6QKX

2-Naphthoyl-CoA Reductase-DiHydroNaphthoyl-CoA complex(NCR-DHNCoA co-crystallized complex)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Low potential enzymatic hydride transfer via highly cooperative and inversely functionalized flavin cofactors.

Willistein, M.Bechtel, D.F.Muller, C.S.Demmer, U.Heimann, L.Kayastha, K.Schunemann, V.Pierik, A.J.Ullmann, G.M.Ermler, U.Boll, M.

(2019) Nat Commun 10: 2074-2074

  • DOI: https://doi.org/10.1038/s41467-019-10078-3
  • Primary Citation of Related Structures:  
    6QKG, 6QKR, 6QKX

  • PubMed Abstract: 

    Hydride transfers play a crucial role in a multitude of biological redox reactions and are mediated by flavin, deazaflavin or nicotinamide adenine dinucleotide cofactors at standard redox potentials ranging from 0 to -340 mV. 2-Naphthoyl-CoA reductase, a key enzyme of oxygen-independent bacterial naphthalene degradation, uses a low-potential one-electron donor for the two-electron dearomatization of its substrate below the redox limit of known biological hydride transfer processes at E°' = -493 mV. Here we demonstrate by X-ray structural analyses, QM/MM computational studies, and multiple spectroscopy/activity based titrations that highly cooperative electron transfer (n = 3) from a low-potential one-electron (FAD) to a two-electron (FMN) transferring flavin cofactor is the key to overcome the resonance stabilized aromatic system by hydride transfer in a highly hydrophobic pocket. The results evidence how the protein environment inversely functionalizes two flavins to switch from low-potential one-electron to hydride transfer at the thermodynamic limit of flavin redox chemistry.


  • Organizational Affiliation

    Microbiology, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NCR714bacterium enrichment culture clone N47Mutation(s): 0 
UniProt
Find proteins for E1YD54 (uncultured Desulfobacterium sp)
Explore E1YD54 
Go to UniProtKB:  E1YD54
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE1YD54
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
J5H
Query on J5H

Download Ideal Coordinates CCD File 
E [auth A]~{S}-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] naphthalene-2-carbothioate
C32 H42 N7 O17 P3 S
DPWZDDZXXDPFNM-YGFBVEKBSA-N
FAD
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
FMN
Query on FMN

Download Ideal Coordinates CCD File 
D [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
B [auth A]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 176.86α = 90
b = 176.86β = 90
c = 49.22γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Cootmodel building
PHASERphasing
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyRTG 1976, SPP 1927

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-15
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Advisory, Data collection, Database references, Refinement description