Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
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Journal
IF	>30 >20 >10 >5 all

Title	Cryo-EM Structures Reveal Relocalization of MetAP in the Presence of Other Protein Biogenesis Factors at the Ribosomal Tunnel Exit.
Journal, issue, pages	J Mol Biol, Vol. 431, Issue 7, Page 1426-1439, Year 2019
Publish date	Mar 29, 2019
Authors	Sayan Bhakta / Shirin Akbar / Jayati Sengupta /
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 ...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.
External links	J Mol Biol / PubMed:30753870
Methods	EM (single particle)
Resolution	10.5 - 14.2 Å
Structure data	9750 6iy7 EMDB-9750: Cryo-EM density map of E. coli 70S ribosome in complex with peptide deformylase enzyme PDB-6iy7: E. coli peptide deformylase crystal structure fitted into the cryo-EM density map of E. coli 70S ribosome in complex with peptide deformylase Method: EM (single particle) / Resolution: 10.5 Å 9752 6iz7 EMDB-9752: Cryo-EM density map of E. coli 70S ribosome in complex with methionine aminopeptidase enzyme PDB-6iz7: E. coli methionine aminopeptidase crystal structure fitted into the cryo-EM density map of E. coli 70S ribosome in complex with methionine aminopeptidase Method: EM (single particle) / Resolution: 11.8 Å 9753 6izi EMDB-9753: Cryo-EM density map of peptide deformylase and methionine aminopeptidase bound to the E. coli 70S ribosome PDB-6izi: Crystal structure of E. coli peptide deformylase and methionine aminopeptidase fitted into the cryo-EM density map of the complex Method: EM (single particle) / Resolution: 11.8 Å 9759 6j0a EMDB-9759: Cryo-EM density map of methionine aminopeptidase enzyme and chaperone trigger factor bound to the E. coli 70S ribosome PDB-6j0a: Crystal structure of E. coli methionine aminopeptidase enzyme and chaperone trigger factor fitted into the cryo-EM density map of the complex Method: EM (single particle) / Resolution: 14.2 Å 9778 6j45 EMDB-9778: Cryo-EM density map of peptide deformylase enzyme and chaperone trigger factor bound to the E. coli 70S ribosome PDB-6j45: Crystal structure of E. coli peptide deformylase enzyme and chaperone trigger factor fitted into the cryo-EM density map of the complex Method: EM (single particle) / Resolution: 12.2 Å
Source	escherichia coli k-12 (bacteria) thermotoga maritima msb8 (bacteria) escherichia coli h591 (bacteria)
Keywords	RIBOSOME / E. coli 70S ribosome / pepdite deformylase / Nascent polypeptide exit tunnel / Protein biogenesis / Methionine aminopeptidase / Methionine excision / Polypeptide exit tunnel / Peptide deformylase / Chaperone / Trigger factor / PPIase