ISDA: 6ZFC

Deposition Date 2020-06-17

Release Date 2020-10-28

Last Version Date 2024-01-24

Entry Detail

PDB ID:

6ZFC

Keywords:

SUGAR BINDING PROTEIN

Title:

Fucose-binding lectin from Burkholderia ambifaria (BamBL) in complex with a fucosyl derivative

Biological Source:

Source Organism:

Burkholderia ambifaria (strain ATCC BAA-244 / AMMD) (Taxon ID: 339670)

Host Organism:

Escherichia coli BL21(DE3)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.65 Å

R-Value Free:

0.20

R-Value Work:

0.17

R-Value Observed:

0.17

Space Group:

I 1 2 1

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:bacterial lectin from Burkholderia ambifaria
Gene (Uniprot):Bamb_5415
Chain IDs:A, B, C, D, E, F
Chain Length:87
Number of Molecules:6
Biological Source:Burkholderia ambifaria (strain ATCC BAA-244 / AMMD)

UniProt ID:Q0B4G1 Pfam ID:PF07938

Ligand Molecules

QJB

Primary Citation

Fucosylated ubiquitin and orthogonally glycosylated mutant A28C: conceptually new ligands for Burkholderia ambifaria lectin (BambL).

Kuhaudomlarp, S, Cerofolini, L, Santarsia, S, Gillon, E, Fallarini, S, Lombardi, G, Denis, M, Giuntini, S, Valori, C, Fragai, M, Imberty, A, Dondoni, A, Nativi, C.Show

Chem Sci 11 12662 12670 (2020)

PMID: 34094460 DOI: 10.1039/d0sc03741a

Abstact

Two orthogonal, metal free click reactions, enabled to glycosylate ubiquitin and its mutant A28C forming two protein scaffolds with high affinity for BambL, a lectin from the human pathogen Burkholderia ambifaria. A new fucoside analogue, with high affinity with BambL, firstly synthetized and co-crystallized with the protein target, provided the insights for sugar determinants grafting onto ubiquitin. Three ubiquitin-based glycosides were thus assembled. Fuc-Ub, presented several copies of the fucoside analogue, with proper geometry for multivalent effect; Rha-A28C, displayed one thio-rhamnose, known for its ability to tuning the immunological response; finally, Fuc-Rha-A28C, included both multiple fucoside analogs and the rhamnose residue. Fuc-Ub and Fuc-Rha-A28C ligands proved high affinity for BambL and unprecedented immune modulatory properties towards macrophages activation.

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Primary Citation of related structures