6OYZ

Crystal structure of MraY bound to capuramycin

Summary for 6OYZ

• Entry DOI: 10.2210/pdb6oyz/pdb
• Descriptor: MraYAA nanobody, Phospho-N-acetylmuramoyl-pentapeptide-transferase, (2~{S},3~{S},4~{S})-2-[(1~{R})-2-azanyl-1-[(2~{S},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-methoxy-4-oxidanyl-oxolan-2-yl]-2-oxidanylidene-ethoxy]-3,4-bis(oxidanyl)-~{N}-[(3~{S})-2-oxidanylideneazepan-3-yl]-3,4-dihydro-2~{H}-pyran-6-carboxamide (3 entities in total)
• Functional Keywords: peptidoglycan biosynthesis, antibiotic target, integral membrane enzyme, translocase, membrane protein/transferase, membrane protein, membrane protein-transferase complex
• Biological source: Lama glama; More
• Total number of polymer chains: 8
• Total formula weight: 224618.86

Authors

Mashalidis, E.H.,Lee, S.Y. (deposition date: 2019-05-15, release date: 2019-07-10, Last modification date: 2023-10-11)

Primary citation

Mashalidis, E.H.,Kaeser, B.,Terasawa, Y.,Katsuyama, A.,Kwon, D.Y.,Lee, K.,Hong, J.,Ichikawa, S.,Lee, S.Y.
Chemical logic of MraY inhibition by antibacterial nucleoside natural products.
Nat Commun, 10:2917-2917, 2019

PubMed Abstract: Novel antibacterial agents are needed to address the emergence of global antibiotic resistance. MraY is a promising candidate for antibiotic development because it is the target of five classes of naturally occurring nucleoside inhibitors with potent antibacterial activity. Although these natural products share a common uridine moiety, their core structures vary substantially and they exhibit different activity profiles. An incomplete understanding of the structural and mechanistic basis of MraY inhibition has hindered the translation of these compounds to the clinic. Here we present crystal structures of MraY in complex with representative members of the liposidomycin/caprazamycin, capuramycin, and mureidomycin classes of nucleoside inhibitors. Our structures reveal cryptic druggable hot spots in the shallow inhibitor binding site of MraY that were not previously appreciated. Structural analyses of nucleoside inhibitor binding provide insights into the chemical logic of MraY inhibition, which can guide novel approaches to MraY-targeted antibiotic design.

PubMed: 31266949
DOI: 10.1038/s41467-019-10957-9

Experimental method

X-RAY DIFFRACTION (3.62 Å)