ISDA

Deposition Date 2022-11-08

Release Date 2023-11-22

Last Version Date 2024-10-16

Entry Detail

PDB ID:

8BK3

Keywords:

ANTIMICROBIAL PROTEIN

Title:

Crystal structure of the transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with diepoxide ketone 1

Biological Source:

Source Organism:

Mycobacterium tuberculosis (Taxon ID: 1773)

Host Organism:

Escherichia coli BL21(DE3)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.15 Å

R-Value Free:

0.25

R-Value Work:

0.21

R-Value Observed:

0.21

Space Group:

P 1 21 1

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:L,D-transpeptidase 2
Chain IDs:A, B
Chain Length:355
Number of Molecules:2
Biological Source:Mycobacterium tuberculosis

UniProt ID:I6Y9J2 Pfam ID:PF17964, PF03734

Ligand Molecules

DMS

EDO

GOL

NO3

QXU

Primary Citation

alpha beta , alpha ' beta '-Diepoxyketones are mechanism-based inhibitors of nucleophilic cysteine enzymes.

de Munnik, M, Lithgow, J, Brewitz, L, Christensen, K.E, Bates, R.H, Rodriguez-Miquel, B, Schofield, C.J.Show

Chem.Commun.(Camb.) 59 12859 12862 (2023)

PMID: 37815791 DOI: 10.1039/d3cc02932h

Abstact

Epoxides are an established class of electrophilic alkylating agents that react with nucleophilic protein residues. We report αβ,α'β'-diepoxyketones (DEKs) as a new type of mechanism-based inhibitors of nucleophilic cysteine enzymes. Studies with the L,D-transpeptidase LdtMt2 from Mycobacterium tuberculosis and the main protease from SARS-CoV-2 (Mpro) reveal that following epoxide ring opening by a nucleophilic cysteine, further reactions can occur, leading to irreversible alkylation.

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Primary Citation of related structures