6TKU

Crystal structure of a capsule-specific depolymerase produced by Klebsiella phage


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and Functional Studies of a Klebsiella Phage Capsule Depolymerase Tailspike: Mechanistic Insights into Capsular Degradation.

Squeglia, F.Maciejewska, B.Latka, A.Ruggiero, A.Briers, Y.Drulis-Kawa, Z.Berisio, R.

(2020) Structure 28: 613

  • DOI: 10.1016/j.str.2020.04.015
  • Primary Citation of Related Structures:  
    6TKU

  • PubMed Abstract: 
  • Capsule polysaccharide is a major virulence factor of Klebsiella pneumoniae, a nosocomial pathogen associated with a wide range of infections. It protects bacteria from harsh environmental conditions, immune system response, and phage infection. To a ...

    Capsule polysaccharide is a major virulence factor of Klebsiella pneumoniae, a nosocomial pathogen associated with a wide range of infections. It protects bacteria from harsh environmental conditions, immune system response, and phage infection. To access cell wall-located receptors, some phages possess tailspike depolymerases that degrade the capsular polysaccharide. Here, we present the crystal structure of a tailspike against Klebsiella, KP32gp38, whose primary sequence shares no similarity to other proteins of known structure. In the trimeric structure of KP32gp38, each chain contains a flexible N-terminal domain, a right-handed parallel β helix domain and two β sandwiches with carbohydrate binding features. The crystal structure and activity assays allowed us to locate the catalytic site. Also, our data provide experimental evidence of a branching architecture of depolymerases in KP32 Klebsiella viruses, as KP32gp38 displays nanomolar affinity to another depolymerase from the same phage, KP32gp37. Results provide a structural framework for enzyme engineering to produce serotype-broad-active enzyme complexes against K. pneumoniae.


    Organizational Affiliation

    Institute of Biostructures and Bioimaging, CNR, Napoli, Italy. Electronic address: rita.berisio@cnr.it.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
depolymerase KP32gp38A584Klebsiella phage KP32Mutation(s): 0 
Gene Names: 38
Find proteins for D1L2X1 (Klebsiella phage KP32)
Explore D1L2X1 
Go to UniProtKB:  D1L2X1
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.726α = 90
b = 71.726β = 90
c = 208.197γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Italian Ministry of EducationItaly2017SFBFER

Revision History 

  • Version 1.0: 2020-04-22
    Type: Initial release
  • Version 1.1: 2020-05-20
    Changes: Database references
  • Version 1.2: 2020-06-10
    Changes: Database references