3WGG

Crystal structure of RSP in complex with alpha-NAD+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.182 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Binding mode of the oxidized alpha-anomer of NAD(+) to RSP, a Rex-family repressor

Zheng, Y.Ko, T.-P.Yang, Y.Shao, W.Guo, R.-T.

(2015) Biochem Biophys Res Commun 456: 733-736

  • DOI: https://doi.org/10.1016/j.bbrc.2014.12.049
  • Primary Citation of Related Structures:  
    3WGG

  • PubMed Abstract: 

    The Rex-family repressors sense redox levels by alternative binding to NADH or NAD(+). RSP is the homologue of Rex in Thermoanaerobacter ethanolicus JW200(T) and regulates ethanol fermentation in this obligate anaerobe. The dimeric repressor binds to DNA by an open conformation. The crystal structure of RSP/α-NAD(+) complex shows a different set of ligand interactions mainly due to the unique configuration of the nicotinamide moiety. The positively charged ring is covered by the Tyr102 side chain and interacts with a sulfate ion adjacent to the N-terminus of helix α8. Consequently, the RSP dimer may be locked in a closed conformation that does not bind to DNA. However, α-NAD(+) does not show a higher affinity to RSP than β-NAD(+). It has to be improved for possible use as an effector in modulating the repressor.


  • Organizational Affiliation

    Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Redox-sensing transcriptional repressor rex
A, B
224Thermoanaerobacter ethanolicus JW 200Mutation(s): 0 
Gene Names: rexrsp
UniProt
Find proteins for D5KM69 (Thermoanaerobacter ethanolicus JW 200)
Explore D5KM69 
Go to UniProtKB:  D5KM69
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD5KM69
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8NA
Query on 8NA

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
alpha-Diphosphopyridine nucleotide
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-OPDHFMQKSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
H [auth B]
I [auth B]
D [auth A],
E [auth A],
F [auth A],
H [auth B],
I [auth B],
J [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.182 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.816α = 90
b = 74.137β = 90
c = 54.764γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-13
    Type: Initial release
  • Version 1.1: 2015-01-28
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description