6XTF

Crystal structure a Thioredoxin Reductase from Gloeobacter violaceus bound to its electron donor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Unexpected diversity of ferredoxin-dependent thioredoxin reductases in cyanobacteria.

Buey, R.M.Fernandez-Justel, D.Gonzalez-Holgado, G.Martinez-Julvez, M.Gonzalez-Lopez, A.Velazquez-Campoy, A.Medina, M.Buchanan, B.B.Balsera, M.

(2021) Plant Physiol 186: 285-296

  • DOI: https://doi.org/10.1093/plphys/kiab072
  • Primary Citation of Related Structures:  
    6XTF

  • PubMed Abstract: 

    Thioredoxin reductases control the redox state of thioredoxins (Trxs)-ubiquitous proteins that regulate a spectrum of enzymes by dithiol-disulfide exchange reactions. In most organisms, Trx is reduced by NADPH via a thioredoxin reductase flavoenzyme (NTR), but in oxygenic photosynthetic organisms, this function can also be performed by an iron-sulfur ferredoxin (Fdx)-dependent thioredoxin reductase (FTR) that links light to metabolic regulation. We have recently found that some cyanobacteria, such as the thylakoid-less Gloeobacter and the ocean-dwelling green oxyphotobacterium Prochlorococcus, lack NTR and FTR but contain a thioredoxin reductase flavoenzyme (formerly tentatively called deeply-rooted thioredoxin reductase or DTR), whose electron donor remained undefined. Here, we demonstrate that Fdx functions in this capacity and report the crystallographic structure of the transient complex between the plant-type Fdx1 and the thioredoxin reductase flavoenzyme from Gloeobacter violaceus. Thereby, our data demonstrate that this cyanobacterial enzyme belongs to the Fdx flavin-thioredoxin reductase (FFTR) family, originally described in the anaerobic bacterium Clostridium pasteurianum. Accordingly, the enzyme hitherto termed DTR is renamed FFTR. Our experiments further show that the redox-sensitive peptide CP12 is modulated in vitro by the FFTR/Trx system, demonstrating that FFTR functionally substitutes for FTR in light-linked enzyme regulation in Gloeobacter. Altogether, we demonstrate the FFTR is spread within the cyanobacteria phylum and propose that, by substituting for FTR, it connects the reduction of target proteins to photosynthesis. Besides, the results indicate that FFTR acquisition constitutes a mechanism of evolutionary adaptation in marine phytoplankton such as Prochlorococcus that live in low-iron environments.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thioredoxin reductase
A, B
320Gloeobacter violaceus PCC 7421Mutation(s): 0 
Gene Names: glr0719
UniProt
Find proteins for Q7NMP6 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
Explore Q7NMP6 
Go to UniProtKB:  Q7NMP6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7NMP6
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ferredoxin
C, D
100Gloeobacter violaceus PCC 7421Mutation(s): 0 
Gene Names: petF
UniProt
Find proteins for Q7NFA3 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421))
Explore Q7NFA3 
Go to UniProtKB:  Q7NFA3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7NFA3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
E [auth A],
S [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
PG4 (Subject of Investigation/LOI)
Query on PG4

Download Ideal Coordinates CCD File 
J [auth A],
T [auth B],
W [auth B]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
FES
Query on FES

Download Ideal Coordinates CCD File 
DA [auth C],
JA [auth D]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
AA [auth B],
L [auth A],
M [auth A]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
BA [auth B]
EA [auth C]
FA [auth C]
G [auth A]
GA [auth C]
BA [auth B],
EA [auth C],
FA [auth C],
G [auth A],
GA [auth C],
HA [auth C],
K [auth A],
KA [auth D],
R [auth A],
U [auth B],
Z [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
CA [auth B]
F [auth A]
H [auth A]
I [auth A]
IA [auth D]
CA [auth B],
F [auth A],
H [auth A],
I [auth A],
IA [auth D],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
V [auth B],
X [auth B],
Y [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 166.741α = 90
b = 181.312β = 90
c = 80.369γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainBFU2016-80343-P

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-28
    Type: Initial release
  • Version 1.1: 2022-02-09
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Refinement description