7P1S

Structure of KDNase from Trichophyton Rubrum in complex with 2,3-didehydro-2,3-dideoxy-D-glycero-D-galacto-nonulosonic acid.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.261 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Kinetic and Structural Characterization of Sialidases (Kdnases) from Ascomycete Fungal Pathogens.

Nejatie, A.Steves, E.Gauthier, N.Baker, J.Nesbitt, J.McMahon, S.A.Oehler, V.Thornton, N.J.Noyovitz, B.Khazaei, K.Byers, B.W.Zandberg, W.F.Gloster, T.M.Moore, M.M.Bennet, A.J.

(2021) ACS Chem Biol 16: 2632-2640

  • DOI: https://doi.org/10.1021/acschembio.1c00666
  • Primary Citation of Related Structures:  
    7P1B, 7P1D, 7P1E, 7P1F, 7P1O, 7P1Q, 7P1R, 7P1S, 7P1U, 7P1V

  • PubMed Abstract: 

    Sialidases catalyze the release of sialic acid from the terminus of glycan chains. We previously characterized the sialidase from the opportunistic fungal pathogen, Aspergillus fumigatus, and showed that it is a Kdnase. That is, this enzyme prefers 3-deoxy-d-glycero-d-galacto-non-2-ulosonates (Kdn glycosides) as the substrate compared to N -acetylneuraminides (Neu5Ac). Here, we report characterization and crystal structures of putative sialidases from two other ascomycete fungal pathogens, Aspergillus terreus ( At S) and Trichophyton rubrum ( Tr S). Unlike A. fumigatus Kdnase ( Af S), hydrolysis with the Neu5Ac substrates was negligible for Tr S and At S; thus, Tr S and At S are selective Kdnases. The second-order rate constant for hydrolysis of aryl Kdn glycosides by At S is similar to that by Af S but 30-fold higher by Tr S. The structures of these glycoside hydrolase family 33 (GH33) enzymes in complex with a range of ligands for both At S and Tr S show subtle changes in ring conformation that mimic the Michaelis complex, transition state, and covalent intermediate formed during catalysis. In addition, they can aid identification of important residues for distinguishing between Kdn and Neu5Ac substrates. When A. fumigatus , A. terreus, and T. rubrum were grown in chemically defined media, Kdn was detected in mycelial extracts, but Neu5Ac was only observed in A. terreus or T. rubrum extracts. The C8 monosaccharide 3-deoxy-d- manno -oct-2-ulosonic acid (Kdo) was also identified in A. fumigatus and T. rubrum samples. A fluorescent Kdn probe was synthesized and revealed the localization of Af S in vesicles at the cell surface.


  • Organizational Affiliation

    Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby V5A 1S6, British Columbia, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Extracellular sialidase/neuraminidase
A, B, C, D
386Trichophyton rubrumMutation(s): 0 
Gene Names: A7C99_5399
UniProt
Find proteins for A0A178EUH2 (Trichophyton rubrum)
Explore A0A178EUH2 
Go to UniProtKB:  A0A178EUH2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A178EUH2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KFN (Subject of Investigation/LOI)
Query on KFN

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
K [auth D]
2,6-anhydro-3-deoxy-D-glycero-D-galacto-non-2-enonic acid
C9 H14 O8
IZHMZNLAOQHCDZ-LRGKAINGSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
L [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.261 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.646α = 90
b = 179.008β = 104.04
c = 97.292γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-20
    Type: Initial release
  • Version 1.1: 2022-05-04
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description