5JRI | pdb_00005jri

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.242 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1073/pnas.1713698114
  • Primary Citation Related Structures: 
    5JRI, 5K0A, 5N0J, 5ODE

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 78.22 kDa 
  • Atom Count: 5,502 
  • Modeled Residue Count: 628 
  • Deposited Residue Count: 660 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Pyridine nucleotide-disulfide oxidoreductase
A, B
330Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: AOY38_16435
UniProt
Find proteins for P74746 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore P74746 
Go to UniProtKB:  P74746
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP74746
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD

Query on FAD



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
M [auth B],
N [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
L [auth A],
O [auth B],
P [auth B],
Q [auth B],
R [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
J [auth A],
K [auth A],
S [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.242 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.734α = 90
b = 79.327β = 90
c = 127.049γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-15
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Database references
  • Version 1.2: 2017-12-13
    Changes: Database references
  • Version 1.3: 2024-10-09
    Changes: Data collection, Database references, Structure summary