6IZ7

E. coli methionine aminopeptidase crystal structure fitted into the cryo-EM density map of E. coli 70S ribosome in complex with methionine aminopeptidase

Summary for 6IZ7

• Entry DOI: 10.2210/pdb6iz7/pdb
• EMDB information: 9750 9752 9753 9759
• Descriptor: Methionine aminopeptidase (1 entity in total)
• Functional Keywords: e. coli 70s ribosome, protein biogenesis, methionine aminopeptidase, methionine excision, polypeptide exit tunnel, ribosome
• Biological source: Escherichia coli K-12
• Total number of polymer chains: 1
• Total formula weight: 29341.78

Authors

Sengupta, J.,Bhakta, S.,Akbar, S. (deposition date: 2018-12-18, release date: 2019-04-17, Last modification date: 2024-03-27)

Primary citation

Bhakta, S.,Akbar, S.,Sengupta, J.
Cryo-EM Structures Reveal Relocalization of MetAP in the Presence of Other Protein Biogenesis Factors at the Ribosomal Tunnel Exit.
J. Mol. Biol., 431:1426-1439, 2019

PubMed Abstract: During protein biosynthesis in bacteria, one of the earliest events that a nascent polypeptide chain goes through is the co-translational enzymatic processing. The event includes two enzymatic pathways: deformylation of the N-terminal methionine by the enzyme peptide deformylase (PDF), followed by methionine excision catalyzed by methionine aminopeptidase (MetAP). During the enzymatic processing, the emerging nascent protein likely remains shielded by the ribosome-associated chaperone trigger factor. The ribosome tunnel exit serves as a stage for recruiting proteins involved in maturation processes of the nascent chain. Co-translational processing of nascent chains is a critical step for subsequent folding and functioning of mature proteins. Here, we present cryo-electron microscopy structures of Escherichia coli (E. coli) ribosome in complex with the nascent chain processing proteins. The structures reveal overlapping binding sites for PDF and MetAP when they bind individually at the tunnel exit site, where L22-L32 protein region provides primary anchoring sites for both proteins. In the absence of PDF, trigger factor can access ribosomal tunnel exit when MetAP occupies its primary binding site. Interestingly, however, in the presence of PDF, when MetAP's primary binding site is already engaged, MetAP has a remarkable ability to occupy an alternative binding site adjacent to PDF. Our study, thus, discloses an unexpected mechanism that MetAP adopts for context-specific ribosome association.

PubMed: 30753870
DOI: 10.1016/j.jmb.2019.02.002

Experimental method

ELECTRON MICROSCOPY (11.8 Å)