5JRI

Structure of an oxidoreductase SeMet-labelled from Synechocystis sp. PCC6803


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.952 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Unprecedented pathway of reducing equivalents in a diflavin-linked disulfide oxidoreductase.

Buey, R.M.Arellano, J.B.Lopez-Maury, L.Galindo-Trigo, S.Velazquez-Campoy, A.Revuelta, J.L.de Pereda, J.M.Florencio, F.J.Schurmann, P.Buchanan, B.B.Balsera, M.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: 12725-12730

  • DOI: 10.1073/pnas.1713698114
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Flavoproteins participate in a wide variety of physiologically relevant processes that typically involve redox reactions. Within this protein superfamily, there exists a group that is able to transfer reducing equivalents from FAD to a redox-active d ...

    Flavoproteins participate in a wide variety of physiologically relevant processes that typically involve redox reactions. Within this protein superfamily, there exists a group that is able to transfer reducing equivalents from FAD to a redox-active disulfide bridge, which further reduces disulfide bridges in target proteins to regulate their structure and function. We have identified a previously undescribed type of flavin enzyme that is exclusive to oxygenic photosynthetic prokaryotes and that is based on the primary sequence that had been assigned as an NADPH-dependent thioredoxin reductase (NTR). However, our experimental data show that the protein does not transfer reducing equivalents from flavins to disulfides as in NTRs but functions in the opposite direction. High-resolution structures of the protein from Gloeobacter violaceus and Synechocystis sp. PCC6803 obtained by X-ray crystallography showed two juxtaposed FAD molecules per monomer in redox communication with an active disulfide bridge in a variant of the fold adopted by NTRs. We have tentatively named the flavoprotein "DDOR" (diflavin-linked disulfide oxidoreductase) and propose that its activity is linked to a thiol-based transfer of reducing equivalents in bacterial membranes. These findings expand the structural and mechanistic repertoire of flavoenzymes with oxidoreductase activity and pave the way to explore new protein engineering approaches aimed at designing redox-active proteins for diverse biotechnological applications.


    Organizational Affiliation

    Metabolic Engineering Group, Departamento de Microbiología y Genética, Universidad de Salamanca, 37007 Salamanca, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyridine nucleotide-disulfide oxidoreductase
A, B
330Synechocystis sp. (strain PCC 6803 / Kazusa)Mutation(s): 0 
Find proteins for P74746 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Go to UniProtKB:  P74746
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.952 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 71.734α = 90.00
b = 79.327β = 90.00
c = 127.049γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SHELXDEphasing
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-11-15
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Database references
  • Version 1.2: 2017-12-13
    Type: Database references