8BKE

Crystal structure of the Klebsiella phage KP34p57 capsular depolymerase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Klebsiella phage KP34gp57 capsular depolymerase structure and function: from a serendipitous finding to the design of active mini-enzymes against K. pneumoniae.

Maciejewska, B.Squeglia, F.Latka, A.Privitera, M.Olejniczak, S.Switala, P.Ruggiero, A.Marasco, D.Kramarska, E.Drulis-Kawa, Z.Berisio, R.

(2023) mBio 14: e0132923-e0132923

  • DOI: https://doi.org/10.1128/mbio.01329-23
  • Primary Citation of Related Structures:  
    8BKE

  • PubMed Abstract: 

    In this work, we determined the structure of Klebsiella phage KP34p57 capsular depolymerase and dissected the role of individual domains in trimerization and functional activity. The crystal structure serendipitously revealed that the enzyme can exist in a monomeric state once deprived of its C-terminal domain. Based on the crystal structure and site-directed mutagenesis, we localized the key catalytic residues in an intra-subunit deep groove. Consistently, we show that C-terminally trimmed KP34p57 variants are monomeric, stable, and fully active. The elaboration of monomeric, fully active phage depolymerases is innovative in the field, as no previous example exists. Indeed, mini phage depolymerases can be combined in chimeric enzymes to extend their activity ranges, allowing their use against multiple serotypes.


  • Organizational Affiliation

    Department of Pathogen Biology and Immunology, University of Wrocław , Wrocław, Poland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein 57A [auth AAA],
B [auth BBB]
638Klebsiella phage KP34Mutation(s): 0 
Gene Names: 57
UniProt
Find proteins for D1L302 (Klebsiella phage KP34)
Explore D1L302 
Go to UniProtKB:  D1L302
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD1L302
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.34α = 90
b = 140.985β = 102.633
c = 81.925γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RESOLVEmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Center for Research and Development (Poland)PolandUMO-2017/26/M/NZ1/00233

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-30
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Database references