1CNE

STRUCTURAL STUDIES ON CORN NITRATE REDUCTASE: REFINED STRUCTURE OF THE CYTOCHROME B REDUCTASE FRAGMENT AT 2.5 ANGSTROMS, ITS ADP COMPLEX AND AN ACTIVE SITE MUTANT AND MODELING OF THE CYTOCHROME B DOMAIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural studies on corn nitrate reductase: refined structure of the cytochrome b reductase fragment at 2.5 A, its ADP complex and an active-site mutant and modeling of the cytochrome b domain.

Lu, G.Lindqvist, Y.Schneider, G.Dwivedi, U.Campbell, W.

(1995) J.Mol.Biol. 248: 931-948

  • DOI: 10.1006/jmbi.1995.0273
  • Primary Citation of Related Structures:  1CNF, 2CND

  • PubMed Abstract: 
  • The refined crystal structures of the recombinant cytochrome b reductase fragment of corn (Zea mays) nitrate reductase, its ADP complex and the active-site mutant Cys242Ser are reported here. The native structure has been refined at 2.5 A resolution ...

    The refined crystal structures of the recombinant cytochrome b reductase fragment of corn (Zea mays) nitrate reductase, its ADP complex and the active-site mutant Cys242Ser are reported here. The native structure has been refined at 2.5 A resolution to a crystallographic R-factor of 18.7% with root-mean-square (r.m.s) deviations from standard bond lengths and angles of 0.013 A and 2.0 degrees. The diffraction pattern of the crystals is highly anisotropic and correction of this effect lowered the crystallographic R-factor by 5% during the refinement. The structure of the enzyme co-crystallized with ADP has been solved at 2.7 A resolution and refined to an R-factor of 18.6% with r.m.s. deviations from standard bond lengths and angles of 0.014 A and 2.1 degrees. It revealed the binding site of the ADP moiety of the NADH cofactor, which is the electron donor for nitrate reduction. Based on this structure, a model of NADH at the active site of the enzyme was built and the implications for electron transfer from NADH to the flavin cofactor are discussed. The crystal structure of an active-site mutant enzyme, Cys242Ser, has been solved by difference Fourier synthesis and refined to an R-factor of 19.0% to 3.0 A resolution with standard deviations of bond lengths and angles of 0.017 A and 2.5 degrees. This structure analysis suggests that the observed decrease in catalytic activity of this mutant might be due to misalignment of the nicotinamide ring in its binding site. A model of the heme-containing domain of nitrate reductase has been built based on the X-ray structure of bovine cytochrome b5 and has been docked with the cytochrome b reductase fragment of nitrate reductase. The model of the complex contains six salt-bridges at the domain-domain interface and a hydrophobic core. In this model, His48, an invariant residue in the cytochrome b reductase family, forms an interaction with the propionic acid group of the D-ring of the heme cofactor. This group is in contact with the C-8 methyl group of the flavin ring. Residues that might influence the redox potential of the flavin cofactor are proposed and their possible role in electron transfer is discussed.


    Related Citations: 
    • Crystallization and Preliminary Crystallographic Studies of the Fad Domain of Corn Nadh:Nitrate Reductase
      Lu, G.,Campbell, W.,Lindqvist, Y.,Schneider, G.
      (1992) J.Mol.Biol. 224: 277
    • Crystal Structure of the Fad Containing Fragment of Corn Nitrate Reductase at 2.5 Angstroms Resolution: Relationship to Other Flavoprotein Reductase
      Lu, G.,Campbell, W.,Lindqvist, Y.,Schneider, G.
      (1995) Structure 2: 809
    • A Method for Processing Diffraction Data from Twinned Crystals and its Application in the Structure Determination of a Fad(Slash)Nadh Binding Fragment of Nitrate Reductase
      Lu, G.,Lindqvist, Y.,Schneider, G.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala Biomedical Center.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NITRATE REDUCTASE
A
270Zea maysEC: 1.7.1.1
Find proteins for P17571 (Zea mays)
Go to UniProtKB:  P17571
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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: 3 Å
  • R-Value Work: 0.190 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 145.200α = 90.00
b = 145.200β = 90.00
c = 47.500γ = 120.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-04-20
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance