9HMX

Structure of SteB-RipA complex from Mycobacterium tuberculosis

Summary for 9HMX

• Entry DOI: 10.2210/pdb9hmx/pdb
• Related: 9HLE
• Descriptor: Peptidoglycan endopeptidase RipA, Copper transporter MctB, HEXANE-1,6-DIOL, ... (4 entities in total)
• Functional Keywords: complex, peptidoglycan hydrolase, cell division, cell cycle
• Biological source: Mycobacterium tuberculosis H37Rv; More
• Total number of polymer chains: 2
• Total formula weight: 51837.36

Authors

Carloni, G.,Wehenkel, A.M.,Alzari, P.M. (deposition date: 2024-12-09, release date: 2025-07-30)

Primary citation

Carloni, G.,Gaday, Q.,Petit, J.,Martinez, M.,Megrian, D.,Sogues, A.,Ben Assaya, M.,Kakonyi, M.,Haouz, A.,Alzari, P.M.,Wehenkel, A.M.
Mechanistic insights into the allosteric regulation of cell wall hydrolase RipA in Mycobacterium tuberculosis.
Biorxiv, 2025

PubMed Abstract: D,L-endopeptidase RipA is the major PG hydrolase required for daughter cell separation in ( ), as RipA defects severely hinder cell division and increase antibiotic vulnerability. Despite extensive studies, the mechanisms governing RipA regulation remain controversial and poorly understood. Here, we report an integrative structural and functional analysis of the SteAB system, a regulatory complex that has been shown to modulate cell separation in the model organism ( ) and is conserved across . Although SteB was previously proposed to act as a mycobacterial outer membrane copper transporter, the crystal structures of the homodimeric protein, alone and in complex with the RipA coiled-coil (CC) domain, rule out this hypothesis. Instead, the high-affinity SteB-RipA interaction, together with computational and biophysical data, strongly supports the role of SteB as a direct RipA activator that releases enzyme autoinhibition upon complex formation. In addition, crystallographic characterization of the cytoplasmic core of SteA revealed a homodimeric organization harboring a conserved functional pocket similar to the phosphonucleotide-binding site of thiamine pyrophosphokinase. These data, coupled with the phenotypic analysis of a knockout mutant of , support a model in which the transmembrane SteAB heterotetramer, driven by cytoplasmic ligand binding, orchestrates the productive periplasmic positioning of RipA, leading to PG hydrolysis activation. These findings shed new light on the regulation of mycobacterial cell wall remodeling, with implications for understanding pathogenesis and identifying novel antimicrobial targets.

PubMed: 40667032
DOI: 10.1101/2025.06.28.662095

Experimental method

X-RAY DIFFRACTION (2.22 Å)