6S8Z | pdb_00006s8z

Elongation Factor P from Corynebacterium glutamicum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.265 (Depositor) 
  • R-Value Work: 
    0.206 (Depositor), 0.253 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6S8Z

This is version 1.2 of the entry. See complete history

Literature

Structure and Function of an Elongation Factor P Subfamily in Actinobacteria.

Pinheiro, B.Scheidler, C.M.Kielkowski, P.Schmid, M.Forne, I.Ye, S.Reiling, N.Takano, E.Imhof, A.Sieber, S.A.Schneider, S.Jung, K.

(2020) Cell Rep 30: 4332-4342.e5

  • DOI: https://doi.org/10.1016/j.celrep.2020.03.009
  • Primary Citation Related Structures: 
    6S8Z

  • PubMed Abstract: 

    Translation of consecutive proline motifs causes ribosome stalling and requires rescue via the action of a specific translation elongation factor, EF-P in bacteria and archaeal/eukaryotic a/eIF5A. In Eukarya, Archaea, and all bacteria investigated so far, the functionality of this translation elongation factor depends on specific and rather unusual post-translational modifications. The phylum Actinobacteria, which includes the genera Corynebacterium, Mycobacterium, and Streptomyces, is of both medical and economic significance. Here, we report that EF-P is required in these bacteria in particular for the translation of proteins involved in amino acid and secondary metabolite production. Notably, EF-P of Actinobacteria species does not need any post-translational modification for activation. While the function and overall 3D structure of this EF-P type is conserved, the loop containing the conserved lysine is flanked by two essential prolines that rigidify it. Actinobacteria's EF-P represents a unique subfamily that works without any modification.


  • Organizational Affiliation
    • Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany.

Macromolecule Content 

  • Total Structure Weight: 20.93 kDa 
  • Atom Count: 1,512 
  • Modeled Residue Count: 185 
  • Deposited Residue Count: 187 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Elongation factor P187Corynebacterium glutamicumMutation(s): 0 
Gene Names: efpCS176_1554
UniProt
Find proteins for Q45288 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534))
Explore Q45288 
Go to UniProtKB:  Q45288
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ45288
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.265 (Depositor) 
  • R-Value Work:  0.206 (Depositor), 0.253 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.201α = 90
b = 38.163β = 93.09
c = 55.356γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyGRK2062

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-26
    Type: Initial release
  • Version 1.1: 2020-04-08
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description