6CK7

Crystal structure of a peptide deformylase from Legionella pneumophila bound to actinonin

Summary for 6CK7

• Entry DOI: 10.2210/pdb6ck7/pdb
• Related: 6CAZ
• Descriptor: Peptide deformylase, ZINC ION, ACTINONIN, ... (5 entities in total)
• Functional Keywords: national institute of allergy and infectious diseases, niaid, structural genomics, legionnaires' disease, formyl-l-methionyl peptide, formate, methionyl peptide, seattle structural genomics center for infectious disease, ssgcid, hydrolase-antibiotic complex, hydrolase/antibiotic
• Biological source: Legionella pneumophila
• Total number of polymer chains: 4
• Total formula weight: 83438.84

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID) (deposition date: 2018-02-27, release date: 2018-03-07, Last modification date: 2025-04-09)

Primary citation

Nguyen, C.L.,Fan, W.,Fisher, S.,Matthews, K.,Norman, J.O.,Abendroth, J.,Barrett, K.F.,Craig, J.K.,Edwards, T.E.,Lorimer, D.D.,McLaughlin, K.J.
Structures of Legionella pneumophila serogroup 1 peptide deformylase bound to nickel(II) and actinonin.
Acta Crystallogr.,Sect.F, 81:163-170, 2025

PubMed Abstract: Legionella pneumophila serogroup 1 is the primary causative agent of Legionnaires' disease, a rare but severe respiratory infection. While the fatality rate of Legionnaires' disease is low in the general population, it is more pronounced in vulnerable communities such as the immunocompromised. Thus, the development of new antimicrobials is of interest for use when existing antibiotics may not be applicable. Peptide deformylases (PDFs) have been under continued investigation as targets for novel antimicrobial compounds. PDF plays an essential role in protein synthesis, removing the N-terminal formyl group from new polypeptides, and is required for growth in most bacteria. Here, we report two crystal structures of L. pneumophila serogroup 1 PDF (LpPDF) bound to either Ni, an active state, or inhibited by actinonin and Zn; the structures were determined to 1.5 and 1.65 Å resolution, respectively, and were solved by the Seattle Structural Genomics Center for Infectious Disease (SSGCID). The SSGCID is charged with determining structures of biologically important proteins and molecules from human pathogens. As actinonin is an antimicrobial natural product that has been used as a reference compound in drug development, these structures will help support the ongoing drug-development process.

PubMed: 40091854
DOI: 10.1107/S2053230X25001876

Experimental method

X-RAY DIFFRACTION (1.65 Å)