6J45 | pdb_00006j45

Crystal structure of E. coli peptide deformylase enzyme and chaperone trigger factor fitted into the cryo-EM density map of the complex

PDB DOI: https://doi.org/10.2210/pdb6J45/pdb
EM Map EMD-9778: EMDB EMDataResource

Classification: RIBOSOME
Organism(s): Escherichia coli H591
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-01-07 Released: 2019-04-17
Deposition Author(s): Sengupta, J., Bhakta, S., Akbar, S.
Funding Organization(s): Council of Scientific & Industrial Research, Department of Science & Technology (India)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 12.2 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Cryo-EM Structures Reveal Relocalization of MetAP in the Presence of Other Protein Biogenesis Factors at the Ribosomal Tunnel Exit.

Bhakta, S., Akbar, S., Sengupta, J.

(2019) J Mol Biology 431: 1426-1439

PubMed: 30753870 Search on PubMed
DOI: https://doi.org/10.1016/j.jmb.2019.02.002
Primary Citation Related Structures:
6IY7, 6IZ7, 6IZI, 6J0A, 6J45

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.

Organizational Affiliation

Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India.

Macromolecule Content

Total Structure Weight: 67.61 kDa
Atom Count: 600
Modeled Residue Count: 600
Deposited Residue Count: 601
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A [auth P]	169	Escherichia coli H591	Mutation(s): 0 Gene Names: def EC: 3.5.1.88

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Trigger factor	B [auth Q]	432	Escherichia coli H591	Mutation(s): 0 Gene Names: tig EC: 5.2.1.8