P38489 (NFNB_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Oxygen-insensitive NAD(P)H nitroreductase
EC=1.-.-.-

Alternative name(s):
Dihydropteridine reductase
EC=1.5.1.34
FMN-dependent nitroreductase

Gene names

Name:	nfnB
Synonyms:	dprA, nfsB, nfsI, ntr
Ordered Locus Names:	b0578, JW0567

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	217 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Reduction of a variety of nitroaromatic compounds using NADH (and to lesser extent NADPH) as source of reducing equivalents; two electrons are transferred. Capable of reducing nitrofurazone, quinones and the anti-tumor agent CB1954 (5-(aziridin-1-yl)-2,4-dinitrobenzamide). The reduction of CB1954 results in the generation of cytotoxic species. Ref.13
Catalytic activity	A 5,6,7,8-tetrahydropteridine + NAD(P)+ = a 6,7-dihydropteridine + NAD(P)H.
Cofactor	FMN.
Enzyme regulation	Subject to competitive inhibition by dicoumarol, nicotinic acid and acetate with respect to NADH. Subject to uncompetitive inhibition by dicoumarol, nicotinic acid and acetate with respect to nitrofurazone and nitrofurantoin. Ref.13
Subunit structure	Homodimer. Ref.10 Ref.11 Ref.12
Sequence similarities	Belongs to the nitroreductase family.
Biophysicochemical properties	Kinetic parameters: KM=350 µM for NADH Ref.13 KM=1850 µM for nitrofurazone

Ontologies

Keywords
Ligand	FMN Flavoprotein NAD NADP
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Cellular_component	cytosol Inferred from direct assay PubMed 16858726. Source: UniProtKB membrane Inferred from direct assay PubMed 16858726. Source: UniProtKB
Molecular_function	6,7-dihydropteridine reductase activity Inferred from direct assay Ref.9. Source: EcoCyc FAD binding Inferred from direct assay Ref.9. Source: EcoCyc FMN binding Inferred from direct assay Ref.11Ref.1. Source: EcoCyc NAD(P)H nitroreductase activity Inferred from mutant phenotype PubMed 338576PubMed 6363380PubMed 7011517. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 217

217

Oxygen-insensitive NAD(P)H nitroreductase

PRO_0000072711

Regions

Nucleotide binding

10 – 14

5

FMN

Nucleotide binding

153 – 158

6

NAD or NADP By similarity

Nucleotide binding

165 – 166

2

FMN

Nucleotide binding

205 – 207

3

FMN

Sites

Binding site

41

1

NAD or NADP; via amide nitrogen

Binding site

71

1

FMN

Experimental info

Sequence conflict

5

1

S → C AA sequence Ref.9

Sequence conflict

10 – 12

3

RHS → CIV AA sequence Ref.9

Sequence conflict

19

1

S → M AA sequence Ref.9

Sequence conflict

21

1

Missing AA sequence Ref.7

Sequence conflict

28

1

E → D AA sequence Ref.7

Sequence conflict

180

1

E → I AA sequence Ref.7

Secondary structure

1

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217

Helix Strand Turn

Details...

Helix

3 – 9

7

Beta strand

14 – 16

3

Helix

24 – 36

13

Helix

40 – 42

3

Beta strand

46 – 51

6

Helix

54 – 61

8

Helix

62 – 64

3

Helix

66 – 71

6

Helix

72 – 77

6

Beta strand

78 – 89

12

Helix

92 – 104

13

Helix

111 – 130

20

Helix

135 – 156

22

Helix

169 – 176

8

Helix

178 – 181

4

Beta strand

183 – 192

10

Helix

199 – 201

3

Helix

210 – 213

4

Beta strand

214 – 217

4

Sequences

	Sequence		Length	Mass (Da)
	P38489 [UniParc]. Last modified October 1, 1994. Version 1. Checksum: A516CEFC3D46AEAC	FASTA	217	23,905
	10 20 30 40 50 60 MDIISVALKR HSTKAFDASK KLTPEQAEQI KTLLQYSPSS TNSQPWHFIV ASTEEGKARV 70 80 90 100 110 120 AKSAAGNYVF NERKMLDASH VVVFCAKTAM DDVWLKLVVD QEDADGRFAT PEAKAANDKG 130 140 150 160 170 180 RKFFADMHRK DLHDDAEWMA KQVYLNVGNF LLGVAALGLD AVPIEGFDAA ILDAEFGLKE 190 200 210 KGYTSLVVVP VGHHSVEDFN ATLPKSRLPQ NITLTEV

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Gene cloning, purification, and characterization of NfsB, a minor oxygen-insensitive nitroreductase from Escherichia coli, similar in biochemical properties to FRase I, the major flavin reductase in Vibrio fischeri." Zenno S., Koike H., Tanokura M., Saigo K. J. Biochem. 120:736-744(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12 / C600 / ATCC 23724 / DSM 3925 / LMG 3041 / NCIB 10222.
[2]	"Physical characterisation of the Escherichia coli B gene encoding nitroreductase and its over-expression in Escherichia coli K12." Michael N.P., Brehm J.K., Anlezark G.M., Minton N.P. FEMS Microbiol. Lett. 124:195-202(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: B.
[3]	"A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map." Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K., Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S., Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K. , Mori H., Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G., Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M., Horiuchi T. DNA Res. 3:137-155(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]	"Sequence of minutes 4-25 of Escherichia coli." Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M., Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D., Namath A., Oefner P., Roberts D., Schramm S., Davis R.W. Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[5]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[6]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[7]	"The bioactivation of 5-(aziridin-1-yl)-2,4-dinitrobenzamide (CB1954) -- I. Purification and properties of a nitroreductase enzyme from Escherichia coli -- a potential enzyme for antibody-directed enzyme prodrug therapy (ADEPT)." Anlezark G.M., Melton R.G., Sherwood R.F., Coles B., Friedlos F., Knox R.J. Biochem. Pharmacol. 44:2289-2295(1992) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-31 AND 139-180, CHARACTERIZATION. Strain: B.
[8]	"Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Link A.J., Robison K., Church G.M. Electrophoresis 18:1259-1313(1997) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-12. Strain: K12 / EMG2.
[9]	"Dihydropteridine reductase from Escherichia coli." Vasudevan S.G., Shaw D.C., Armarego W.L.F. Biochem. J. 255:581-588(1988) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-20, CHARACTERIZATION AS A DIHYDROPTERIDINE REDUCT.
[10]	"Crystal structure of FMN-dependent nitroreductase from Escherichia coli B: a prodrug-activating enzyme." Parkinson G.N., Skelly J.V., Neidle S. J. Med. Chem. 43:3624-3631(2000) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.06 ANGSTROMS) IN COMPLEX WITH FMN, SUBUNIT. Strain: B.
[11]	"The structure of Escherichia coli nitroreductase complexed with nicotinic acid: three crystal forms at 1.7 A, 1.8 A and 2.4 A resolution." Lovering A.L., Hyde E.I., Searle P.F., White S.A. J. Mol. Biol. 309:203-213(2001) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEX WITH NICOTININC ACID AND FMN, SUBUNIT. Strain: K12 / DH5-alpha.
[12]	"Studies on the nitroreductase prodrug-activating system. Crystal structures of complexes with the inhibitor dicoumarol and dinitrobenzamide prodrugs and of the enzyme active form." Johansson E., Parkinson G.N., Denny W.A., Neidle S. J. Med. Chem. 46:4009-4020(2003) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEXES WITH FMN; DICOUMAROL AND DINITROBENZAMIDE PRODRUGS, SUBUNIT.
[13]	"Structural and mechanistic studies of Escherichia coli nitroreductase with the antibiotic nitrofurazone. Reversed binding orientations in different redox states of the enzyme." Race P.R., Lovering A.L., Green R.M., Ossor A., White S.A., Searle P.F., Wrighton C.J., Hyde E.I. J. Biol. Chem. 280:13256-13264(2005) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEX WITH FMN; ACETATE AND THE ANTIBIOTIC NITROFURAZONE, FUNCTION, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

D25414 Genomic DNA. Translation: BAA05004.1.
U07860 Genomic DNA. Translation: AAC43263.1.
U82598 Genomic DNA. Translation: AAB40776.1.
U00096 Genomic DNA. Translation: AAC73679.1.
AP009048 Genomic DNA. Translation: BAA35218.1.

PIR

I67685.
S01818.

RefSeq

NP_415110.1. NC_000913.2.
YP_488865.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1DS7	X-ray	2.06	A/B	1-217	[»]
1ICR	X-ray	1.70	A/B	1-217	[»]
1ICU	X-ray	1.80	A/B/C/D	1-217	[»]
1ICV	X-ray	2.40	A/B/C/D	1-217	[»]
1IDT	X-ray	2.00	A/B	1-217	[»]
1OO5	X-ray	2.50	A/B	1-217	[»]
1OO6	X-ray	2.00	A/B	1-217	[»]
1OON	X-ray	2.49	A/B	1-217	[»]
1OOQ	X-ray	2.00	A/B	1-217	[»]
1YKI	X-ray	1.70	A/B/C/D	1-217	[»]
1YLR	X-ray	1.70	A/B	1-217	[»]
1YLU	X-ray	2.00	A/B	1-217	[»]

ProteinModelPortal

P38489.

SMR

P38489. Positions 1-217.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-10330N.

IntAct

P38489. 12 interactions.

STRING

511145.b0578.

2D gel databases

SWISS-2DPAGE

P38489.

Proteomic databases

PaxDb

P38489.

PRIDE

P38489.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC73679; AAC73679; b0578.
BAA35218; BAA35218; BAA35218.

GeneID

12933919.
945778.

KEGG

ecj:Y75_p0565.
eco:b0578.

PATRIC

32116324. VBIEscCol129921_0602.

Organism-specific databases

EchoBASE

EB4146.

EcoGene

EG20151. nfnB.

Phylogenomic databases

eggNOG

COG0778.

HOGENOM

HOG000146740.

KO

K10679.

OMA

DACPIEG.

ProtClustDB

PRK11053.

Enzyme and pathway databases

BioCyc

EcoCyc:DIHYDROPTERIREDUCT-MONOMER.
ECOL316407:JW0567-MONOMER.
MetaCyc:DIHYDROPTERIREDUCT-MONOMER.

Gene expression databases

Genevestigator

P38489.

Family and domain databases

Gene3D

3.40.109.10. 1 hit.

InterPro

IPR000415. Nitroreductase-like.
[Graphical view]

Pfam

PF00881. Nitroreductase. 1 hit.
[Graphical view]

SUPFAM

SSF55469. Nitroreductase. 1 hit.

ProtoNet

Search...

Other

ChEMBL

CHEMBL1075080.

DrugBank

DB01093. Dimethyl sulfoxide.

EvolutionaryTrace

P38489.

Entry information

Entry name

NFNB_ECOLI

Accession

Primary (citable) accession number: P38489
Secondary accession number(s): P19575

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1994
Last sequence update:	October 1, 1994
Last modified:	May 1, 2013
This is version 115 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program