7P1R

Structure of Trichophyton Rubrum KDNase in complex with 2,3-difluoro-KDN

PDB DOI: https://doi.org/10.2210/pdb7P1R/pdb

Classification: CARBOHYDRATE
Organism(s): Trichophyton rubrum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-07-02 Released: 2021-10-20
Deposition Author(s): Gloster, T.M., McMahon, S.A.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.213
R-Value Work: 0.184
R-Value Observed: 0.185

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 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

PubMed: 34724608 Search on PubMed
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.

Macromolecule Content

Total Structure Weight: 170.86 kDa
Atom Count: 13,789
Modelled Residue Count: 1,530
Deposited Residue Count: 1,544
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Extracellular sialidase/neuraminidase	A, B, C, D	386	Trichophyton rubrum	Mutation(s): 0 Gene Names: A7C99_5399
UniProt
Find proteins for A0A178EUH2 (Trichophyton rubrum) Explore A0A178EUH2 Go to UniProtKB: A0A178EUH2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A178EUH2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FKD (Subject of Investigation/LOI) Query on FKD Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain T [auth D] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain P [auth C] mmCIF format, chain T [auth D]	H [auth A], L [auth B], P [auth C], T [auth D]	3-deoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid C₉ H₁₅ F O₉ KOWJBKIDVGQXJZ-QMFVTVPYSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain Q [auth D] SDF format, chain R [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D]	E [auth A] F [auth A] I [auth B] J [auth B] M [auth C] E [auth A], F [auth A], I [auth B], J [auth B], M [auth C], N [auth C], Q [auth D], R [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain Q [auth D] Focus chain R [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain Q [auth D] Focus chain R [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain S [auth D] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain O [auth C] mmCIF format, chain S [auth D]	G [auth A], K [auth B], O [auth C], S [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth D] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth D]