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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 paper
NCBI PubMed ID: 32571186
Publication DOI: 10.1134/S0006297920050053
Journal NLM ID: 0376536
Publisher: 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
Location inside paper: p.571, Fig.2, table S4, oligosaccharide 3-7
Compound class: CPS
Contained glycoepitopes: IEDB_130648,IEDB_137473,IEDB_1391961,IEDB_141584,IEDB_885822

Methods: 13C NMR, 1H NMR, NMR-2D, DNA techniques, GPC, enzymatic digestion, HR-ESI-MS
Comments, role: Cleavage of O-deacetylated CPS from A. baumannii 28 by the phage FriI depolymerase gp49. NMR data for the major nonasaccharide 4 (n=1), chemical shifts (δ, ppm) of aDQuipNAc4NAc residue at the reducing end of OS: 1H: 5.10 4.04 3.98 3.78 3.97 1.13, 13C: 92.2 54.3 75.1 58.3 68.0 17.9.

Related record ID(s): 5049, 5050, 5051, 5052, 5054, 5055, 25166, 25167, 25168, 25169, 25170, 32134
NCBI Taxonomy refs (TaxIDs): 470
Show glycosyltransferases

NMR conditions: in D2O at 293 K [as TSV]

13C NMR data:
Linkage	Residue	C1	C2	C3	C4	C5	C6
3,4,3,3,4,2	Ac	174.9-176.1	23.3-23.9
3,4,3,3,4	aDGalpN	99.9	49.6	77.4	69.5	71.7	61.8
3,4,3,3,2	Ac	174.9-176.1	23.3-23.9
3,4,3,3	aDGalpNA	98.7-98.8	50.5	67.8	78.7-78.9	71.7	173.3
3,4,3,2	Ac	174.9-176.1	23.3-23.9
3,4,3,4	Ac	174.9-176.1	23.3-23.9
3,4,3	bDQuipN4N	102.6	56.2	77.4	58.3	72.2	17.9
3,4,3,3,4,3,3,4,2	Ac	174.9-176.1	23.3-23.9
3,4,3,3,4,3,3,4	aDGalpN	99.9	51.1	68.7	69.7	72.2	61.9
3,4,3,3,4,3,3,2	Ac	174.9-176.1	23.3-23.9
3,4,3,3,4,3,3	aDGalpNA	98.7-98.8	50.5	67.8	78.7-78.9	71.7	173.3
3,4,3,3,4,3,2	Ac	174.9-176.1	23.3-23.9
3,4,3,3,4,3,4	Ac	174.9-176.1	23.3-23.9
3,4,3,3,4,3	bDQuipN4N	102.6	56.2	77.4	58.3	72.2	17.9
3,4,2	Ac	174.9-176.1	23.3-23.9
3,4	aDGalpN	99.9	49.6	77.4	69.5	71.7	61.8
3,2	Ac	174.9-176.1	23.3-23.9
3	aDGalpNA	98.7-98.8	50.5	67.8	78.7-78.9	71.7	173.4
2	Ac	174.9-176.1	23.3-23.9
4	Ac	174.9-176.1	23.3-23.9
	bDQuipN4N	95.8	57.5	77.4	58.4	72.4	17.9


1H NMR data:
Linkage	Residue	H1	H2	H3	H4	H5	H6
3,4,3,3,4,2	Ac	-	1.94-2.09
3,4,3,3,4	aDGalpN	4.91	4.28	3.98	4.21	4.27	3.66-3.68
3,4,3,3,2	Ac	-	1.94-2.09
3,4,3,3	aDGalpNA	5.22-5.23	4.23	3.93	4.42	4.29	-
3,4,3,2	Ac	-	1.94-2.09
3,4,3,4	Ac	-	1.94-2.09
3,4,3	bDQuipN4N	4.63	3.77	3.88	3.77	3.51	1.17
3,4,3,3,4,3,3,4,2	Ac	-	1.94-2.09
3,4,3,3,4,3,3,4	aDGalpN	4.97	4.18	3.95	4.03	4.27	3.66-3.68
3,4,3,3,4,3,3,2	Ac	-	1.94-2.09
3,4,3,3,4,3,3	aDGalpNA	5.22-5.23	4.23	3.93	4.42	4.29	-
3,4,3,3,4,3,2	Ac	-	1.94-2.09
3,4,3,3,4,3,4	Ac	-	1.94-2.09
3,4,3,3,4,3	bDQuipN4N	4.63	3.77	3.88	3.77	3.51	1.17
3,4,2	Ac	-	1.94-2.09
3,4	aDGalpN	4.91	4.28	3.98	4.21	4.27	3.66-3.68
3,2	Ac	-	1.94-2.09
3	aDGalpNA	5.22-5.23	4.23	3.93	4.42	4.32	-
2	Ac	-	1.94-2.09
4	Ac	-	1.94-2.09
	bDQuipN4N	4.71	3.72	3.85	3.78	3.53	1.17


1H/13C HSQC data:
Linkage	Residue	C1/H1	C2/H2	C3/H3	C4/H4	C5/H5	C6/H6
3,4,3,3,4,2	Ac		23.3-23.9/1.94-2.09
3,4,3,3,4	aDGalpN	99.9/4.91	49.6/4.28	77.4/3.98	69.5/4.21	71.7/4.27	61.8/3.66-3.68
3,4,3,3,2	Ac		23.3-23.9/1.94-2.09
3,4,3,3	aDGalpNA	98.7-98.8/5.22-5.23	50.5/4.23	67.8/3.93	78.7-78.9/4.42	71.7/4.29	
3,4,3,2	Ac		23.3-23.9/1.94-2.09
3,4,3,4	Ac		23.3-23.9/1.94-2.09
3,4,3	bDQuipN4N	102.6/4.63	56.2/3.77	77.4/3.88	58.3/3.77	72.2/3.51	17.9/1.17
3,4,3,3,4,3,3,4,2	Ac		23.3-23.9/1.94-2.09
3,4,3,3,4,3,3,4	aDGalpN	99.9/4.97	51.1/4.18	68.7/3.95	69.7/4.03	72.2/4.27	61.9/3.66-3.68
3,4,3,3,4,3,3,2	Ac		23.3-23.9/1.94-2.09
3,4,3,3,4,3,3	aDGalpNA	98.7-98.8/5.22-5.23	50.5/4.23	67.8/3.93	78.7-78.9/4.42	71.7/4.29	
3,4,3,3,4,3,2	Ac		23.3-23.9/1.94-2.09
3,4,3,3,4,3,4	Ac		23.3-23.9/1.94-2.09
3,4,3,3,4,3	bDQuipN4N	102.6/4.63	56.2/3.77	77.4/3.88	58.3/3.77	72.2/3.51	17.9/1.17
3,4,2	Ac		23.3-23.9/1.94-2.09
3,4	aDGalpN	99.9/4.91	49.6/4.28	77.4/3.98	69.5/4.21	71.7/4.27	61.8/3.66-3.68
3,2	Ac		23.3-23.9/1.94-2.09
3	aDGalpNA	98.7-98.8/5.22-5.23	50.5/4.23	67.8/3.93	78.7-78.9/4.42	71.7/4.32	
2	Ac		23.3-23.9/1.94-2.09
4	Ac		23.3-23.9/1.94-2.09
	bDQuipN4N	95.8/4.71	57.5/3.72	77.4/3.85	58.4/3.78	72.4/3.53	17.9/1.17

¹H NMR data:

Linkage	Residue	H1	H2	H3	H4	H5	H6
3,4,3,3,4,2	Ac		1.94 2.09
3,4,3,3,4	aDGalpN	4.91	4.28	3.98	4.21	4.27	3.66 3.68
3,4,3,3,2	Ac		1.94 2.09
3,4,3,3	aDGalpNA	5.22 5.23	4.23	3.93	4.42	4.29
3,4,3,2	Ac		1.94 2.09
3,4,3,4	Ac		1.94 2.09
3,4,3	bDQuipN4N	4.63	3.77	3.88	3.77	3.51	1.17
3,4,3,3,4,3,3,4,2	Ac		1.94 2.09
3,4,3,3,4,3,3,4	aDGalpN	4.97	4.18	3.95	4.03	4.27	3.66 3.68
3,4,3,3,4,3,3,2	Ac		1.94 2.09
3,4,3,3,4,3,3	aDGalpNA	5.22 5.23	4.23	3.93	4.42	4.29
3,4,3,3,4,3,2	Ac		1.94 2.09
3,4,3,3,4,3,4	Ac		1.94 2.09
3,4,3,3,4,3	bDQuipN4N	4.63	3.77	3.88	3.77	3.51	1.17
3,4,2	Ac		1.94 2.09
3,4	aDGalpN	4.91	4.28	3.98	4.21	4.27	3.66 3.68
3,2	Ac		1.94 2.09
3	aDGalpNA	5.22 5.23	4.23	3.93	4.42	4.32
2	Ac		1.94 2.09
4	Ac		1.94 2.09
	bDQuipN4N	4.71	3.72	3.85	3.78	3.53	1.17

¹³C NMR data:

Linkage	Residue	C1	C2	C3	C4	C5	C6
3,4,3,3,4,2	Ac	174.9 176.1	23.3 23.9
3,4,3,3,4	aDGalpN	99.9	49.6	77.4	69.5	71.7	61.8
3,4,3,3,2	Ac	174.9 176.1	23.3 23.9
3,4,3,3	aDGalpNA	98.7 98.8	50.5	67.8	78.7 78.9	71.7	173.3
3,4,3,2	Ac	174.9 176.1	23.3 23.9
3,4,3,4	Ac	174.9 176.1	23.3 23.9
3,4,3	bDQuipN4N	102.6	56.2	77.4	58.3	72.2	17.9
3,4,3,3,4,3,3,4,2	Ac	174.9 176.1	23.3 23.9
3,4,3,3,4,3,3,4	aDGalpN	99.9	51.1	68.7	69.7	72.2	61.9
3,4,3,3,4,3,3,2	Ac	174.9 176.1	23.3 23.9
3,4,3,3,4,3,3	aDGalpNA	98.7 98.8	50.5	67.8	78.7 78.9	71.7	173.3
3,4,3,3,4,3,2	Ac	174.9 176.1	23.3 23.9
3,4,3,3,4,3,4	Ac	174.9 176.1	23.3 23.9
3,4,3,3,4,3	bDQuipN4N	102.6	56.2	77.4	58.3	72.2	17.9
3,4,2	Ac	174.9 176.1	23.3 23.9
3,4	aDGalpN	99.9	49.6	77.4	69.5	71.7	61.8
3,2	Ac	174.9 176.1	23.3 23.9
3	aDGalpNA	98.7 98.8	50.5	67.8	78.7 78.9	71.7	173.4
2	Ac	174.9 176.1	23.3 23.9
4	Ac	174.9 176.1	23.3 23.9
	bDQuipN4N	95.8	57.5	77.4	58.4	72.4	17.9

There is only one chemically distinct structure:

CC(=O)N[C@H]1[C@H](O[C@H]2[C@@H](O)[C@@H](CO)O[C@H](O[C@H]3[C@@H](C(=O)O)O[C@H](O[C@@H]4[C@@H](NC(C)=O)[C@H](O[C@H]5[C@@H](O)[C@@H](CO)O[C@H](O[C@H]6[C@@H](C(=O)O)O[C@H](O[C@H]7[C@H](NC(C)=O)[C@@H](C)O[C@@H](O)[C@@H]7NC(C)=O)[C@H](NC(C)=O)[C@H]6O)[C@@H]5NC(C)=O)O[C@H](C)[C@H]4NC(C)=O)[C@H](NC(C)=O)[C@H]3O)[C@@H]2NC(C)=O)O[C@H](C)[C@@H](NC(C)=O)[C@@H]1O[C@H]1O[C@H](C(=O)O)[C@H](O[C@H]2O[C@H](CO)[C@H](O)[C@H](O)[C@H]2NC(C)=O)[C@H](O)[C@H]1NC(C)=O

SVG MW SMILES 3D mol Ionize

Warning = sub-repeat ending at bDQuipN4N: variable unit count (0-4) was assumed to be 0