Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 70.21 kDa 
• Atom Count: 5521 
• Modelled Residue Count: 622 
• Deposited Residue Count: 622 
• Unique protein chains: 1

2Q0L

Helicobacter pylori thioredoxin reductase reduced by sodium dithionite in complex with NADP+

• DOI: 10.2210/pdb2Q0L/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Helicobacter pylori 26695
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-05-22 Released: 2007-07-03 
• Deposition Author(s): Sandalova, T., Gustafsson, T., Lu, J., Holmgren, A., Schneider, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.193 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 

Literature

High-resolution structures of oxidized and reduced thioredoxin reductase from Helicobacter pylori.

Gustafsson, T.N., Sandalova, T., Lu, J., Holmgren, A., Schneider, G.

(2007) Acta Crystallogr D Biol Crystallogr 63: 833-843

• PubMed: 17582174 
• DOI: 10.1107/S0907444907026303
• Primary Citation of Related Structures:  
  2Q0L, 2Q0K


• PubMed Abstract: 
  

The crystal structures of homodimeric thioredoxin reductase (TrxR) from the gastric pathogen Helicobacter pylori in complex with NADP(+) have been determined for the oxidized and reduced form of the enzyme at 1.7 and 1.45 A resolution, respectively. The enzyme subunit is built up of FAD- and NAD(P)H-binding domains, each of which contain variants of the Rossmann fold typical of nucleotide-binding proteins. The majority of the amino-acid residues binding the cofactors FAD and NAD(P)H are conserved in the low-molecular-weight thioredoxin reductases. In the reduced species the isoalloxazine ring of FAD is bent along an axis passing through the N5 and N10 atoms with an angle of 22 degrees and the ribityl moiety adopts an unusual conformation. Well defined electron density shows the position of the whole NADP(+) molecule with a binding mode similar to that observed in the Escherichia coli TrxR-thioredoxin complex, although the orientation of the NAD(P)H-binding domain is different. Rigid-body rotation of this domain to the orientation observed in the E. coli TrxR-thioredoxin complex positions NADP(+) adjacent to the FAD molecule, suitable for electron transfer, without any readjustments of the conformation of NADP(+). A comparison of the binding surfaces of thioredoxin and thioredoxin reductases from H. pylori and E. coli shows that the overall surface charge distribution in these proteins is conserved and that residue substitutions that change the shape of the binding surface may account for the species-specific recognition of thioredoxin by TrxR.

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Organizational Affiliation: 

The Medical Nobel Institute for Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin reductase	A, B	311	Helicobacter pylori 26695	Mutation(s): 0  Gene Names: trxB, HP_0825 EC: 1.8.1.9
Find proteins for P56431 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore P56431  Go to UniProtKB:  P56431

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A], E [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
NAP	D [auth A], F [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.193 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.451	α = 90
b = 99.455	β = 97.94
c = 64.765	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-05-22 
• Released Date: 2007-07-03 
Deposition Author(s): Sandalova, T., Gustafsson, T., Lu, J., Holmgren, A., Schneider, G.

Revision History  

• Version 1.0: 2007-07-03
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance