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P38501

- NIR_ALCFA

UniProt

P38501 - NIR_ALCFA

Protein

Copper-containing nitrite reductase

Gene

nirK

Organism
Alcaligenes faecalis
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 99 (01 Oct 2014)
      Sequence version 1 (01 Oct 1994)
      Previous versions | rss
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    Functioni

    Catalytic activityi

    Nitric oxide + H2O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H+.

    Cofactori

    Binds 1 Cu2+ ion. The Cu2+ ion is held by residues from each of 2 monomers of the trimer. Nitrite is bound to the Cu2+ ion site. Pseudoazurin is the physiological electron donor for the Cu-NIR in vitro By similarity.By similarity
    Binds 1 Cu+ ion. The Cu+ ion is bound within a single monomer By similarity.By similarity
    FAD.By similarity

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi131 – 1311Copper 1; type 11 Publication
    Metal bindingi136 – 1361Copper 2; type 2
    Metal bindingi171 – 1711Copper 2; type 2
    Metal bindingi172 – 1721Copper 1; type 1
    Metal bindingi181 – 1811Copper 1; type 1
    Metal bindingi186 – 1861Copper 1; type 1
    Metal bindingi342 – 3421Copper 2; type 21 Publication

    GO - Molecular functioni

    1. copper ion binding Source: InterPro
    2. nitrite reductase (NO-forming) activity Source: UniProtKB-EC

    GO - Biological processi

    1. denitrification pathway Source: UniProtKB-UniPathway
    2. nitrate assimilation Source: UniProtKB-KW

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Nitrate assimilation

    Keywords - Ligandi

    Copper, FAD, Flavoprotein, Metal-binding

    Enzyme and pathway databases

    SABIO-RKP38501.
    UniPathwayiUPA00652; UER00707.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Copper-containing nitrite reductase (EC:1.7.2.1)
    Alternative name(s):
    Cu-NIR
    Gene namesi
    Name:nirK
    Synonyms:nir
    OrganismiAlcaligenes faecalis
    Taxonomic identifieri511 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesAlcaligenaceaeAlcaligenes

    Subcellular locationi

    GO - Cellular componenti

    1. periplasmic space Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Periplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi171 – 1711H → K: Loses nitrite-reducing activity. 1 Publication
    Mutagenesisi186 – 1861M → E: Contains only a type II copper atom and fails to catalyze the reduction of nitrite. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 3333Tat-type signal1 PublicationPROSITE-ProRule annotationAdd
    BLAST
    Chaini34 – 376343Copper-containing nitrite reductasePRO_0000002987Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei34 – 341Pyrrolidone carboxylic acid

    Post-translational modificationi

    Predicted to be exported by the Tat system. The position of the signal peptide cleavage has been experimentally proven.

    Keywords - PTMi

    Pyrrolidone carboxylic acid

    Expressioni

    Inductioni

    Under anaerobic growth conditions and by nitrite.

    Interactioni

    Subunit structurei

    Homotrimer.

    Structurei

    Secondary structure

    1
    376
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi42 – 476
    Beta strandi50 – 523
    Beta strandi74 – 8714
    Beta strandi94 – 1007
    Beta strandi103 – 1053
    Beta strandi109 – 1124
    Beta strandi116 – 1238
    Helixi141 – 1477
    Beta strandi154 – 1618
    Beta strandi166 – 1716
    Helixi178 – 1836
    Beta strandi187 – 1937
    Beta strandi209 – 21911
    Helixi235 – 2384
    Helixi239 – 2479
    Beta strandi252 – 2565
    Turni260 – 2634
    Helixi265 – 2673
    Beta strandi269 – 2724
    Beta strandi276 – 28611
    Beta strandi290 – 2934
    Beta strandi297 – 3015
    Beta strandi306 – 3083
    Beta strandi311 – 3166
    Beta strandi323 – 3308
    Beta strandi335 – 3439
    Helixi344 – 3485
    Beta strandi353 – 3608
    Turni364 – 3663
    Beta strandi367 – 3748

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1AQ8X-ray2.00A/B/C34-376[»]
    1AS6X-ray1.80A/B/C34-376[»]
    1AS7X-ray2.00A/B/C34-376[»]
    1AS8X-ray1.85A/B/C34-376[»]
    1ET5X-ray1.90A40-376[»]
    1ET7X-ray1.70A40-376[»]
    1ET8X-ray1.80A40-376[»]
    1J9QX-ray1.65A/B/C40-376[»]
    1J9RX-ray2.00A/B/C40-376[»]
    1J9SX-ray1.90A/B/C40-376[»]
    1J9TX-ray1.95A/B/C40-376[»]
    1L9OX-ray1.70A/B/C40-376[»]
    1L9PX-ray1.75A/B/C40-376[»]
    1L9QX-ray1.70A/B/C40-376[»]
    1L9RX-ray1.78A/B/C40-376[»]
    1L9SX-ray1.78A/B/C40-376[»]
    1L9TX-ray1.75A/B/C40-376[»]
    1NPJX-ray1.90A/B/C34-376[»]
    1NPNX-ray1.80A/B/C34-376[»]
    1NTDX-ray2.30A34-376[»]
    1SJMX-ray1.40A/B/C40-376[»]
    1SNRX-ray1.31A/B/C40-376[»]
    1ZDQX-ray1.80A/B/C40-375[»]
    1ZDSX-ray1.55A/B/C40-375[»]
    2AFNX-ray2.00A/B/C34-376[»]
    2B08X-ray1.90A/B/C37-376[»]
    2E86X-ray1.50A/B/C40-376[»]
    2FJSX-ray1.85A/B/C40-376[»]
    2P80NMR-A/B/C40-376[»]
    2PP7X-ray1.65A/B/C40-376[»]
    2PP8X-ray1.50A/B/C40-376[»]
    2PP9X-ray1.80A/B/C40-376[»]
    2PPAX-ray1.69A/B/C40-376[»]
    2PPCX-ray1.58A/B/C40-376[»]
    2PPDX-ray1.80A/B/C34-376[»]
    2PPEX-ray1.75A/B/C34-376[»]
    2PPFX-ray1.65A/B/C40-376[»]
    3H4FX-ray2.10A/B/C40-375[»]
    3H4HX-ray1.60A/B/C41-375[»]
    3H56X-ray1.50A40-375[»]
    ProteinModelPortaliP38501.
    SMRiP38501. Positions 40-376.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP38501.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini34 – 211178Plastocyanin-like 1Add
    BLAST
    Domaini212 – 376165Plastocyanin-like 2Add
    BLAST

    Domaini

    The type I copper site in NIR plays a crucial role for electron transfer from pseudoazurin to the type II copper site of NIR, which comprises the catalytic center of NIR for the reduction of nitrite.

    Sequence similaritiesi

    Belongs to the multicopper oxidase family.Curated
    Contains 2 plastocyanin-like domains.Curated

    Keywords - Domaini

    Repeat, Signal

    Family and domain databases

    Gene3Di2.60.40.420. 2 hits.
    InterProiIPR001117. Cu-oxidase.
    IPR011707. Cu-oxidase_3.
    IPR008972. Cupredoxin.
    IPR001287. NO2-reductase_Cu.
    IPR006311. TAT_signal.
    [Graphical view]
    PfamiPF00394. Cu-oxidase. 1 hit.
    PF07732. Cu-oxidase_3. 1 hit.
    [Graphical view]
    PRINTSiPR00695. CUNO2RDTASE.
    SUPFAMiSSF49503. SSF49503. 2 hits.
    TIGRFAMsiTIGR02376. Cu_nitrite_red. 1 hit.
    PROSITEiPS51318. TAT. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    P38501-1 [UniParc]FASTAAdd to Basket

    « Hide

    MAEQMQISRR TILAGAALAG ALAPVLATTS AWGQGAVRKA TAAEIAALPR    50
    QKVELVDPPF VHAHSQVAEG GPKVVEFTMV IEEKKIVIDD AGTEVHAMAF 100
    NGTVPGPLMV VHQDDYLELT LINPETNTLM HNIDFHAATG ALGGGGLTEI 150
    NPGEKTILRF KATKPGVFVY HCAPPGMVPW HVVSGMNGAI MVLPREGLHD 200
    GKGKALTYDK IYYVGEQDFY VPRDENGKYK KYEAPGDAYE DTVKVMRTLT 250
    PTHVVFNGAV GALTGDKAMT AAVGEKVLIV HSQANRDTRP HLIGGHGDYV 300
    WATGKFNTPP DVDQETWFIP GGAAGAAFYT FQQPGIYAYV NHNLIEAFEL 350
    GAAAHFKVTG EWNDDLMTSV LAPSGT 376
    Length:376
    Mass (Da):40,332
    Last modified:October 1, 1994 - v1
    Checksum:i0AD918988301BF29
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    D13155 Genomic DNA. Translation: BAA02440.1.
    PIRiI39582.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    D13155 Genomic DNA. Translation: BAA02440.1 .
    PIRi I39582.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1AQ8 X-ray 2.00 A/B/C 34-376 [» ]
    1AS6 X-ray 1.80 A/B/C 34-376 [» ]
    1AS7 X-ray 2.00 A/B/C 34-376 [» ]
    1AS8 X-ray 1.85 A/B/C 34-376 [» ]
    1ET5 X-ray 1.90 A 40-376 [» ]
    1ET7 X-ray 1.70 A 40-376 [» ]
    1ET8 X-ray 1.80 A 40-376 [» ]
    1J9Q X-ray 1.65 A/B/C 40-376 [» ]
    1J9R X-ray 2.00 A/B/C 40-376 [» ]
    1J9S X-ray 1.90 A/B/C 40-376 [» ]
    1J9T X-ray 1.95 A/B/C 40-376 [» ]
    1L9O X-ray 1.70 A/B/C 40-376 [» ]
    1L9P X-ray 1.75 A/B/C 40-376 [» ]
    1L9Q X-ray 1.70 A/B/C 40-376 [» ]
    1L9R X-ray 1.78 A/B/C 40-376 [» ]
    1L9S X-ray 1.78 A/B/C 40-376 [» ]
    1L9T X-ray 1.75 A/B/C 40-376 [» ]
    1NPJ X-ray 1.90 A/B/C 34-376 [» ]
    1NPN X-ray 1.80 A/B/C 34-376 [» ]
    1NTD X-ray 2.30 A 34-376 [» ]
    1SJM X-ray 1.40 A/B/C 40-376 [» ]
    1SNR X-ray 1.31 A/B/C 40-376 [» ]
    1ZDQ X-ray 1.80 A/B/C 40-375 [» ]
    1ZDS X-ray 1.55 A/B/C 40-375 [» ]
    2AFN X-ray 2.00 A/B/C 34-376 [» ]
    2B08 X-ray 1.90 A/B/C 37-376 [» ]
    2E86 X-ray 1.50 A/B/C 40-376 [» ]
    2FJS X-ray 1.85 A/B/C 40-376 [» ]
    2P80 NMR - A/B/C 40-376 [» ]
    2PP7 X-ray 1.65 A/B/C 40-376 [» ]
    2PP8 X-ray 1.50 A/B/C 40-376 [» ]
    2PP9 X-ray 1.80 A/B/C 40-376 [» ]
    2PPA X-ray 1.69 A/B/C 40-376 [» ]
    2PPC X-ray 1.58 A/B/C 40-376 [» ]
    2PPD X-ray 1.80 A/B/C 34-376 [» ]
    2PPE X-ray 1.75 A/B/C 34-376 [» ]
    2PPF X-ray 1.65 A/B/C 40-376 [» ]
    3H4F X-ray 2.10 A/B/C 40-375 [» ]
    3H4H X-ray 1.60 A/B/C 41-375 [» ]
    3H56 X-ray 1.50 A 40-375 [» ]
    ProteinModelPortali P38501.
    SMRi P38501. Positions 40-376.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Enzyme and pathway databases

    UniPathwayi UPA00652 ; UER00707 .
    SABIO-RK P38501.

    Miscellaneous databases

    EvolutionaryTracei P38501.

    Family and domain databases

    Gene3Di 2.60.40.420. 2 hits.
    InterProi IPR001117. Cu-oxidase.
    IPR011707. Cu-oxidase_3.
    IPR008972. Cupredoxin.
    IPR001287. NO2-reductase_Cu.
    IPR006311. TAT_signal.
    [Graphical view ]
    Pfami PF00394. Cu-oxidase. 1 hit.
    PF07732. Cu-oxidase_3. 1 hit.
    [Graphical view ]
    PRINTSi PR00695. CUNO2RDTASE.
    SUPFAMi SSF49503. SSF49503. 2 hits.
    TIGRFAMsi TIGR02376. Cu_nitrite_red. 1 hit.
    PROSITEi PS51318. TAT. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Cloning and characterization of a nitrite reductase gene from Alcaligenes faecalis and its expression in Escherichia coli."
      Nishiyama M., Suzuki J., Kukimoto M., Ohnuki T., Horinouchi S., Beppu T.
      J. Gen. Microbiol. 139:725-733(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 34-48 AND 192-240.
      Strain: S-6.
    2. "X-ray structure and site-directed mutagenesis of a nitrite reductase from Alcaligenes faecalis S-6: roles of two copper atoms in nitrite reduction."
      Kukimoto M., Nishiyama M., Murphy M.E.P., Turley S., Adman E.T., Horinouchi S., Beppu T.
      Biochemistry 33:5246-5252(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS), MUTAGENESIS.
      Strain: S-6.
    3. "Structure of Alcaligenes faecalis nitrite reductase and a copper site mutant, M150E, that contains zinc."
      Murphy M.E., Turley S., Kukimoto M., Nishiyama M., Horinouchi S., Sasaki H., Tanokura M., Adman E.T.
      Biochemistry 34:12107-12117(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
    4. "Structure of nitrite bound to copper-containing nitrite reductase from Alcaligenes faecalis. Mechanistic implications."
      Murphy M.E., Turley S., Adman E.T.
      J. Biol. Chem. 272:28455-28460(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).

    Entry informationi

    Entry nameiNIR_ALCFA
    AccessioniPrimary (citable) accession number: P38501
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1994
    Last sequence update: October 1, 1994
    Last modified: October 1, 2014
    This is version 99 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Direct protein sequencing

    Documents

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

    External Data

    Dasty 3