6QKR | pdb_00006qkr

2-Naphthoyl-CoA Reductase-2-Naphthoyl-CoA complex(NCR-NCoA-soaked complex)

• PDB DOI: https://doi.org/10.2210/pdb6QKR/pdb

• Classification: FLAVOPROTEIN
• Organism(s): bacterium enrichment culture clone N47
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-01-30 Released: 2019-05-15 
• Deposition Author(s): Kayastha, K., Ermler, U.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.218 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

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

• PubMed: 31061390 
• DOI: https://doi.org/10.1038/s41467-019-10078-3
• Primary Citation 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.

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Organizational Affiliation: 
• Microbiology, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany.
Biochemistry, Faculty of Chemistry, University of Kaiserslautern, Erwin-Schrödinger-Straße 52, 67663, Kaiserslautern, Germany.
Biophysics, Department of Physics, University of Kaiserslautern, Erwin-Schrödinger-Straße 46, 67663, Kaiserslautern, Germany.
Max-Planck-Institute for Biophysics Frankfurt, Max-von-Laue-Str. 3, 60438, Frankfurt, Germany.
Computational Biochemistry, University of Bayreuth, Universitätsstrasse 30, NW I, 95447, Bayreuth, Germany.
Max-Planck-Institute for Biophysics Frankfurt, Max-von-Laue-Str. 3, 60438, Frankfurt, Germany. [e-mail].
Microbiology, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 160.87 kDa 
• Atom Count: 10,716 
• Modeled Residue Count: 1,324 
• Deposited Residue Count: 1,428 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NCR	A, B	714	bacterium enrichment culture clone N47	Mutation(s): 0
UniProt
Find proteins for E1YD54 (uncultured Desulfobacterium sp) Explore E1YD54  Go to UniProtKB:  E1YD54

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
J5H	F [auth A], J [auth B]	~{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	D [auth A], H [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
FMN	E [auth A], I [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
SF4	C [auth A], G [auth B]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.218 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.67	α = 90
b = 86.05	β = 90.67
c = 96.9	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
PHASER	phasing
ARP/wARP	model building
Coot	model building
PHENIX	refinement
BUSTER	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-05-15 
Deposition Author(s): Kayastha, K., Ermler, U.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	RTG 1976, SPP 1927

Revision History  

• Version 1.0: 2019-05-15
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary