7Z0W

E. coli NfsA bound to NADP+

PDB DOI: https://doi.org/10.2210/pdb7Z0W/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-02-23 Released: 2022-07-20
Deposition Author(s): White, S.A., Grainger, A., Parr, R., Day, M.A., Jarrom, D., Graziano, A., Searle, P.F., Hyde, E.I.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free:
0.187 (Depositor), 0.190 (DCC)
R-Value Work:
0.153 (Depositor), 0.160 (DCC)
R-Value Observed:
0.155 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

PubMed: 35648111 Search on PubMedSearch on PubMed Central
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.

Macromolecule Content

Total Structure Weight: 219.38 kDa
Atom Count: 16,522
Modelled Residue Count: 1,899
Deposited Residue Count: 1,920
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxygen-insensitive NADPH nitroreductase	A, B, C, D, E A, B, C, D, E, F, G, H	240	Escherichia coli K-12	Mutation(s): 0 Gene Names: nfsA, mda18, mdaA, ybjB, b0851, JW0835 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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P17117
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATR (Subject of Investigation/LOI) Query on ATR Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain P [auth D] MOL2 format, chain K [auth B] MOL2 format, chain P [auth D] mmCIF format, chain K [auth B] mmCIF format, chain P [auth D]	K [auth B], P [auth D]	2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ YPTPYQSAVGGMFN-KQYNXXCUSA-N		Interactions Focus chain K [auth B] Focus chain P [auth D] Interactions & Density Focus chain K [auth B] Focus chain P [auth D]
FMN Query on FMN Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain Q [auth E] SDF format, chain R [auth F] SDF format, chain T [auth H] SDF format, chain M [auth C] SDF format, chain O [auth D] SDF format, chain S [auth G] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth F] MOL2 format, chain T [auth H] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] MOL2 format, chain S [auth G] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain Q [auth E] mmCIF format, chain R [auth F] mmCIF format, chain T [auth H] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D] mmCIF format, chain S [auth G]	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		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth G] Focus chain T [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth G] Focus chain T [auth H]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain L [auth B]	L [auth B], N [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain N [auth C] Interactions & Density Focus chain L [auth B] Focus chain N [auth C]