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P72181

- NIRS_PARPN

UniProt

P72181 - NIRS_PARPN

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Protein
Nitrite reductase
Gene
nirS
Organism
Paracoccus pantotrophus (Thiosphaera pantotropha)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

Catalytic activityi

Nitric oxide + H2O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H+.
NH3 + H2O + acceptor = hydroxylamine + reduced acceptor.

Cofactori

Binds 2 heme groups per subunit.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi46 – 461Iron (heme axial ligand)
Binding sitei94 – 941Heme (covalent)
Binding sitei97 – 971Heme (covalent)
Metal bindingi98 – 981Iron (heme axial ligand)
Metal bindingi229 – 2291Iron (heme D1 proximal ligand)

GO - Molecular functioni

  1. electron carrier activity Source: InterPro
  2. heme binding Source: InterPro
  3. hydroxylamine reductase activity Source: UniProtKB-EC
  4. metal ion binding Source: UniProtKB-KW
  5. nitrite reductase (NO-forming) activity Source: UniProtKB-EC
Complete GO annotation...

GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Electron transport, Transport

    Keywords - Ligandi

    Heme, Iron, Metal-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Nitrite reductase (EC:1.7.2.1)
    Alternative name(s):
    Cytochrome cd1
    Cytochrome oxidase
    Hydroxylamine reductase (EC:1.7.99.1)
    Gene namesi
    Name:nirS
    OrganismiParacoccus pantotrophus (Thiosphaera pantotropha)
    Taxonomic identifieri82367 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhodobacteralesRhodobacteraceaeParacoccus

    Subcellular locationi

    GO - Cellular componenti

    1. periplasmic space Source: UniProtKB-SubCell
    Complete GO annotation...

    Keywords - Cellular componenti

    Periplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 2929
    Add
    BLAST
    Chaini30 – 596567Nitrite reductase
    PRO_0000006575Add
    BLAST

    Interactioni

    Subunit structurei

    Homodimer.

    Structurei

    Secondary structure

    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi39 – 413
    Helixi42 – 454
    Beta strandi50 – 556
    Helixi61 – 633
    Helixi80 – 9314
    Helixi95 – 984
    Beta strandi105 – 1073
    Helixi112 – 1187
    Helixi120 – 1278
    Beta strandi132 – 1343
    Turni136 – 1383
    Beta strandi142 – 1443
    Helixi146 – 15712
    Helixi168 – 1747
    Beta strandi176 – 1794
    Helixi181 – 1833
    Helixi194 – 1963
    Beta strandi197 – 2026
    Turni203 – 2064
    Beta strandi207 – 2126
    Turni213 – 2153
    Beta strandi218 – 2236
    Beta strandi228 – 2336
    Beta strandi239 – 2446
    Beta strandi247 – 2537
    Beta strandi256 – 2583
    Beta strandi261 – 2666
    Beta strandi269 – 2768
    Turni283 – 2853
    Beta strandi286 – 2938
    Beta strandi296 – 3016
    Turni302 – 3043
    Beta strandi307 – 3126
    Turni318 – 3203
    Beta strandi323 – 3253
    Beta strandi329 – 3346
    Beta strandi336 – 34510
    Turni346 – 3494
    Beta strandi350 – 3556
    Beta strandi359 – 36810
    Beta strandi371 – 3788
    Beta strandi384 – 3896
    Helixi390 – 3923
    Beta strandi394 – 3996
    Turni400 – 4034
    Beta strandi404 – 4107
    Beta strandi412 – 4165
    Beta strandi422 – 4265
    Turni427 – 4293
    Beta strandi430 – 44718
    Turni450 – 4523
    Turni454 – 4563
    Beta strandi459 – 4657
    Beta strandi481 – 4866
    Helixi493 – 4964
    Beta strandi499 – 5035
    Helixi504 – 5063
    Beta strandi510 – 5123
    Beta strandi516 – 5194
    Helixi521 – 5255
    Beta strandi533 – 5397
    Beta strandi543 – 5519
    Beta strandi559 – 5646
    Turni565 – 5684
    Beta strandi569 – 5746
    Beta strandi581 – 5877
    Helixi588 – 5925

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1AOFX-ray2.00A/B30-596[»]
    1AOMX-ray1.80A/B30-596[»]
    1AOQX-ray1.80A/B30-596[»]
    1DY7X-ray1.60A/B30-596[»]
    1E2RX-ray1.59A/B30-596[»]
    1GQ1X-ray1.40A/B30-596[»]
    1H9XX-ray2.10A/B30-596[»]
    1H9YX-ray2.40A/B30-596[»]
    1HCMX-ray2.50A/B30-596[»]
    1HJ3X-ray1.60A/B30-596[»]
    1HJ4X-ray1.60A/B30-596[»]
    1HJ5X-ray1.46A/B30-596[»]
    1QKSX-ray1.28A/B30-596[»]
    ProteinModelPortaliP72181.
    SMRiP72181. Positions 38-596.

    Miscellaneous databases

    EvolutionaryTraceiP72181.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini77 – 16286Cytochrome c
    Add
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni30 – 7647N-terminal tail
    Add
    BLAST
    Regioni163 – 596434D1-heme domain
    Add
    BLAST

    Sequence similaritiesi

    Keywords - Domaini

    Signal

    Family and domain databases

    Gene3Di1.10.760.10. 1 hit.
    2.130.10.10. 1 hit.
    2.140.10.20. 1 hit.
    InterProiIPR009056. Cyt_c-like_dom.
    IPR003143. Cyt_cd1_C.
    IPR011048. Haem_d1.
    IPR015943. WD40/YVTN_repeat-like_dom.
    [Graphical view]
    PfamiPF13442. Cytochrome_CBB3. 1 hit.
    [Graphical view]
    SUPFAMiSSF46626. SSF46626. 2 hits.
    SSF51004. SSF51004. 1 hit.
    PROSITEiPS51007. CYTC. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    P72181-1 [UniParc]FASTAAdd to Basket

    « Hide

    MRQRTPFARP GLLASAALAL VLGPLAASAQ EQVAPPKDPA AALEDHKTRT    50
    DNRYEPSLDN LAQQDVAAPG APEGVSALSD AQYNEANKIY FERCAGCHGV 100
    LRKGATGKAL TPDLTRDLGF DYLQSFITYG SPAGMPNWGT SGELSAEQVD 150
    LMANYLLLDP AAPPEFGMKE MRESWKVHVA PEDRPTQQEN DWDLENLFSV 200
    TLRDAGQIAL IDGATYEIKS VLDTGYAVHI SRLSASGRYL FVIGRDGKVN 250
    MIDLWMKEPT TVAEIKIGSE ARSIETSKME GWEDKYAIAG AYWPPQYVIM 300
    DGETLEPKKI QSTRGMTYDE QEYHPEPRVA AILASHYRPE FIVNVKETGK 350
    ILLVDYTDLD NLKTTEISAE RFLHDGGLDG SHRYFITAAN ARNKLVVIDT 400
    KEGKLVAIED TGGQTPHPGR GANFVHPTFG PVWATSHMGD DSVALIGTDP 450
    EGHPDNAWKI LDSFPALGGG SLFIKTHPNS QYLYVDATLN PEAEISGSVA 500
    VFDIKAMTGD GSDPEFKTLP IAEWAGITEG QPRVVQGEFN KDGTEVWFSV 550
    WNGKDQESAL VVVDDKTLEL KHVIKDERLV TPTGKFNVYN TMTDTY 596
    Length:596
    Mass (Da):65,383
    Last modified:November 8, 2002 - v2
    Checksum:iABAD0C871E8FB7F1
    GO

    Sequence conflict

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti28 – 281S → A in AAB17878. 1 Publication
    Sequence conflicti76 – 761S → T in AAB17878. 1 Publication
    Sequence conflicti130 – 1301G → A in AAB17878. 1 Publication
    Sequence conflicti214 – 2141A → T in AAB17878. 1 Publication

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U75413 Genomic DNA. Translation: AAB17878.1.
    AJ401462 Genomic DNA. Translation: CAC03621.1.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U75413 Genomic DNA. Translation: AAB17878.1 .
    AJ401462 Genomic DNA. Translation: CAC03621.1 .

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1AOF X-ray 2.00 A/B 30-596 [» ]
    1AOM X-ray 1.80 A/B 30-596 [» ]
    1AOQ X-ray 1.80 A/B 30-596 [» ]
    1DY7 X-ray 1.60 A/B 30-596 [» ]
    1E2R X-ray 1.59 A/B 30-596 [» ]
    1GQ1 X-ray 1.40 A/B 30-596 [» ]
    1H9X X-ray 2.10 A/B 30-596 [» ]
    1H9Y X-ray 2.40 A/B 30-596 [» ]
    1HCM X-ray 2.50 A/B 30-596 [» ]
    1HJ3 X-ray 1.60 A/B 30-596 [» ]
    1HJ4 X-ray 1.60 A/B 30-596 [» ]
    1HJ5 X-ray 1.46 A/B 30-596 [» ]
    1QKS X-ray 1.28 A/B 30-596 [» ]
    ProteinModelPortali P72181.
    SMRi P72181. Positions 38-596.
    ModBasei Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Miscellaneous databases

    EvolutionaryTracei P72181.

    Family and domain databases

    Gene3Di 1.10.760.10. 1 hit.
    2.130.10.10. 1 hit.
    2.140.10.20. 1 hit.
    InterProi IPR009056. Cyt_c-like_dom.
    IPR003143. Cyt_cd1_C.
    IPR011048. Haem_d1.
    IPR015943. WD40/YVTN_repeat-like_dom.
    [Graphical view ]
    Pfami PF13442. Cytochrome_CBB3. 1 hit.
    [Graphical view ]
    SUPFAMi SSF46626. SSF46626. 2 hits.
    SSF51004. SSF51004. 1 hit.
    PROSITEi PS51007. CYTC. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Transcriptional analysis of the nirS gene, encoding cytochrome cd1 nitrite reductase, of Paracoccus pantotrophus LMD 92.63."
      Saunders N.F.W., Ferguson S.J., Baker S.C.
      Microbiology 146:509-516(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: LMD 92.63.
    2. "The cytochrome c domain of dimeric cytochrome cd(1) of Paracoccus pantotrophus can be produced at high levels as a monomeric holoprotein using an improved c-type cytochrome expression system in Escherichia coli."
      Gordon E.H.J., Steensma E., Ferguson S.J.
      Biochem. Biophys. Res. Commun. 281:788-794(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    3. "The anatomy of a bifunctional enzyme: structural basis for reduction of oxygen to water and synthesis of nitric oxide by cytochrome cd1."
      Fueloep V., Moir J.W.B., Ferguson S.J., Hajdu J.
      Cell 81:369-377(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS).
    4. "Cytochrome cd1 structure: unusual haem environments in a nitrite reductase and analysis of factors contributing to beta-propeller folds."
      Baker S.C., Saunders N.F.W., Willis A.C., Ferguson S.J., Fueloep V., Hajdu J.
      J. Mol. Biol. 269:440-455(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.2 ANGSTROMS).
    5. "Haem-ligand switching during catalysis in crystals of a nitrogen-cycle enzyme."
      Williams P.A., Fueloep V., Garman E.F., Saunders N.F.W., Ferguson S.J., Hajdu J.
      Nature 389:406-412(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
    6. "Proton-coupled structural changes upon binding of carbon monoxide to cytochrome cd1: a combined flash photolysis and X-ray crystallography study."
      Sjoegren T., Svensson-Ek M., Hajdu J., Brzezinski P.
      Biochemistry 39:10967-10974(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
    7. "X-ray crystallographic study of cyanide binding provides insights into the structure-function relationship for cytochrome cd1 nitrite reductase from Paracoccus pantotrophus."
      Jafferji A., Allen J.W.A., Ferguson S.J., Fueloep V.
      J. Biol. Chem. 275:25089-25094(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.59 ANGSTROMS).
    8. "Structure of the bound dioxygen species in the cytochrome oxidase reaction of cytochrome cd1 nitrite reductase."
      Sjoegren T., Hajdu J.
      J. Biol. Chem. 276:13072-13076(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.46 ANGSTROMS).
    9. "The structure of an alternative form of Paracoccus pantotrophus cytochrome cd1 nitrite reductase."
      Sjoegren T., Hajdu J.
      J. Biol. Chem. 276:29450-29455(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).

    Entry informationi

    Entry nameiNIRS_PARPN
    AccessioniPrimary (citable) accession number: P72181
    Secondary accession number(s): Q9FCQ0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: November 8, 2002
    Last modified: April 16, 2014
    This is version 95 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure

    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

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