3D8X

Crystal Structure of Saccharomyces cerevisiae NDPPH Dependent Thioredoxin Reductase 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 

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This is version 1.3 of the entry. See complete history


Literature

Crystal structure of Saccharomyces cerevisiae cytoplasmic thioredoxin reductase Trr1 reveals the structural basis for species-specific recognition of thioredoxin

Zhang, Z.Bao, R.Zhang, Y.Yu, J.Zhou, C.-Z.Chen, Y.

(2009) Biochim Biophys Acta 1794: 124-128

  • DOI: https://doi.org/10.1016/j.bbapap.2008.09.011
  • Primary Citation of Related Structures:  
    3D8X

  • PubMed Abstract: 

    Thioredoxin reductase (TrxR) is a member of the pyridine nucleotide-disulfide oxidoreductase family of the flavoenzymes. It can use a dithiol-disulfide active-site to transfer reducing equivalents from NADPH to thioredoxin (Trx), via the cofactor FAD. In Saccharomyces cerevisiae, the cytoplasmic thioredoxin reductase Trr1 plays an important role in multiple cellular events under the control of transcription factor Yap1 and/or Rho5. Here we present the crystal structure of Trr1 at the resolution of 2.8 A, the first fungal TrxR structure. Structural analysis shows it shares a very similar overall structure to Escherichia coli TrxR. However, fine comparisons indicate some distinct differences at the Trx recognition sites. These differences might be responsible to the species-specific recognition of Trx, which has been demonstrated by previous biochemical assays.


  • Organizational Affiliation

    Protein Research Institute, Tongji University, Shanghai 200092, People's Republic of China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thioredoxin reductase 1
A, B
326Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: TRR1
EC: 1.8.1.9
UniProt
Find proteins for P29509 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P29509 
Go to UniProtKB:  P29509
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29509
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
NDP
Query on NDP

Download Ideal Coordinates CCD File 
D [auth A]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.229α = 90
b = 125.004β = 114.16
c = 60.967γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
AUTOMARdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-12-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2013-11-20
    Changes: Non-polymer description
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description