3GRS

REFINED STRUCTURE OF GLUTATHIONE REDUCTASE AT 1.54 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Refined structure of glutathione reductase at 1.54 A resolution.

Karplus, P.A.Schulz, G.E.

(1987) J.Mol.Biol. 195: 701-729

  • Also Cited By: 1ZDL

  • PubMed Abstract: 
  • The crystal structure of human glutathione reductase has been established at 1.54 A resolution using a restrained least-squares refinement method. Based on 77,690 independent reflections of better than 10 A resolution, a final R-factor of 18.6% was o ...

    The crystal structure of human glutathione reductase has been established at 1.54 A resolution using a restrained least-squares refinement method. Based on 77,690 independent reflections of better than 10 A resolution, a final R-factor of 18.6% was obtained with a model obeying standard geometry within 0.025 A in bond lengths and 2.4 degrees in bond angles. The final 2Fo-Fc electron density map allows for the distinction of carbon, nitrogen and oxygen atoms with temperature factors below about 25 A2. Apart from 461 amino acid residues and the prosthetic group FAD, the model contains 524 solvent molecules, about 118 of which can be considered an integral part of the enzyme. The largest solvent cluster is at the dimer interface and contains 104 interconnected solvent molecules, part of which are organized in a warped sheet-like structure. The main-chain dihedral angles are well-concentrated in the allowed regions of the Ramachandran plot. The spread of dihedral angles in beta-pleated sheets is much larger than in alpha-helices and especially in alpha-helix cores, indicating the higher plasticity of beta-structures. The analysis revealed a large amount of 3(10)-helix. The side-chain conformations cluster at the staggered positions, and show well-defined preferences. Also, a mobility gradient is observed for side-chains. Non-polar and polar side-chains show average temperature factor increases per bond of 10% and 25%, respectively. A number of alternative conformations of internal side-chains, in particular serines and methionines, have been detected. The extended FAD molecule also shows a mobility gradient between the very rigid flavin (mean value of B) = 8.7 A2) and the more mobile adenine (mean value of B = 16.2 A2). The entire active center is particularly well ordered, with temperature factors around 10 A2. The dimer interface consists of a rigid contact area, which is well conserved in the Escherichia coli enzyme, and a flexible area that is not. Altogether, the buried surfaces at the crystal contacts are half as large as at the dimer interface, but less specific. The refined structure shows clearly that there are no buried cations compensating the charge of the pyrophosphate moiety of FAD. The flavin deviates slightly from standard geometry, which is possibly caused by the polypeptide environment. In contrast to an earlier interpretation, atom N5 of the flavin can accommodate a proton, and it is conceivable that this proton proceeds to the redox-active disulfide.(ABSTRACT TRUNCATED AT 400 WORDS)


    Related Citations: 
    • The Catalytic Mechanism of Glutathione Reductase as Derived from X-Ray Diffraction Analyses of Reaction Intermediates
      Pai, E.F.,Schulz, G.E.
      (1983) J.Biol.Chem. 258: 1752
    • The C-Terminal Fragment of Human Glutathione Reductase Contains the Postulated Catalytic Histidine
      Untucht-Grau, R.,Schulz, G.E.,Schirmer, R.H.
      (1979) FEBS Lett. 105: 244
    • Low Resolution Structure of Human Erythrocyte Glutathione Reductase
      Zappe, H.A.,Krohne-Ehrich, G.,Schulz, G.E.
      (1977) J.Mol.Biol. 113: 141
    • Inhibition of Human Glutathione Reductase by the Nitrosourea Drugs 1,3-Bis(2-Chloroethyl)-1-Nitrosurea and 1-(2-Chloroethyl)-3-(2-Hydroxyethyl)-1-Nitrosourea
      Karplus, P.A.,Krauth-Siegel, R.L.,Schirmer, R.H.,Schulz, G.E.
      (1988) Eur.J.Biochem. 171: 193
    • The Structure of the Flavoenzyme Glutathione Reductase
      Schulz, G.E.,Schirmer, R.H.,Sachsenheimer, W.,Pai, E.F.
      (1978) Nature 273: 120
    • Gene Duplication in Glutathione Reductase
      Schulz, G.E.
      (1980) J.Mol.Biol. 138: 335
    • Interaction of a Glutathione S-Conjugate with Glutathione Reductase. Kinetic and X-Ray Crystallographic Studies
      Bilzer, M.,Krauth-Siegel, R.L.,Schirmer, R.H.,Akerboom, T.P.M.,Sies, H.,Schulz, G.E.
      (1984) Eur.J.Biochem. 138: 373
    • Three-Dimensional Structure of Glutathione Reductase at 2 Angstroms Resolution
      Thieme, R.,Pai, E.F.,Schirmer, R.H.,Schulz, G.E.
      (1981) J.Mol.Biol. 152: 763
    • Fad-Binding Site of Glutathione Reductase
      Schulz, G.E.,Schirmer, R.H.,Pai, E.F.
      (1982) J.Mol.Biol. 160: 287
    • Comparison of the Three-Dimensional Protein and Nucleotide Structure of the Fad-Binding Domain of P-Hydroxybenzoate Hydroxylase with the Fad-as Well as Nadph-Binding Domains of Glutathione Reductase
      Wierenga, R.K.,Drenth, J.,Schulz, G.E.
      (1983) J.Mol.Biol. 167: 725
    • Crystals of Human Erythrocyte Glutathione Reductase
      Schulz, G.E.,Zappe, H.,Worthington, D.J.,Rosemeyer, M.A.
      (1975) FEBS Lett. 54: 86
    • Glutathione Reductase from Human Erythrocytes. The Sequences of the Nadph Domain and of the Interface Domain
      Krauth-Siegel, R.L.,Blatterspiel, R.,Saleh, M.,Schiltz, E.,Schirmer, R.H.,Untucht-Grau, R.
      (1982) Eur.J.Biochem. 121: 259


    Organizational Affiliation

    Institut für Organische Chemie und Biochemie der Universität, Freiburg i.Br., F.R. Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUTATHIONE REDUCTASE
A
478Homo sapiensMutation(s): 0 
Gene Names: GSR (GLUR, GRD1)
EC: 1.8.1.7
Find proteins for P00390 (Homo sapiens)
Go to Gene View: GSR
Go to UniProtKB:  P00390
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
FAD
Query on FAD

Download SDF File 
Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Work: 0.186 
  • Space Group: B 1 1 2
Unit Cell:
Length (Å)Angle (°)
a = 119.800α = 90.00
b = 84.500β = 90.00
c = 63.200γ = 58.70
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1988-04-16
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance