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P37062

- NAPE_ENTFA

UniProt

P37062 - NAPE_ENTFA

Protein

NADH peroxidase

Gene

npr

Organism
Enterococcus faecalis (strain ATCC 700802 / V583)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 120 (01 Oct 2014)
      Sequence version 2 (23 Apr 2003)
      Previous versions | rss
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    Functioni

    Peroxidase whose active site is a redox-active cysteine-sulfenic acid.

    Catalytic activityi

    NADH + H2O2 = NAD+ + 2 H2O.

    Cofactori

    Binds 1 FAD per subunit.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei10 – 101Proton acceptor1 Publication
    Binding sitei32 – 321FAD2 Publications
    Active sitei42 – 421Redox-active1 Publication
    Binding sitei42 – 421FAD2 Publications
    Binding sitei132 – 1321FAD2 Publications
    Binding sitei160 – 1601NAD; via amide nitrogen1 Publication
    Binding sitei179 – 1791NAD1 Publication
    Binding sitei188 – 1881NAD1 Publication
    Binding sitei243 – 2431NAD; via amide nitrogen1 Publication
    Binding sitei281 – 2811FAD2 Publications
    Binding sitei297 – 2971NAD; via carbonyl oxygen1 Publication
    Binding sitei299 – 2991FAD; via amide nitrogen2 Publications
    Binding sitei328 – 3281NAD; via carbonyl oxygen1 Publication

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi7 – 115FAD2 Publications
    Nucleotide bindingi110 – 1134FAD2 Publications

    GO - Molecular functioni

    1. flavin adenine dinucleotide binding Source: InterPro
    2. NADH peroxidase activity Source: UniProtKB-EC

    GO - Biological processi

    1. cell redox homeostasis Source: InterPro

    Keywords - Molecular functioni

    Oxidoreductase, Peroxidase

    Keywords - Ligandi

    FAD, Flavoprotein, NAD

    Enzyme and pathway databases

    BioCyciEFAE226185:GHI1-1199-MONOMER.
    SABIO-RKP37062.

    Protein family/group databases

    PeroxiBasei4010. EfNadPrx01.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    NADH peroxidase (EC:1.11.1.1)
    Short name:
    NPXase
    Short name:
    Npx
    Gene namesi
    Name:npr
    Ordered Locus Names:EF_1211
    OrganismiEnterococcus faecalis (strain ATCC 700802 / V583)
    Taxonomic identifieri226185 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesEnterococcaceaeEnterococcus
    ProteomesiUP000001415: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 447447NADH peroxidasePRO_0000184705Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei42 – 421Cysteine sulfenic acid (-SOH)1 Publication

    Keywords - PTMi

    Oxidation

    Interactioni

    Subunit structurei

    Homotetramer.2 Publications

    Protein-protein interaction databases

    STRINGi226185.EF1211.

    Structurei

    Secondary structure

    1
    447
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi2 – 65
    Helixi10 – 2213
    Beta strandi26 – 3914
    Helixi41 – 433
    Helixi44 – 485
    Helixi55 – 573
    Beta strandi58 – 603
    Helixi63 – 686
    Beta strandi72 – 754
    Beta strandi77 – 837
    Turni84 – 874
    Beta strandi88 – 936
    Turni94 – 963
    Beta strandi99 – 1035
    Beta strandi105 – 1095
    Beta strandi113 – 1153
    Turni121 – 1244
    Beta strandi125 – 1295
    Helixi133 – 14412
    Beta strandi151 – 1555
    Helixi159 – 17012
    Beta strandi174 – 18310
    Turni184 – 1885
    Helixi191 – 20212
    Turni203 – 2053
    Beta strandi206 – 2116
    Beta strandi214 – 2185
    Beta strandi220 – 2223
    Beta strandi225 – 2306
    Beta strandi232 – 2343
    Beta strandi236 – 2405
    Beta strandi244 – 2474
    Helixi249 – 2513
    Turni252 – 2543
    Beta strandi276 – 2783
    Helixi280 – 2823
    Beta strandi285 – 2873
    Turni288 – 2914
    Beta strandi292 – 2943
    Helixi299 – 31113
    Beta strandi313 – 3153
    Beta strandi327 – 3315
    Beta strandi334 – 3407
    Helixi343 – 3497
    Beta strandi354 – 36310
    Beta strandi372 – 3798
    Turni381 – 3833
    Beta strandi385 – 39511
    Helixi400 – 40910
    Helixi414 – 4185
    Turni426 – 4283
    Helixi434 – 44512

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1F8WX-ray2.45A1-447[»]
    1JOAX-ray2.80A1-447[»]
    1NHPX-ray2.00A1-447[»]
    1NHQX-ray2.00A1-447[»]
    1NHRX-ray2.10A1-447[»]
    1NHSX-ray2.00A1-447[»]
    1NPXX-ray2.16A1-447[»]
    2NPXX-ray2.40A1-447[»]
    ProteinModelPortaliP37062.
    SMRiP37062. Positions 1-447.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP37062.

    Family & Domainsi

    Sequence similaritiesi

    Keywords - Domaini

    Redox-active center

    Phylogenomic databases

    eggNOGiCOG0446.
    KOiK05910.
    OMAiMSCGMEL.
    OrthoDBiEOG6QVRCJ.

    Family and domain databases

    Gene3Di3.30.390.30. 1 hit.
    InterProiIPR016156. FAD/NAD-linked_Rdtase_dimer.
    IPR013027. FAD_pyr_nucl-diS_OxRdtase.
    IPR004099. Pyr_nucl-diS_OxRdtase_dimer.
    IPR023753. Pyr_nucl-diS_OxRdtase_FAD/NAD.
    IPR001327. Pyr_OxRdtase_NAD-bd_dom.
    [Graphical view]
    PfamiPF00070. Pyr_redox. 1 hit.
    PF07992. Pyr_redox_2. 2 hits.
    PF02852. Pyr_redox_dim. 1 hit.
    [Graphical view]
    PRINTSiPR00368. FADPNR.
    SUPFAMiSSF55424. SSF55424. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P37062-1 [UniParc]FASTAAdd to Basket

    « Hide

    MKVIVLGSSH GGYEAVEELL NLHPDAEIQW YEKGDFISFL SCGMQLYLEG    50
    KVKDVNSVRY MTGEKMESRG VNVFSNTEIT AIQPKEHQVT VKDLVSGEER 100
    VENYDKLIIS PGAVPFELDI PGKDLDNIYL MRGRQWAIKL KQKTVDPEVN 150
    NVVVIGSGYI GIEAAEAFAK AGKKVTVIDI LDRPLGVYLD KEFTDVLTEE 200
    MEANNITIAT GETVERYEGD GRVQKIVTDK NAYDADLVVV AVGVRPNTAW 250
    LKGTLELHPN GLIKTDEYMR TSEPDVFAVG DATLIKYNPA DTEVNIALAT 300
    NARKQGRFAV KNLEEPVKPF PGVQGSSGLA VFDYKFASTG INEVMAQKLG 350
    KETKAVTVVE DYLMDFNPDK QKAWFKLVYD PETTQILGAQ LMSKADLTAN 400
    INAISLAIQA KMTIEDLAYA DFFFQPAFDK PWNIINTAAL EAVKQER 447
    Length:447
    Mass (Da):49,566
    Last modified:April 23, 2003 - v2
    Checksum:i3FAF85AF5BB2A70B
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti226 – 2261I → V in CAA44611. (PubMed:1719212)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X62755 Genomic DNA. Translation: CAA44611.1.
    AE016830 Genomic DNA. Translation: AAO81008.1.
    PIRiS18332.
    RefSeqiNP_814938.1. NC_004668.1.

    Genome annotation databases

    EnsemblBacteriaiAAO81008; AAO81008; EF_1211.
    GeneIDi1200111.
    KEGGiefa:EF1211.
    PATRICi21852806. VBIEntFae7065_1134.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X62755 Genomic DNA. Translation: CAA44611.1 .
    AE016830 Genomic DNA. Translation: AAO81008.1 .
    PIRi S18332.
    RefSeqi NP_814938.1. NC_004668.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1F8W X-ray 2.45 A 1-447 [» ]
    1JOA X-ray 2.80 A 1-447 [» ]
    1NHP X-ray 2.00 A 1-447 [» ]
    1NHQ X-ray 2.00 A 1-447 [» ]
    1NHR X-ray 2.10 A 1-447 [» ]
    1NHS X-ray 2.00 A 1-447 [» ]
    1NPX X-ray 2.16 A 1-447 [» ]
    2NPX X-ray 2.40 A 1-447 [» ]
    ProteinModelPortali P37062.
    SMRi P37062. Positions 1-447.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 226185.EF1211.

    Protein family/group databases

    PeroxiBasei 4010. EfNadPrx01.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAO81008 ; AAO81008 ; EF_1211 .
    GeneIDi 1200111.
    KEGGi efa:EF1211.
    PATRICi 21852806. VBIEntFae7065_1134.

    Phylogenomic databases

    eggNOGi COG0446.
    KOi K05910.
    OMAi MSCGMEL.
    OrthoDBi EOG6QVRCJ.

    Enzyme and pathway databases

    BioCyci EFAE226185:GHI1-1199-MONOMER.
    SABIO-RK P37062.

    Miscellaneous databases

    EvolutionaryTracei P37062.

    Family and domain databases

    Gene3Di 3.30.390.30. 1 hit.
    InterProi IPR016156. FAD/NAD-linked_Rdtase_dimer.
    IPR013027. FAD_pyr_nucl-diS_OxRdtase.
    IPR004099. Pyr_nucl-diS_OxRdtase_dimer.
    IPR023753. Pyr_nucl-diS_OxRdtase_FAD/NAD.
    IPR001327. Pyr_OxRdtase_NAD-bd_dom.
    [Graphical view ]
    Pfami PF00070. Pyr_redox. 1 hit.
    PF07992. Pyr_redox_2. 2 hits.
    PF02852. Pyr_redox_dim. 1 hit.
    [Graphical view ]
    PRINTSi PR00368. FADPNR.
    SUPFAMi SSF55424. SSF55424. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Cloning, sequence and overexpression of NADH peroxidase from Streptococcus faecalis 10C1. Structural relationship with the flavoprotein disulfide reductases."
      Ross R.P., Claiborne A.
      J. Mol. Biol. 221:857-871(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE.
      Strain: ATCC 11700 / DSM 20409 / NCIMB 8661 / 10C1.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 700802 / V583.
    3. "The non-flavin redox center of the streptococcal NADH peroxidase. I. Thiol reactivity and redox behavior in the presence of urea."
      Poole L.B., Claiborne A.
      J. Biol. Chem. 264:12322-12329(1989) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 1-51.
      Strain: ATCC 11700 / DSM 20409 / NCIMB 8661 / 10C1.
    4. "Structure of NADH peroxidase from Streptococcus faecalis 10C1 refined at 2.16-A resolution."
      Stehle T., Ahmed S.A., Claiborne A., Schulz G.E.
      J. Mol. Biol. 221:1325-1344(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.16 ANGSTROMS).
      Strain: ATCC 11700 / DSM 20409 / NCIMB 8661 / 10C1.
    5. "NADH binding site and catalysis of NADH peroxidase."
      Stehle T., Claiborne A., Schulz G.E.
      Eur. J. Biochem. 211:221-226(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) IN COMPLEX WITH NAD AND FAD.
      Strain: ATCC 11700 / DSM 20409 / NCIMB 8661 / 10C1.
    6. "Structure of the native cysteine-sulfenic acid redox center of enterococcal NADH peroxidase refined at 2.8-A resolution."
      Yeh J.I., Claiborne A., Hol W.G.J.
      Biochemistry 35:9951-9957(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) IN COMPLEX WITH FAD, ACTIVE SITE, OXIDATION AT CYS-42.
      Strain: ATCC 11700 / DSM 20409 / NCIMB 8661 / 10C1.
    7. "13C NMR analysis of the cysteine-sulfenic acid redox center of enterococcal NADH peroxidase."
      Crane E.J. III, Vervoort J., Clairborne A.
      Biochemistry 36:8611-8618(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: STRUCTURE BY NMR.
      Strain: ATCC 11700 / DSM 20409 / NCIMB 8661 / 10C1.

    Entry informationi

    Entry nameiNAPE_ENTFA
    AccessioniPrimary (citable) accession number: P37062
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 1, 1994
    Last sequence update: April 23, 2003
    Last modified: October 1, 2014
    This is version 120 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    The active site is the redox-active Cys-42 oxidized to Cys-SOH. The oxidized form is stabilized by a hydrogen bond formation with His-10.

    Keywords - Technical termi

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

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3