7Z0W

E. coli NfsA bound to NADP+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.155 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

The 3D-structure, kinetics and dynamics of the E. coli nitroreductase NfsA with NADP + provide glimpses of its catalytic mechanism.

White, S.A.Christofferson, A.J.Grainger, A.I.Day, M.A.Jarrom, D.Graziano, A.E.Searle, P.F.Hyde, E.I.

(2022) FEBS Lett 596: 2425-2440

  • DOI: https://doi.org/10.1002/1873-3468.14413
  • Primary Citation of Related Structures:  
    7Q0O, 7Z0W

  • PubMed Abstract: 

    Nitroreductases activate nitroaromatic antibiotics and cancer prodrugs to cytotoxic hydroxylamines and reduce quinones to quinols. Using steady-state and stopped-flow kinetics, we show that the Escherichia coli nitroreductase NfsA is 20-50 fold more active with NADPH than with NADH and that product release may be rate-limiting. The crystal structure of NfsA with NADP + shows that a mobile loop forms a phosphate-binding pocket. The nicotinamide ring and nicotinamide ribose are mobile, as confirmed in molecular dynamics (MD) simulations. We present a model of NADPH bound to NfsA. Only one NADP + is seen bound to the NfsA dimers, and MD simulations show that binding of a second NADP(H) cofactor is unfavourable, suggesting that NfsA and other members of this protein superfamily may have a half-of-sites mechanism.


  • Organizational Affiliation

    School of Biosciences, University of Birmingham, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Oxygen-insensitive NADPH nitroreductase
A, B, C, D, E
A, B, C, D, E, F, G, H
240Escherichia coli K-12Mutation(s): 0 
Gene Names: nfsAmda18mdaAybjBb0851JW0835
EC: 1 (PDB Primary Data), 1.5.1.38 (PDB Primary Data)
UniProt
Find proteins for P17117 (Escherichia coli (strain K12))
Explore P17117 
Go to UniProtKB:  P17117
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17117
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATR (Subject of Investigation/LOI)
Query on ATR

Download Ideal Coordinates CCD File 
K [auth B],
P [auth D]
2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE
C10 H16 N5 O13 P3
YPTPYQSAVGGMFN-KQYNXXCUSA-N
FMN
Query on FMN

Download Ideal Coordinates CCD File 
I [auth A]
J [auth B]
M [auth C]
O [auth D]
Q [auth E]
I [auth A],
J [auth B],
M [auth C],
O [auth D],
Q [auth E],
R [auth F],
S [auth G],
T [auth H]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
L [auth B],
N [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.155 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.766α = 90
b = 110.757β = 103.84
c = 112.25γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-20
    Type: Initial release
  • Version 1.1: 2022-10-05
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description