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- PDB-6j0a: Crystal structure of E. coli methionine aminopeptidase enzyme and... -

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Basic information

Entry
Database: PDB / ID: 6j0a
TitleCrystal structure of E. coli methionine aminopeptidase enzyme and chaperone trigger factor fitted into the cryo-EM density map of the complex
Components
  • Methionine aminopeptidaseMethionyl aminopeptidase
  • Trigger factor
KeywordsRIBOSOME / E. coli 70S ribosome / Protein biogenesis / Chaperone / Methionine aminopeptidase / Trigger factor / Polypeptide exit tunnel
Function / homology
Function and homology information


'de novo' cotranslational protein folding / initiator methionyl aminopeptidase activity / methionyl aminopeptidase / metalloaminopeptidase activity / protein unfolding / chaperone-mediated protein folding / protein folding chaperone / regulation of DNA-templated transcription elongation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity ...'de novo' cotranslational protein folding / initiator methionyl aminopeptidase activity / methionyl aminopeptidase / metalloaminopeptidase activity / protein unfolding / chaperone-mediated protein folding / protein folding chaperone / regulation of DNA-templated transcription elongation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / ferrous iron binding / protein transport / ribosome binding / cell cycle / cell division / proteolysis / DNA binding / cytosol / cytoplasm
Similarity search - Function
Transcription elongation factor GreA/GreB, C-terminal domain superfamily / Trigger factor / Trigger factor, C-terminal / Trigger factor, ribosome-binding, bacterial / Trigger factor ribosome-binding domain superfamily / Bacterial trigger factor protein (TF) / Bacterial trigger factor protein (TF) C-terminus / Trigger factor, C-terminal domain superfamily / Trigger factor/SurA domain superfamily / Methionine aminopeptidase subfamily 1 signature. ...Transcription elongation factor GreA/GreB, C-terminal domain superfamily / Trigger factor / Trigger factor, C-terminal / Trigger factor, ribosome-binding, bacterial / Trigger factor ribosome-binding domain superfamily / Bacterial trigger factor protein (TF) / Bacterial trigger factor protein (TF) C-terminus / Trigger factor, C-terminal domain superfamily / Trigger factor/SurA domain superfamily / Methionine aminopeptidase subfamily 1 signature. / Peptidase M24A, methionine aminopeptidase, subfamily 1 / Peptidase M24, methionine aminopeptidase / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like
Similarity search - Domain/homology
Methionine aminopeptidase / Trigger factor
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Thermotoga maritima MSB8 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 14.2 Å
AuthorsSengupta, J. / Bhakta, S. / Akbar, 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 22, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 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: Methionine aminopeptidase
Q: Trigger factor


Theoretical massNumber of molelcules
Total (without water)77,3032
Polymers77,3032
Non-polymers00
Water0
1


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

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Components

#1: Protein Methionine aminopeptidase / Methionyl aminopeptidase / MetAP / Peptidase M / Coordinate model: Cα atoms only


Mass: 29341.775 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: map, b0168, JW0163 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AE18, methionyl aminopeptidase
#2: Protein Trigger factor / TF / PPIase / Coordinate model: Cα atoms only


Mass: 47961.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Strain: MSB8 / Gene: tig, TM_0694 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9WZF8, peptidylprolyl isomerase
Sequence detailsAuthors state that the conflict is due to the low resolutrion range. They did not determine the ...Authors state that the conflict is due to the low resolutrion range. They did not determine the accurate model of the E. coli trigger factor.

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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 methionine aminopeptidase enzyme and chaperone trigger factor
Type: RIBOSOME / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
11Escherichia coli K-12 (bacteria)83333K-12
21Thermotoga maritima MSB8 (bacteria)243274
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
11Escherichia coli (E. coli)562
21Escherichia coli BL21(DE3) (bacteria)469008BL21(DE3)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
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 FIELDBright-field microscopy
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: 14.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19500 / Symmetry type: POINT
Atomic model building

3D fitting-ID: 1 / Pdb chain-ID: A / Source name: PDB / Type: experimental model

IDPDB-IDAccession codeInitial refinement model-ID
11C21

1c21

1C211
23GU0

3gu0

3GU02

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