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Protein

NADPH dehydrogenase

Gene

namA

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.1 Publication

Catalytic activityi

NADPH + acceptor = NADP+ + reduced acceptor.1 Publication

Cofactori

FMN1 Publication

Enzyme regulationi

Inhibited by p-hydroxybenzaldehyde (pHBA) and p-nitrophenol (pNP).

Kineticsi

The highest catalytic efficiency was observed with N-ethylmaleimide for which the KM is inferior to 1.0 µM.

  1. KM=19 µM for duroquinone1 Publication
  2. KM=109 µM for nitroglycerin1 Publication
  3. KM=293 µM for cyclohex-2-enone1 Publication
  4. KM=705 µM for 2,4,6-trinitrotoluene1 Publication
  5. KM=841 µM for menadione1 Publication
  6. KM=2602 µM for trans-hex-2-enal1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei28 – 281Substrate1 Publication
    Binding sitei60 – 601FMN1 Publication
    Binding sitei102 – 1021FMN1 Publication
    Binding sitei215 – 2151FMN1 Publication

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi23 – 264FMN1 Publication
    Nucleotide bindingi307 – 3082FMN1 Publication

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Detoxification, Stress response

    Keywords - Ligandi

    Flavoprotein, FMN, NADP

    Enzyme and pathway databases

    BioCyciBSUB:BSU23820-MONOMER.
    SABIO-RKP54550.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    NADPH dehydrogenase (EC:1.6.99.11 Publication)
    Alternative name(s):
    Xenobiotic reductase
    Gene namesi
    Name:namA
    Synonyms:yqjM
    Ordered Locus Names:BSU23820
    OrganismiBacillus subtilis (strain 168)
    Taxonomic identifieri224308 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
    Proteomesi
    • UP000001570 Componenti: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methionineiRemoved1 Publication
    Chaini2 – 338337NADPH dehydrogenasePRO_0000216119Add
    BLAST

    Proteomic databases

    PaxDbiP54550.

    Expressioni

    Inductioni

    By toxic xenobiotic compounds (2,4,6-trinitrotoluene and nitroglycerin), and in response to oxidative stress (hydrogen peroxide and paraquat).1 Publication

    Interactioni

    Subunit structurei

    Homotetramer. Composed of a dimer of active dimers.2 Publications

    Protein-protein interaction databases

    STRINGi224308.Bsubs1_010100013071.

    Structurei

    Secondary structure

    1
    338
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi4 – 63Combined sources
    Beta strandi9 – 113Combined sources
    Beta strandi14 – 229Combined sources
    Beta strandi33 – 353Combined sources
    Helixi39 – 5012Combined sources
    Beta strandi54 – 6411Combined sources
    Helixi65 – 673Combined sources
    Beta strandi73 – 753Combined sources
    Helixi79 – 813Combined sources
    Helixi82 – 9413Combined sources
    Beta strandi98 – 1047Combined sources
    Helixi107 – 1093Combined sources
    Beta strandi117 – 1215Combined sources
    Helixi136 – 15520Combined sources
    Beta strandi159 – 1657Combined sources
    Helixi170 – 1756Combined sources
    Turni177 – 1793Combined sources
    Beta strandi187 – 1893Combined sources
    Helixi190 – 20718Combined sources
    Beta strandi212 – 2176Combined sources
    Helixi228 – 24013Combined sources
    Beta strandi245 – 2495Combined sources
    Turni262 – 2654Combined sources
    Helixi266 – 27611Combined sources
    Beta strandi279 – 2824Combined sources
    Helixi289 – 2979Combined sources
    Beta strandi302 – 3065Combined sources
    Helixi308 – 3125Combined sources
    Helixi316 – 3238Combined sources
    Helixi332 – 3343Combined sources
    Turni335 – 3373Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1Z41X-ray1.30A/B1-338[»]
    1Z42X-ray1.85A/B1-338[»]
    1Z44X-ray1.40A/B1-338[»]
    1Z48X-ray1.80A/B1-338[»]
    ProteinModelPortaliP54550.
    SMRiP54550. Positions 2-338.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP54550.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni164 – 1674Substrate binding1 Publication

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105CCY. Bacteria.
    COG1902. LUCA.
    HOGENOMiHOG000116232.
    InParanoidiP54550.
    KOiK00354.
    OMAiGYQTRFA.
    OrthoDBiEOG60PHD0.
    PhylomeDBiP54550.

    Family and domain databases

    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_01614. NamA.
    InterProiIPR013785. Aldolase_TIM.
    IPR023663. NADPH_DH.
    IPR001155. OxRdtase_FMN_N.
    [Graphical view]
    PfamiPF00724. Oxidored_FMN. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P54550-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MARKLFTPIT IKDMTLKNRI VMSPMCMYSS HEKDGKLTPF HMAHYISRAI
    60 70 80 90 100
    GQVGLIIVEA SAVNPQGRIT DQDLGIWSDE HIEGFAKLTE QVKEQGSKIG
    110 120 130 140 150
    IQLAHAGRKA ELEGDIFAPS AIAFDEQSAT PVEMSAEKVK ETVQEFKQAA
    160 170 180 190 200
    ARAKEAGFDV IEIHAAHGYL IHEFLSPLSN HRTDEYGGSP ENRYRFLREI
    210 220 230 240 250
    IDEVKQVWDG PLFVRVSASD YTDKGLDIAD HIGFAKWMKE QGVDLIDCSS
    260 270 280 290 300
    GALVHADINV FPGYQVSFAE KIREQADMAT GAVGMITDGS MAEEILQNGR
    310 320 330
    ADLIFIGREL LRDPFFARTA AKQLNTEIPA PVQYERGW
    Length:338
    Mass (Da):37,584
    Last modified:January 23, 2007 - v3
    Checksum:iBDC52D34236326FE
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    D84432 Genomic DNA. Translation: BAA12619.1.
    AL009126 Genomic DNA. Translation: CAB14314.1.
    PIRiE69964.
    RefSeqiNP_390263.1. NC_000964.3.
    WP_003230377.1. NZ_JNCM01000036.1.

    Genome annotation databases

    EnsemblBacteriaiCAB14314; CAB14314; BSU23820.
    GeneIDi938698.
    KEGGibsu:BSU23820.
    PATRICi18976589. VBIBacSub10457_2485.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    D84432 Genomic DNA. Translation: BAA12619.1.
    AL009126 Genomic DNA. Translation: CAB14314.1.
    PIRiE69964.
    RefSeqiNP_390263.1. NC_000964.3.
    WP_003230377.1. NZ_JNCM01000036.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1Z41X-ray1.30A/B1-338[»]
    1Z42X-ray1.85A/B1-338[»]
    1Z44X-ray1.40A/B1-338[»]
    1Z48X-ray1.80A/B1-338[»]
    ProteinModelPortaliP54550.
    SMRiP54550. Positions 2-338.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi224308.Bsubs1_010100013071.

    Proteomic databases

    PaxDbiP54550.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiCAB14314; CAB14314; BSU23820.
    GeneIDi938698.
    KEGGibsu:BSU23820.
    PATRICi18976589. VBIBacSub10457_2485.

    Phylogenomic databases

    eggNOGiENOG4105CCY. Bacteria.
    COG1902. LUCA.
    HOGENOMiHOG000116232.
    InParanoidiP54550.
    KOiK00354.
    OMAiGYQTRFA.
    OrthoDBiEOG60PHD0.
    PhylomeDBiP54550.

    Enzyme and pathway databases

    BioCyciBSUB:BSU23820-MONOMER.
    SABIO-RKP54550.

    Miscellaneous databases

    EvolutionaryTraceiP54550.

    Family and domain databases

    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_01614. NamA.
    InterProiIPR013785. Aldolase_TIM.
    IPR023663. NADPH_DH.
    IPR001155. OxRdtase_FMN_N.
    [Graphical view]
    PfamiPF00724. Oxidored_FMN. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 2-11, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, INDUCTION.
      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] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.3 ANGSTROMS) IN COMPLEX WITH FMN AND SUBSTRATES, SUBUNIT.

    Entry informationi

    Entry nameiNAMA_BACSU
    AccessioniPrimary (citable) accession number: P54550
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1996
    Last sequence update: January 23, 2007
    Last modified: February 17, 2016
    This is version 112 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Forms a charge transfer complex with a variety of phenolic compounds.

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Bacillus subtilis
      Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.