,4,2 | Ac | 174.6
176.1 | 23.2
23.7 | |
| 3,3,4 | aLFucpN | 97.6 | 50.7 | 68.5
68.7 | 72.4 | 67.9
68.5 | 16.5 |
| 3,3 | aDGalpNA | 99.3 | 49.6 | 78.0 | 74.7 | 72.0 | ? |
| 3,2 | Ac | 174.6
176.1 | 23.2
23.7 | |
| 3 | aLFucpN | 98.2
98.6 | 50.1 | 73.9 | 72.4 | 67.9
68.5 | 16.8 |
| 2 | Ac | 174.6
176.1 | 23.2
23.7 | |
| | aDGlcpN | 92.3 | 55.5 | 76.4 | 69.7 | 72.8 | 61.9 |
|
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The spectrum also has 2 signals at unknown positions (not plotted). |
There is only one chemically distinct structure:
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Found 1 record.
Displayed record 1
