8IQ9

Crystal structure of trimeric K2-2 TSP in complex with tetrasaccharide and octasaccharide

Summary for 8IQ9

• Entry DOI: 10.2210/pdb8iq9/pdb
• Descriptor: K2-2 TSP, alpha-D-glucopyranuronic acid-(1-3)-beta-D-mannopyranose-(1-4)-alpha-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-4)-[alpha-D-glucopyranuronic acid-(1-3)]beta-D-mannopyranose-(1-4)-alpha-D-glucopyranose-(1-3)-beta-D-glucopyranose, alpha-D-glucopyranuronic acid-(1-3)-beta-D-mannopyranose-(1-4)-alpha-D-glucopyranose-(1-3)-beta-D-glucopyranose, ... (6 entities in total)
• Functional Keywords: bacteriophage, tailspike protein, klebsiella pneumoniae k2, hydrolase
• Biological source: Klebsiella phage VLC6
• Total number of polymer chains: 3
• Total formula weight: 200376.29

Authors

Ye, T.J.,Ko, T.P.,Huang, K.F.,Wu, S.H. (deposition date: 2023-03-16, release date: 2024-02-21, Last modification date: 2024-04-03)

Primary citation

Ye, T.J.,Fung, K.M.,Lee, I.M.,Ko, T.P.,Lin, C.Y.,Wong, C.L.,Tu, I.F.,Huang, T.Y.,Yang, F.L.,Chang, Y.P.,Wang, J.T.,Lin, T.L.,Huang, K.F.,Wu, S.H.
Klebsiella pneumoniae K2 capsular polysaccharide degradation by a bacteriophage depolymerase does not require trimer formation.
Mbio, 15:e0351923-e0351923, 2024

PubMed Abstract: K2-capsular is a hypervirulent pathogen that causes fatal infections. Here, we describe a phage tailspike protein, named K2-2, that specifically depolymerizes the K2 capsular polysaccharide (CPS) of into tetrasaccharide repeating units. Nearly half of the products contained -acetylation, which was thought crucial to the immunogenicity of CPS. The product-bound structures of this trimeric enzyme revealed intersubunit carbohydrate-binding grooves, each accommodating three tetrasaccharide units of K2 CPS. The catalytic residues and the key interactions responsible for K2 CPS recognition were identified and verified by site-directed mutagenesis. Further biophysical and functional characterization, along with the structure of a tetrameric form of K2-2, demonstrated that the formation of intersubunit catalytic center does not require trimerization, which could be nearly completely disrupted by a single-residue mutation in the C-terminal domain. Our findings regarding the assembly and catalysis of K2-2 provide cues for the development of glycoconjugate vaccines against infection.IMPORTANCEGenerating fragments of capsular polysaccharides from pathogenic bacteria with crucial antigenic determinants for vaccine development continues to pose challenges. The significance of the C-terminal region of phage tailspike protein (TSP) in relation to its folding and trimer formation remains largely unexplored. The polysaccharide depolymerase described here demonstrates the ability to depolymerize the K2 CPS of into tetrasaccharide fragments while retaining the vital -acetylation modification crucial for immunogenicity. By carefully characterizing the enzyme, elucidating its three-dimensional structures, conducting site-directed mutagenesis, and assessing the antimicrobial efficacy of the mutant enzymes against K2 , we offer valuable insights into the mechanism by which this enzyme recognizes and depolymerizes the K2 CPS. Our findings, particularly the discovery that trimer formation is not required for depolymerizing activity, challenge the current understanding of trimer-dependent TSP activity and highlight the catalytic mechanism of the TSP with an intersubunit catalytic center.

PubMed: 38349137
DOI: 10.1128/mbio.03519-23

Experimental method

X-RAY DIFFRACTION (1.58 Å)