Wide‐open conformation of UDP‐MurNc‐tripeptide ligase revealed by the substrate‐free structure of MurE from Acinetobacter baumannii

Abstract

MurE ligase catalyzes the attachment of meso‐diaminopimelic acid to the UDP‐MurNAc‐l‐Ala‐d‐Glu using ATP and producing UDP‐MurNAc‐l‐Ala‐d‐Glu‐meso‐A2pm during bacterial cell wall biosynthesis. Owing to the critical role of this enzyme, MurE is considered an attractive target for antibacterial drugs. Despite extensive studies on MurE ligase, the structural dynamics of its conformational changes are still elusive. In this study, we present the substrate‐free structure of MurE from Acinetobacter baumannii, which is an antibiotic‐resistant superbacterium that has threatened global public health. The structure revealed that MurE has a wide‐open conformation and undergoes wide‐open, intermediately closed, and fully closed dynamic conformational transition. Unveiling structural dynamics of MurE will help to understand the working mechanism of this ligase and to design next‐generation antibiotics targeting MurE.

Structural characterisation of methanogen pseudomurein cell wall peptide ligases homologous to bacterial MurE/F murein peptide ligases

“…Rigid-body conformational flexibility for the C-terminal domain is observed for bacterial Mur ligases; Thermotoga maritima MurD exhibits different C-terminal domain orientations for the two molecules in the asymmetric unit [46], closure of the C-terminal domain (relative to the rest of the structure) is seen for Streptococcus pneumoniae MurF upon inhibitor binding [47] and further analysis is presented by Jung et al . [48]. The observation of domain-based rigid-body conformational changes upon inhibitor/substrate binding has led to the proposal of a Mur ligase enzymatic mechanism involving a transition from an open apo structure to a closed substrate-bound conformation [8, 48, 49].…”

“…[48]. The observation of domain-based rigid-body conformational changes upon inhibitor/substrate binding has led to the proposal of a Mur ligase enzymatic mechanism involving a transition from an open apo structure to a closed substrate-bound conformation [8, 48, 49].…”

“…The enzymatic mechanism is associated with an open apo Mur substrate-binding conformation followed by closure of the tertiary structure through the movement of the C-terminal domain towards the middle domain [8]. Rigid-body movement has been observed for the MurD C-terminal domain in the absence of substrates [46, 61] suggesting a relatively low energy barrier for the different conformational states for the Mur [8, 48] and pMurE ligases. The presence of the conserved P-loop ATP-binding site and UDP-binding surface for pMurE suggests that a similar catalytic mechanism is possible for pMurE, but the absence of a successful chemical synthesis of the methanogen pMur N α -UDP-Glu γ -peptide substrates to date means that the specific pMurE catalytic mechanism remains untested.…”

The crystal structure of Mycobacterium thermoresistibile MurE ligase reveals the binding mode of the substrate m-diaminopimelate

“…Based on the structural data reported so far and its comparison with the structure herein described, we can have a more complete scenario of the dynamic motions of MurE in the presence of different ligands. Thus, starting from ligand-free form (Jung et al, 2021), MurE should have the most wide-open conformation, which is also described for MurC, MurD and MurF (Basavannacharya et al, 2010a;Seo et al, 2021;Šink et al, 2016;Yan et al, 2000). In contrast, upon the binding of UAG or nucleotide, MurE should adopt a closed conformation (Gordon et al, 2001;Kouidmi et al, 2014;Smith, 2006).…”

“…So far, most of the structures solved for MurE consist of the complex with UAG substrate (Basavannacharya et al, 2010b) or UMT product (Gordon et al, 2001;Ruane et al, 2013) or ADP (Favini-Stabile et al, 2013). Only recently, the structure of a MurE in its apo form was reported (Jung et al, 2021). To our knowledge, there is no structure of any MurE in the presence of the free amino acid L-Lys or m-DAP and consequently, the conformational changes triggered by the binding of this substrate are unknown.…”