Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 54521.32 
• Atom Count: 3762 
• Residue Count: 488 
• Unique protein chains: 1

2NVK

Crystal Structure of Thioredoxin Reductase from Drosophila melanogaster

• DOI: 10.2210/pdb2NVK/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli
• Mutation(s): 2 


• Deposited: 2006-11-13 Released: 2007-04-24 
• Deposition Author(s): Eckenroth, B.E., Rould, M.A., Hondal, R.J., Everse, S.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.247 
• R-Value Work: 0.198 

Literature

Structural and Biochemical Studies Reveal Differences in the Catalytic Mechanisms of Mammalian and Drosophila melanogaster Thioredoxin Reductases.

Eckenroth, B.E., Rould, M.A., Hondal, R.J., Everse, S.J.

(2007) Biochemistry 46: 4694-4705

• PubMed: 17385893 
• DOI: 10.1021/bi602394p


• PubMed Abstract: 
  

Thioredoxin reductase (TR) from Drosophila melanogaster (DmTR) is a member of the glutathione reductase (GR) family of pyridine nucleotide disulfide oxidoreductases and catalyzes the reduction of the redox-active disulfide bond of thioredoxin. DmTR is notable for having high catalytic activity without the presence of a selenocysteine (Sec) residue (which is essential for the mammalian thioredoxin reductases). We report here the X-ray crystal structure of DmTR at 2.4 A resolution (Rwork = 19.8%, Rfree = 24.7%) in which the enzyme was truncated to remove the C-terminal tripeptide sequence Cys-Cys-Ser. We also demonstrate that tetrapeptides equivalent to the oxidized C-terminal active sites of both mouse mitochondrial TR (mTR3) and DmTR are substrates for the truncated forms of both enzymes. This truncated enzyme/peptide substrate system examines the kinetics of the ring-opening step that occurs during the enzymatic cycle of TR. The ring-opening step is 300-500-fold slower when Sec is replaced with Cys in mTR3 when using this system. Conversely, when Cys is replaced with Sec in DmTR, the rate of ring opening is only moderately increased (5-36-fold). Structures of these tetrapeptides were oriented in the active site of both enzymes using oxidized glutathione bound to GR as a template. DmTR has a more open tetrapeptide binding pocket than the mouse enzyme and accommodates the peptide Ser-Cys-Cys-Ser(ox) in a cis conformation that allows for the protonation of the leaving-group Cys by His464', which helps to explain why this TR can function without the need for Sec. In contrast, mTR3 shows a narrower pocket. One possible result of this narrower interface is that the mammalian redox-active tetrapeptide Gly-Cys-Sec-Gly may adopt a trans conformation for a better fit. This places the Sec residue farther away from the protonating histidine residue, but the lower pKa of Sec in comparison to that of Cys eliminates the need for Sec to be protonated.

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Organizational Affiliation: 

Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, Vermont 05405, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Thioredoxin Reductase	X	488	Drosophila melanogaster	Mutation(s): 2  Gene Names: Trxr-1 (GR) EC: 1.8.1.9
Find proteins for P91938 (Drosophila melanogaster) Go to UniProtKB:  P91938

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
FAD	X	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
NAP	X	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.247 
• R-Value Work: 0.198 
• Space Group: H 3 2

Unit Cell:

Length (Å)	Angle (°)
a = 151.487	α = 90.00
b = 151.487	β = 90.00
c = 134.259	γ = 120.00

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CNS	phasing
DENZO	data reduction
SCALEPACK	data scaling
MAR345	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-11-13 
• Released Date: 2007-04-24 
• Deposition Author(s): Eckenroth, B.E., Rould, M.A., Hondal, R.J., Everse, S.J.

Revision History 

• Version 1.0: 2007-04-24
  Type: Initial release
• Version 1.1: 2008-05-01
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Advisory, Derived calculations, Version format compliance
• Version 1.3: 2017-10-18
  Type: Refinement description