6RR3

CRYSTAL STRUCTURE OF FAD-CONTAINING FERREDOXIN-NADP REDUCTASE FROM BRUCELLA OVIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 

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Ligand Structure Quality Assessment 


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Literature

Towards the competent conformation for catalysis in the ferredoxin-NADP+reductase from the Brucella ovis pathogen.

Perez-Amigot, D.Taleb, V.Boneta, S.Anoz-Carbonell, E.Sebastian, M.Velazquez-Campoy, A.Polo, V.Martinez-Julvez, M.Medina, M.

(2019) Biochim Biophys Acta Bioenerg 1860: 148058-148058

  • DOI: 10.1016/j.bbabio.2019.148058
  • Primary Citation of Related Structures:  
    6RR3, 6RRA

  • PubMed Abstract: 
  • Brucella ovis encodes a bacterial subclass 1 ferredoxin-NADP(H) reductase (BoFPR) that, by similarity with other FPRs, is expected either to deliver electrons from NADPH to the redox-based metabolism and/or to oxidize NADPH to regulate the soxRS regulon that protects bacteria against oxidative damage ...

    Brucella ovis encodes a bacterial subclass 1 ferredoxin-NADP(H) reductase (BoFPR) that, by similarity with other FPRs, is expected either to deliver electrons from NADPH to the redox-based metabolism and/or to oxidize NADPH to regulate the soxRS regulon that protects bacteria against oxidative damage. Such potential roles for the pathogen survival under infection conditions make of interest to understand and to act on the BoFPR mechanism. Here, we investigate the NADP + /H interaction and NADPH oxidation by hydride transfer (HT) to BoFPR. Crystal structures of BoFPR in free and in complex with NADP + hardly differ. The latter shows binding of the NADP + adenosine moiety, while its redox-reactive nicotinamide protrudes towards the solvent. Nonetheless, pre-steady-state kinetics show formation of a charge-transfer complex (CTC-1) prior to the hydride transfer, as well as conversion of CTC-1 into a second charge-transfer complex (CTC-2) concomitantly with the HT event. Thus, during catalysis nicotinamide and flavin reacting rings stack. Kinetic data also identify the HT itself as the rate limiting step in the reduction of BoFPR by NADPH, as well as product release limiting the overall reaction. Using all-atom molecular dynamics simulations with a thermal effect approach we are able to visualise a potential transient catalytically competent interaction of the reacting rings. Simulations indicate that the architecture of the FAD folded conformation in BoFPR might be key in catalysis, pointing to its adenine as an element to orient the reactive atoms in conformations competent for HT.


    Organizational Affiliation

    Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain. Electronic address: mmedina@unizar.es.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ferredoxin-NADP reductaseA257Brucella ovis ATCC 25840Mutation(s): 0 
Gene Names: fprBOV_0348
EC: 1.18.1.2
UniProt
Find proteins for A0A0H3ASL8 (Brucella ovis (strain ATCC 25840 / 63/290 / NCTC 10512))
Explore A0A0H3ASL8 
Go to UniProtKB:  A0A0H3ASL8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3ASL8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
B [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.068α = 90
b = 39.068β = 90
c = 164.911γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainBIO2016-75183-P

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-21
    Type: Initial release
  • Version 1.1: 2019-09-11
    Changes: Data collection, Database references