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- PDB-6iy7: E. coli peptide deformylase crystal structure fitted into the cry... -

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Basic information

Entry
Database: PDB / ID: 6iy7
TitleE. coli peptide deformylase crystal structure fitted into the cryo-EM density map of E. coli 70S ribosome in complex with peptide deformylase
ComponentsPeptide deformylase
KeywordsRIBOSOME / E. coli 70S ribosome / pepdite deformylase / Nascent polypeptide exit tunnel
Function / homology
Function and homology information


co-translational protein modification / peptide deformylase / peptide deformylase activity / ferrous iron binding / ribosome binding / hydrolase activity / translation / zinc ion binding / cytosol
Similarity search - Function
Peptide deformylase / Peptide deformylase superfamily / Polypeptide deformylase
Similarity search - Domain/homology
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10.5 Å
AuthorsSengupta, J. / Akbar, S. / Bhakta, S.
Funding support India, 2items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research India
Department of Science & Technology (India)SB/SO/BB-0025/2014 India
CitationJournal: J Mol Biol / Year: 2019
Title: Cryo-EM Structures Reveal Relocalization of MetAP in the Presence of Other Protein Biogenesis Factors at the Ribosomal Tunnel Exit.
Authors: Sayan Bhakta / Shirin Akbar / Jayati Sengupta /
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.
History
DepositionDec 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Structure summary / Category: em_entity_assembly / Item: _em_entity_assembly.name
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Assembly

Deposited unit
P: Peptide deformylase


Theoretical massNumber of molelcules
Total (without water)19,3571
Polymers19,3571
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Peptide deformylase / PDF / Polypeptide deformylase / Coordinate model: Cα atoms only


Mass: 19357.447 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: def / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6K3, peptide deformylase

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: E. coli 70S ribosome in complex with peptide deformylase
Type: RIBOSOME / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K-12
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 10 e/Å2 / Film or detector model: FEI EAGLE (4k x 4k)
Image scansWidth: 4096 / Height: 4096

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Processing

EM softwareName: SPIDER / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 10.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44000 / Symmetry type: POINT
Atomic model buildingPDB-ID: 1BS7

1bs7


Pdb chain-ID: A / Accession code: 1BS7 / Source name: PDB / Type: experimental model

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