3JQQ

Crystal structure of the H286K mutant of Ferredoxin-NADP+ reductase from Plasmodium falciparum in complex with 2'P-AMP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.259 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Plasmodium falciparum ferredoxin-NADP+ reductase His286 plays a dual role in NADP(H) binding and catalysis

Crobu, D., Canevari, G., Milani, M., Pandini, V., Vanoni, M.A., Bolognesi, M., Zanetti, G., Aliverti, A.

(2009) Biochemistry 48: 9525-9533

  • DOI: 10.1021/bi9013209
  • Primary Citation of Related Structures:  
    3JQR, 3JQP, 3JQQ

  • PubMed Abstract: 

    • The NADP-binding site of Plasmodium falciparum ferredoxin-NADP(+) reductase contains two basic residues, His286 and Lys249, conserved within the Plasmodium genus, but not in other plant-type homologues. Previous crystal studies indicated that His286 ...

    The NADP-binding site of Plasmodium falciparum ferredoxin-NADP(+) reductase contains two basic residues, His286 and Lys249, conserved within the Plasmodium genus, but not in other plant-type homologues. Previous crystal studies indicated that His286 interacts with the adenine ring and with the 5'-phosphate of 2'-P-AMP, a ligand that mimics the adenylate moiety of NADP(H). Here we show that replacement of His286 with aliphatic residues results both in a decrease in the affinity of the enzyme for NADPH and in a decrease in k(cat), due to a lowered hydride-transfer rate. Unexpectedly, the mutation to Gln produces an enzyme more active than the wild-type one, whereas the change to Lys destabilizes the nicotinamide-isoalloxazine interaction, decreasing k(cat). On the basis of the crystal structure of selected mutants complexed with 2'-P-AMP, we conclude that the His286 side chain plays a dual role in catalysis both by providing binding energy for NADPH and by favoring the catalytically competent orientation of its nicotinamide ring. For the latter function, the H-bonding potential rather than the positively charged state of the His286 imidazole seems sufficient. Furthermore, we show that the Lys249Ala mutation decreases K(m)(NADPH) and K(d) for NADP(+) or 2'-P-AMP by a factor of 10. We propose that the Lys249 side chain participates in substrate recognition by interacting with the 2'-phosphate of NADP(H) and that this interaction was not observed in the crystal form of the enzyme-2'-P-AMP complex due to a conformational perturbation of the substrate-binding loop induced by dimerization.

    Organizational Affiliation: 

    Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita degli Studi di Milano, via Celoria 26, 20133 Milano, Italy.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ferredoxin NADP reductaseA, B, C, D, E, F316Plasmodium falciparumMutation(s): 1 
Gene Names: PfFNR, PFF1115w
EC: 1.18.1.2
Find proteins for C6KT68 (Plasmodium falciparum (isolate 3D7))
Explore C6KT68 
Go to UniProtKB:  C6KT68
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD
Download CCD File 
A, B, C, D, E, F
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N		 Ligand Interaction
A2P
Query on A2P
Download CCD File 
A, B, C, D, E, F
ADENOSINE-2'-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
AEOBEOJCBAYXBA-KQYNXXCUSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
A2PKi:  2900   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.259 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.243α = 90
b = 124.243β = 90
c = 134.255γ = 120
Software Package:
Software NamePurpose
DNAdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance