8BNY

Structure of the tetramerization domain of pLS20 conjugation repressor Rco


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

A tetramerization domain in prokaryotic and eukaryotic transcription regulators homologous to p53.

Bernardo, N.Crespo, I.Cuppari, A.Meijer, W.J.J.Boer, D.R.

(2023) Acta Crystallogr D Struct Biol 79: 259-267

  • DOI: https://doi.org/10.1107/S2059798323001298
  • Primary Citation of Related Structures:  
    8BNY

  • PubMed Abstract: 

    Transcriptional regulation usually requires the action of several proteins that either repress or activate a promotor of an open reading frame. These proteins can counteract each other, thus allowing tight regulation of the transcription of the corresponding genes, where tight repression is often linked to DNA looping or cross-linking. Here, the tetramerization domain of the bacterial gene repressor Rco from Bacillus subtilis plasmid pLS20 (Rco pLS20 ) has been identified and its structure is shown to share high similarity to the tetramerization domain of the well known p53 family of human tumor suppressors, despite lacking clear sequence homology. In Rco pLS20 , this tetramerization domain is responsible for inducing DNA looping, a process that involves multiple tetramers. In accordance, it is shown that Rco pLS20 can form octamers. This domain was named TetD loop and its occurrence was identified in other Bacillus species. The TetD loop fold was also found in the structure of a transcriptional repressor from Salmonella phage SPC32H. It is proposed that the TetD loop fold has evolved through divergent evolution and that the TetD loop originates from a common ancestor predating the occurrence of multicellular life.


  • Organizational Affiliation

    Experiments Division, ALBA Synchrotron Light Source, Carrer de la Llum 2-26, 08290 Cerdanyola del Vallès, Catalunya, Spain.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Immunity repressor protein
A, B, C, D
161Bacillus subtilisMutation(s): 0 
UniProt
Find proteins for E9RIY8 (Bacillus subtilis subsp. natto)
Explore E9RIY8 
Go to UniProtKB:  E9RIY8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE9RIY8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.328α = 90
b = 36.182β = 90
c = 109.532γ = 90
Software Package:
Software NamePurpose
autoPROCdata processing
Arcimboldophasing
PHENIXrefinement
Cootmodel building
PHENIXmodel building
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainBIO2016-77883-C2-2-P
Spanish Ministry of Economy and CompetitivenessSpainFIS2015-72574-EXP

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-19
    Type: Initial release