title: Structural basis for the inhibition of Mycobacterium tuberculosis L,D-transpeptidase by meropenem, a drug effective against extensively drug-resistant strains.
abstract: Difficulty in the treatment of tuberculosis and growing drug resistance in Mycobacterium tuberculosis (Mtb) are a global health issue. Carbapenems inactivate L,D-transpeptidases; meropenem, when administered with clavulanate, showed in vivo activity against extensively drug-resistant Mtb strains. LdtMt2 (Rv2518c), one of two functional L,D-transpeptidases in Mtb, is predominantly expressed over LdtMt1 (Rv0116c). Here, the crystal structure of N-terminally truncated LdtMt2 (residues Leu131-Ala408) is reported in both ligand-free and meropenem-bound forms. The structure of meropenem-inhibited LdtMt2 provides a detailed structural view of the interactions between a carbapenem drug and Mtb L,D-transpeptidase. The structures revealed that the catalytic L,D-transpeptidase domain of LdtMt2 is preceded by a bacterial immunogloblin-like Big_5 domain and is followed by an extended C-terminal tail that interacts with both domains. Furthermore, it is shown using mass analyses that meropenem acts as a suicide inhibitor of LdtMt2. Upon acylation of the catalytic Cys354 by meropenem, the `active-site lid' undergoes a large conformational change to partially cover the active site so that the bound meropenem is accessible to the bulk solvent via three narrow paths. This work will facilitate structure-guided discovery of L,D-transpeptidase inhibitors as novel antituberculosis drugs against drug-resistant Mtb.
authors.affiliation: Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea.
authors.forename: Hyoun Sook
authors.initials: HS
authors.lastname: Kim
authors.forename: Jieun
authors.initials: J
authors.lastname: Kim
authors.forename: Ha Na
authors.initials: HN
authors.lastname: Im
authors.forename: Ji Young
authors.initials: JY
authors.lastname: Yoon
authors.forename: Doo Ri
authors.initials: DR
authors.lastname: An
authors.forename: Hye Jin
authors.initials: HJ
authors.lastname: Yoon
authors.forename: Jin Young
authors.initials: JY
authors.lastname: Kim
authors.forename: Hye Kyeoung
authors.initials: HK
authors.lastname: Min
authors.forename: Soon-Jong
authors.initials: SJ
authors.lastname: Kim
authors.forename: Jae Young
authors.initials: JY
authors.lastname: Lee
authors.forename: Byung Woo
authors.initials: BW
authors.lastname: Han
authors.forename: Se Won
authors.initials: SW
authors.lastname: Suh
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D018360:Crystallography, X-Ray; D004352:Drug Resistance, Microbial / Q000187:drug effects*; D004791:Enzyme Inhibitors / Q000494:pharmacology*; D000077731:Meropenem; D009169:Mycobacterium tuberculosis / Q000187:drug effects / Q000201:enzymology; D010458:Peptidyl Transferases / Q000037:antagonists & inhibitors* / Q000737:chemistry*; D013845:Thienamycins / Q000494:pharmacology*
chemical_list: D000900:Anti-Bacterial Agents; D004791:Enzyme Inhibitors; D013845:Thienamycins; D010458:Peptidyl Transferases; D000077731:Meropenem
keywords: LdtMt2; Mt2594; Mycobacterium tuberculosis; Rv2518c; antituberculosis drug discovery; carbapenem; l,d-transpeptidases; meropenem; peptidoglycans