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P38501

- NIR_ALCFA

UniProt

P38501 - NIR_ALCFA

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Protein
Copper-containing nitrite reductase
Gene
nirK, nir
Organism
Alcaligenes faecalis
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+.

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.
Binds 1 Cu+ ion. The Cu+ ion is bound within a single monomer 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
Complete GO annotation...

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
Complete GO annotation...

Keywords - Cellular componenti

Periplasm

Pathology & Biotechi

Mutagenesis

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

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 3333Tat-type signal1 Publication
Add
BLAST
Chaini34 – 376343Copper-containing nitrite reductase
PRO_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

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.

Miscellaneous databases

EvolutionaryTraceiP38501.

Family & Domainsi

Domains and Repeats

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

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 16, 2013
This is version 98 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

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