2Q0L

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

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 

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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

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

  • 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 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.

    Organizational Affiliation: 

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thioredoxin reductaseA, B311Helicobacter pylori 26695Mutation(s): 0 
Gene Names: trxB, HP_0825
EC: 1.8.1.9
UniProt
Find proteins for P56431 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore P56431 
Go to UniProtKB:  P56431
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56431
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / 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		 Ligand Interaction
NAP
Query on NAP
Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]		NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N		 Ligand Interaction
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 = 50.451α = 90
b = 99.455β = 97.94
c = 64.765γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
MOSFLMdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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