3KM5

Crystal Structure Analysis of the K2 Cleaved Adhesin Domain of Lys-gingipain (Kgp)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

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This is version 1.2 of the entry. See complete history


Literature

Structure determination and analysis of a haemolytic gingipain adhesin domain from Porphyromonas gingivalis

Li, N.Yun, P.Nadkarni, M.A.Ghadikolaee, N.B.Nguyen, K.-A.Lee, M.Hunter, N.Collyer, C.A.

(2010) Mol Microbiol 76: 861-873

  • DOI: 10.1111/j.1365-2958.2010.07123.x
  • Primary Citation of Related Structures:  
    3KM5

  • PubMed Abstract: 
  • Porphyromonas gingivalis is an obligately anaerobic bacterium recognized as an aetiological agent of adult periodontitis. P. gingivalis produces cysteine proteinases, the gingipains. The crystal structure of a domain within the haemagglutinin region of the lysine gingipain (Kgp) is reported here ...

    Porphyromonas gingivalis is an obligately anaerobic bacterium recognized as an aetiological agent of adult periodontitis. P. gingivalis produces cysteine proteinases, the gingipains. The crystal structure of a domain within the haemagglutinin region of the lysine gingipain (Kgp) is reported here. The domain was named K2 as it is the second of three homologous structural modules in Kgp. The K2 domain structure is a 'jelly-roll' fold with two anti-parallel beta-sheets. This fold topology is shared with adhesive domains from functionally diverse receptors such as MAM domains, ephrin receptor ligand binding domains and a number of carbohydrate binding modules. Possible functions of K2 were investigated. K2 induced haemolysis of erythrocytes in a dose-dependent manner that was augmented by the blocking of anion transport. Further, cysteine-activated arginine gingipain RgpB, which degrades glycophorin A, sensitized erythrocytes to the haemolytic effect of K2. Cleaved K2, similar to that found in extracted Kgp, lacks the haemolytic activity indicating that autolysis of Kgp may be a staged process which is artificially enhanced by extraction of the protein. The data indicate a functional role for K2 in the integrated capacity conferred by Kgp to enable the porphyrin auxotroph P. gingivalis to capture essential haem from erythrocytes.


    Organizational Affiliation

    School of Molecular Bioscience, The University of Sydney, NSW, Australia.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lysine specific cysteine proteaseA, B180Porphyromonas gingivalis W83Mutation(s): 0 
Gene Names: kgphagAPG_1837
UniProt
Find proteins for P59915 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83))
Explore P59915 
Go to UniProtKB:  P59915
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP59915
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 29.911α = 90
b = 59.858β = 94.23
c = 85.672γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXCDphasing
SHELXEmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-31
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description