Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | 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: 48.87 kDa 
• Atom Count: 3817 
• Modelled Residue Count: 424 
• Deposited Residue Count: 424 
• Unique protein chains: 1

1JAY

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

• PDB DOI: 10.2210/pdb1JAY/pdb

• Classification: STRUCTURAL GENOMICS
• Organism(s): Archaeoglobus fulgidus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2001-06-01 Released: 2001-12-21 
• Deposition Author(s): Warkentin, E., Mamat, B., Thauer, R., Ermler, U., Shima, S.

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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 

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

• PubMed: 11726492 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coenzyme F420H2:NADP+ Oxidoreductase (FNO)	A, B	212	Archaeoglobus fulgidus	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
F42	E [auth A], H [auth B]	COENZYME F420 C29 H36 N5 O18 P GEHSZWRGPHDXJO-NALJQGANSA-N
NAP	D [auth A], G [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
NA	C [auth A], F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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 = 54.9	α = 90
b = 69.8	β = 90
c = 145.5	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-06-01 
• Released Date: 2001-12-21 
Deposition Author(s): Warkentin, E., Mamat, B., Thauer, R., Ermler, U., Shima, S.

Revision History  

• 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