2X3H

COLIPHAGE K5A LYASE

• PDB DOI: https://doi.org/10.2210/pdb2X3H/pdb

• Classification: LYASE
• Organism(s): Vectrevirus K15
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-02-04 Released: 2010-06-02 
• Deposition Author(s): Thompson, J.E., Pourhossein, M., Goldrick, M., Hudson, T., Derrick, J.P., Roberts, I.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.203 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 

Literature

The K5 Lyase Kfla Combines a Viral Tail Spike Structure with a Bacterial Polysaccharide Lyase Mechanism.

Thompson, J.E., Pourhossein, M., Waterhouse, A., Hudson, T., Goldrick, M., Derrick, J.P., Roberts, I.S.

(2010) J Biol Chem 285: 23963

• PubMed: 20519506 
• DOI: https://doi.org/10.1074/jbc.M110.127571
• Primary Citation of Related Structures:  
  2X3H


• PubMed Abstract: 
  

  K5 lyase A (KflA) is a tail spike protein (TSP) encoded by a K5A coliphage, which cleaves K5 capsular polysaccharide, a glycosaminoglycan with the repeat unit [-4)-betaGlcA-(1,4)- alphaGlcNAc(1-], displayed on the surface of Escherichia coli K5 strains. The crystal structure of KflA reveals a trimeric arrangement, with each monomer containing a right-handed, single-stranded parallel beta-helix domain. Stable trimer formation by the intertwining of strands in the C-terminal domain, followed by proteolytic maturation, is likely to be catalyzed by an autochaperone as described for K1F endosialidase. The structure of KflA represents the first bacteriophage tail spike protein combining polysaccharide lyase activity with a single-stranded parallel beta-helix fold. We propose a catalytic site and mechanism representing convergence with the syn-beta-elimination site of heparinase II from Pedobacter heparinus.

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Organizational Affiliation: 

Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 170.09 kDa 
• Atom Count: 11,734 
• Modelled Residue Count: 1,494 
• Deposited Residue Count: 1,626 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
K5 LYASE	A, B, C	542	Vectrevirus K15	Mutation(s): 0  EC: 4.2.2.7
UniProt
Find proteins for O09496 (Escherichia virus K5) Explore O09496  Go to UniProtKB:  O09496

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BR	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth C], L [auth C], M [auth C], N [auth C], O [auth C]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.203 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.53	α = 90
b = 130.4	β = 90
c = 145.74	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-02 
Deposition Author(s): Thompson, J.E., Pourhossein, M., Goldrick, M., Hudson, T., Derrick, J.P., Roberts, I.S.

Revision History  

• Version 1.0: 2010-06-02
  Type: Initial release
  
• Version 1.1: 2011-05-07
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-05-08
  Changes: Data collection, Derived calculations, Experimental preparation, Other
• Version 1.4: 2019-10-30
  Changes: Advisory, Data collection, Derived calculations, Other