P54550 (NAMA_BACSU) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
NADPH dehydrogenase
EC=1.6.99.1

Alternative name(s):
Xenobiotic reductase

Gene names

Name:	namA
Ordered Locus Names:	BSU23820

Organism

Bacillus subtilis

Taxonomic identifier

1423 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Bacillales › Bacillaceae › Bacillus

Protein attributes

Sequence length	338 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the reduction of the double bond of an array of alpha, beta-unsaturated aldehydes and ketones. It also reduces the nitro group of nitroester and nitroaromatic compounds. It could have a role in detoxification processes. HAMAP MF_01614
Catalytic activity	NADPH + acceptor = NADP+ + reduced acceptor. HAMAP MF_01614
Cofactor	FMN.
Enzyme regulation	Inhibited by p-hydroxybenzaldehyde (pHBA) and p-nitrophenol (pNP). HAMAP MF_01614
Subunit structure	Homotetramer. Composed of a dimer of active dimers. Ref.4
Induction	By toxic xenobiotic compounds (2,4,6-trinitrotoluene and nitroglycerin), and in response to oxidative stress (hydrogen peroxide and paraquat). HAMAP MF_01614
Miscellaneous	Forms a charge transfer complex with a variety of phenolic compounds. HAMAP MF_01614
Sequence similarities	Belongs to the NADH:flavin oxidoreductase/NADH oxidase family. NamA subfamily.
Biophysicochemical properties	Kinetic parameters: The highest catalytic efficiency was observed with N-ethylmaleimide for which the KM is inferior to 1.0 µM. KM=19 µM for duroquinone KM=109 µM for nitroglycerin KM=293 µM for cyclohex-2-enone KM=705 µM for 2,4,6-trinitrotoluene KM=841 µM for menadione KM=2602 µM for trans-hex-2-enal

Ontologies

Keywords
Ligand	FMN Flavoprotein NADP
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Molecular function	FMN binding Inferred from electronic annotation. Source: InterPro NADPH dehydrogenase activity Inferred from electronic annotation. Source: EC pentaerythritol trinitrate reductase activity Inferred from electronic annotation. Source: EC trichloro-p-hydroquinone reductive dehalogenase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.3

Chain

2 – 338

337

NADPH dehydrogenase HAMAP MF_01614

PRO_0000216119

Regions

Nucleotide binding

23 – 27

5

FMN HAMAP MF_01614

Sites

Binding site

28

1

Substrate

Binding site

164

1

Substrate

Binding site

167

1

Substrate

Binding site

215

1

FMN

Binding site

308

1

FMN

Secondary structure

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338

Helix Strand Turn

Details...

Helix

4 – 6

3

Beta strand

9 – 11

3

Beta strand

14 – 22

9

Beta strand

33 – 35

3

Helix

39 – 50

12

Beta strand

54 – 64

11

Helix

65 – 67

3

Helix

79 – 81

3

Helix

82 – 94

13

Beta strand

98 – 104

7

Helix

107 – 109

3

Beta strand

117 – 121

5

Helix

136 – 155

20

Beta strand

159 – 165

7

Helix

170 – 175

6

Turn

177 – 179

3

Beta strand

187 – 189

3

Helix

190 – 207

18

Beta strand

212 – 217

6

Helix

228 – 240

13

Beta strand

245 – 249

5

Turn

262 – 265

4

Helix

266 – 276

11

Beta strand

279 – 282

4

Helix

289 – 297

9

Beta strand

302 – 306

5

Helix

308 – 312

5

Helix

316 – 323

8

Helix

332 – 334

3

Turn

335 – 337

3

Sequences

	Sequence		Length	Mass (Da)
	P54550 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: BDC52D34236326FE	FASTA	338	37,584
	10 20 30 40 50 60 MARKLFTPIT IKDMTLKNRI VMSPMCMYSS HEKDGKLTPF HMAHYISRAI GQVGLIIVEA 70 80 90 100 110 120 SAVNPQGRIT DQDLGIWSDE HIEGFAKLTE QVKEQGSKIG IQLAHAGRKA ELEGDIFAPS 130 140 150 160 170 180 AIAFDEQSAT PVEMSAEKVK ETVQEFKQAA ARAKEAGFDV IEIHAAHGYL IHEFLSPLSN 190 200 210 220 230 240 HRTDEYGGSP ENRYRFLREI IDEVKQVWDG PLFVRVSASD YTDKGLDIAD HIGFAKWMKE 250 260 270 280 290 300 QGVDLIDCSS GALVHADINV FPGYQVSFAE KIREQADMAT GAVGMITDGS MAEEILQNGR 310 320 330 ADLIFIGREL LRDPFFARTA AKQLNTEIPA PVQYERGW

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Systematic sequencing of the 283 kb 210 degrees-232 degrees region of the Bacillus subtilis genome containing the skin element and many sporulation genes." Mizuno M., Masuda S., Takemaru K., Hosono S., Sato T., Takeuchi M., Kobayashi Y. Microbiology 142:3103-3111(1996) [PubMed: 8969508] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: 168 / JH642.
[2]	"The complete genome sequence of the Gram-positive bacterium Bacillus subtilis." Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V. , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A. Nature 390:249-256(1997) [PubMed: 9384377] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: 168.
[3]	"Characterization of yqjM, an old yellow enzyme homolog from Bacillus subtilis involved in the oxidative stress response." Fitzpatrick T.B., Amrhein N., Macheroux P. J. Biol. Chem. 278:19891-19897(2003) [PubMed: 12660247] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-11, CHARACTERIZATION. Strain: 168.
[4]	"The 1.3 A crystal structure of the flavoprotein YqjM reveals a novel class of old yellow enzymes." Kitzing K., Fitzpatrick T.B., Wilken C., Sawa J., Bourenkov G.P., Macheroux P., Clausen T. J. Biol. Chem. 280:27904-27913(2005) [PubMed: 15890652] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.3 ANGSTROMS) IN COMPLEX WITH FMN AND SUBSTRATES, SUBUNIT.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

D84432 Genomic DNA. Translation: BAA12619.1.
AL009126 Genomic DNA. Translation: CAB14314.1.

PIR

E69964.

RefSeq

NP_390263.1. NC_000964.3.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1Z41	X-ray	1.30	A/B	1-338	[»]
1Z42	X-ray	1.85	A/B	1-338	[»]
1Z44	X-ray	1.40	A/B	1-338	[»]
1Z48	X-ray	1.80	A/B	1-338	[»]

ProteinModelPortal

P54550.

SMR

P54550. Positions 2-338.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBBACT00000001737; EBBACP00000001737; EBBACG00000001735.

GeneID

938698.

GenomeReviews

Gene locus BSU23820 in contig AL009126_GR.

KEGG

bsu:BSU23820.

NMPDR

fig|224308.1.peg.2387.

PATRIC

18976589. VBIBacSub10457_2485.

Organism-specific databases

GenoList

BSU23820. [Micado]

Phylogenomic databases

GeneTree

EBGT00050000002219.

HOGENOM

HBG583461.

OMA

WVEDGWN.

PhylomeDB

P54550.

ProtClustDB

PRK13523.

Enzyme and pathway databases

BioCyc

BSUB:BSU23820-MONOMER.

Family and domain databases

HAMAP

MF_01614. NamA.
[Tree]

InterPro

IPR013785. Aldolase_TIM.
IPR023663. NADPH_DH.
IPR001155. OxRdtase_FMN_N.
[Graphical view]

Gene3D

G3DSA:3.20.20.70. Aldolase_TIM. 1 hit.

KO

K00540.

Pfam

PF00724. Oxidored_FMN. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

NAMA_BACSU

Accession

Primary (citable) accession number: P54550

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1996
Last sequence update:	January 23, 2007
Last modified:	January 25, 2012
This is version 84 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program