1JAY

Structure of Coenzyme F420H2:NADP+ Oxidoreductase (FNO) with its substrates bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 

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This is version 1.3 of the entry. See complete history


Literature

Structures of F420H2:NADP+ oxidoreductase with and without its substrates bound.

Warkentin, E.Mamat, B.Sordel-Klippert, M.Wicke, M.Thauer, R.K.Iwata, M.Iwata, S.Ermler, U.Shima, S.

(2001) EMBO J 20: 6561-6569

  • DOI: 10.1093/emboj/20.23.6561
  • Primary Citation of Related Structures:  
    1JAX, 1JAY

  • PubMed Abstract: 
  • Cofactor F420 is a 5'-deazaflavin derivative first discovered in methanogenic archaea but later found also to be present in some bacteria. As a coenzyme, it is involved in hydride transfer reactions and as a prosthetic group in the DNA photolyase reaction ...

    Cofactor F420 is a 5'-deazaflavin derivative first discovered in methanogenic archaea but later found also to be present in some bacteria. As a coenzyme, it is involved in hydride transfer reactions and as a prosthetic group in the DNA photolyase reaction. We report here for the first time on the crystal structure of an F420-dependent oxidoreductase bound with F420. The structure of F420H2:NADP+ oxidoreductase resolved to 1.65 A contains two domains: an N-terminal domain characteristic of a dinucleotide-binding Rossmann fold and a smaller C-terminal domain. The nicotinamide and the deazaflavin part of the two coenzymes are bound in the cleft between the domains such that the Si-faces of both face each other at a distance of 3.1 A, which is optimal for hydride transfer. Comparison of the structures bound with and without substrates reveals that of the two substrates NADP has to bind first, the binding being associated with an induced fit.


    Organizational Affiliation

    Max-Planck-Institut für Biophysik, Heinrich-Hoffmann-Strasse 7, D-60596 Frankfurt/Main, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Coenzyme F420H2:NADP+ Oxidoreductase (FNO)A, B212Archaeoglobus fulgidusMutation(s): 0 
Gene Names: AF0892
EC: 1.5.1.40
UniProt
Find proteins for O29370 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16))
Explore O29370 
Go to UniProtKB:  O29370
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO29370
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F42
Query on F42

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
COENZYME F420
C29 H36 N5 O18 P
GEHSZWRGPHDXJO-NALJQGANSA-N
 Ligand Interaction
NAP
Query on NAP

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.9α = 90
b = 69.8β = 90
c = 145.5γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-12-21
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2014-11-12
    Changes: Structure summary