3KEQ

Crystal structure of a Rex-family transcriptional regulatory protein from Streptococcus agalactiae complexed with NAD+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.227 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

NAD+ pool depletion as a signal for the Rex regulon involved in Streptococcus agalactiae virulence.

Franza, T.Rogstam, A.Thiyagarajan, S.Sullivan, M.J.Derre-Bobillot, A.Bauer, M.C.Goh, K.G.K.Da Cunha, V.Glaser, P.Logan, D.T.Ulett, G.C.von Wachenfeldt, C.Gaudu, P.

(2021) PLoS Pathog 17: e1009791-e1009791

  • DOI: https://doi.org/10.1371/journal.ppat.1009791
  • Primary Citation of Related Structures:  
    3KEO, 3KEQ, 3KET

  • PubMed Abstract: 

    In many Gram-positive bacteria, the redox-sensing transcriptional repressor Rex controls central carbon and energy metabolism by sensing the intra cellular balance between the reduced and oxidized forms of nicotinamide adenine dinucleotide; the NADH/NAD+ ratio. Here, we report high-resolution crystal structures and characterization of a Rex ortholog (Gbs1167) in the opportunistic pathogen, Streptococcus agalactiae, also known as group B streptococcus (GBS). We present structures of Rex bound to NAD+ and to a DNA operator which are the first structures of a Rex-family member from a pathogenic bacterium. The structures reveal the molecular basis of DNA binding and the conformation alterations between the free NAD+ complex and DNA-bound form of Rex. Transcriptomic analysis revealed that GBS Rex controls not only central metabolism, but also expression of the monocistronic rex gene as well as virulence gene expression. Rex enhances GBS virulence after disseminated infection in mice. Mechanistically, NAD+ stabilizes Rex as a repressor in the absence of NADH. However, GBS Rex is unique compared to Rex regulators previously characterized because of its sensing mechanism: we show that it primarily responds to NAD+ levels (or growth rate) rather than to the NADH/NAD+ ratio. These results indicate that Rex plays a key role in GBS pathogenicity by modulating virulence factor gene expression and carbon metabolism to harvest nutrients from the host.


  • Organizational Affiliation

    Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Redox-sensing transcriptional repressor rex
A, B
212Streptococcus agalactiae serogroup IIIMutation(s): 0 
Gene Names: gbs1167rex
UniProt
Find proteins for Q8E565 (Streptococcus agalactiae serotype III (strain NEM316))
Explore Q8E565 
Go to UniProtKB:  Q8E565
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8E565
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
C [auth A]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.227 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.67α = 90
b = 71.47β = 90
c = 113.88γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-05-16
    Changes: Advisory, Data collection
  • Version 1.3: 2021-09-08
    Changes: Advisory, Database references, Derived calculations
  • Version 1.4: 2023-11-01
    Changes: Data collection, Refinement description