7UWT | pdb_00007uwt

Structure of Oxygen-Insensitive NAD(P)H-dependent Nitroreductase NfsB_Vv F70A/F108Y (NTR 2.0) in complex with FMN at 1.85 Angstroms resolution

PDB DOI: https://doi.org/10.2210/pdb7UWT/pdb

Classification: OXIDOREDUCTASE
Organism(s): Vibrio vulnificus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2022-05-03 Released: 2022-05-18
Deposition Author(s): Sharrock, A.V., Arcus, V., Mumm, J.S., Ackerley, D.F.
Funding Organization(s): National Institutes of Health/Office of the Director, National Institutes of Health/National Institute of Mental Health (NIH/NIMH), Health Research Council (HRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.196 (Depositor), 0.203 (DCC)
R-Value Work:
0.165 (Depositor), 0.176 (DCC)
R-Value Observed:
0.166 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

The Crystal Structure of Engineered Nitroreductase NTR 2.0 and Impact of F70A and F108Y Substitutions on Substrate Specificity.

Sharrock, A.V., Mumm, J.S., Bagdziunas, G., Cenas, N., Arcus, V.L., Ackerley, D.F.

(2023) Int J Mol Sci 24

PubMed: 37047605 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.3390/ijms24076633
Primary Citation Related Structures:
7UWT

PubMed Abstract:
Bacterial nitroreductase enzymes that convert prodrugs to cytotoxins are valuable tools for creating transgenic targeted ablation models to study cellular function and cell-specific regeneration paradigms. We recently engineered a nitroreductase ("NTR 2.0") for substantially enhanced reduction of the prodrug metronidazole, which permits faster cell ablation kinetics, cleaner interrogations of cell function, ablation of previously recalcitrant cell types, and extended ablation paradigms useful for modelling chronic diseases. To provide insight into the enhanced enzymatic mechanism of NTR 2.0, we have solved the X-ray crystal structure at 1.85 Angstroms resolution and compared it to the parental enzyme, NfsB from Vibrio vulnificus . We additionally present a survey of reductive activity with eight alternative nitroaromatic substrates, to provide access to alternative ablation prodrugs, and explore applications such as remediation of dinitrotoluene pollutants. The predicted binding modes of four key substrates were investigated using molecular modelling.

Organizational Affiliation

School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand.

Macromolecule Content

Total Structure Weight: 51.32 kDa
Atom Count: 3,637
Modeled Residue Count: 434
Deposited Residue Count: 434
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydropteridine reductase	A, B	217	Vibrio vulnificus	Mutation(s): 2 Gene Names: FORC53_4366, JS85_12320 EC: 1.5.1.34
UniProt
Find proteins for Q7MCD2 (Vibrio vulnificus (strain YJ016)) Explore Q7MCD2 Go to UniProtKB: Q7MCD2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7MCD2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P4K Query on P4K Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B]	G [auth B], H [auth B], I [auth B]	polyethylene glycol C₃₀ H₆₂ O₁₅ WWPGFZAAWXFBTF-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B]
FMN (Subject of Investigation/LOI) Query on FMN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.196 (Depositor), 0.203 (DCC)
R-Value Work: 0.165 (Depositor), 0.176 (DCC)
R-Value Observed: 0.166 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.43	α = 90
b = 137.36	β = 90
c = 107.04	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
MOSFLM	data reduction
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-05-18

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/Office of the Director	United States	R01OD020376
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)	United States	R01MH126731
Health Research Council (HRC)	New Zealand	19-750