1QG0 | pdb_00001qg0

WILD-TYPE PEA FNR

• PDB DOI: https://doi.org/10.2210/pdb1QG0/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Lathyrus oleraceus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-04-18 Released: 1999-04-27 
• Deposition Author(s): Deng, Z., Aliverti, A., Zanetti, G., Arakaki, A.K., Ottado, J., Orellano, E.G., Calcaterra, N.B., Ceccarelli, E.A., Carrillo, N., Karplus, P.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.273 (Depositor) 
• R-Value Work: 
  0.218 (Depositor), 0.222 (DCC) 

Starting Model: experimental

Literature

A productive NADP+ binding mode of ferredoxin-NADP+ reductase revealed by protein engineering and crystallographic studies.

Deng, Z., Aliverti, A., Zanetti, G., Arakaki, A.K., Ottado, J., Orellano, E.G., Calcaterra, N.B., Ceccarelli, E.A., Carrillo, N., Karplus, P.A.

(1999) Nat Struct Biol 6: 847-853

• PubMed: 10467097 
• DOI: https://doi.org/10.1038/12307
• Primary Citation Related Structures: 
  1QFY, 1QFZ, 1QG0, 1QGA


• PubMed Abstract: 
  

  The flavoenzyme ferredoxin-NADP+ reductase (FNR) catalyzes the production of NADPH during photosynthesis. Whereas the structures of FNRs from spinach leaf and a cyanobacterium as well as many of their homologs have been solved, none of these studies has yielded a productive geometry of the flavin-nicotinamide interaction. Here, we show that this failure occurs because nicotinamide binding to wild type FNR involves the energetically unfavorable displacement of the C-terminal Tyr side chain. We used mutants of this residue (Tyr 308) of pea FNR to obtain the structures of productive NADP+ and NADPH complexes. These structures reveal a unique NADP+ binding mode in which the nicotinamide ring is not parallel to the flavin isoalloxazine ring, but lies against it at an angle of approximately 30 degrees, with the C4 atom 3 A from the flavin N5 atom.

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Organizational Affiliation: 
• Section of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, New York 14853, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 71.26 kDa 
• Atom Count: 5,030 
• Modeled Residue Count: 592 
• Deposited Residue Count: 616 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (FERREDOXIN:NADP+ REDUCTASE)	A, B	308	Lathyrus oleraceus	Mutation(s): 0  EC: 1.18.1.2
UniProt
Find proteins for P10933 (Pisum sativum) Explore P10933  Go to UniProtKB:  P10933

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A], D [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.273 (Depositor) 
• R-Value Work:  0.218 (Depositor), 0.222 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.9	α = 90
b = 94.1	β = 90
c = 140.2	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-04-27 
Deposition Author(s): Deng, Z., Aliverti, A., Zanetti, G., Arakaki, A.K., Ottado, J., Orellano, E.G., Calcaterra, N.B., Ceccarelli, E.A., Carrillo, N., Karplus, P.A.

Revision History  

• Version 1.0: 1999-04-27
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description