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Protein

Copper-containing nitrite reductase

Gene

nirK

Organism
Alcaligenes faecalis
Status
Reviewed-Annotation score: 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

Protein has several cofactor binding sites:
  • Cu2+By similarityNote: 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
  • Cu+By similarityNote: Binds 1 Cu+ ion. The Cu+ ion is bound within a single monomer.By similarity
  • FADBy similarity

Pathwayi: nitrate reduction (denitrification)

This protein is involved in step 2 of the subpathway that synthesizes dinitrogen from nitrate.
Proteins known to be involved in the 4 steps of the subpathway in this organism are:
  1. no protein annotated in this organism
  2. Copper-containing nitrite reductase (nirK)
  3. no protein annotated in this organism
  4. no protein annotated in this organism
This subpathway is part of the pathway nitrate reduction (denitrification), which is itself part of Nitrogen metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes dinitrogen from nitrate, the pathway nitrate reduction (denitrification) and in Nitrogen metabolism.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi131Copper 1; type 11 Publication1
Metal bindingi136Copper 2; type 21
Metal bindingi171Copper 2; type 21
Metal bindingi172Copper 1; type 11
Metal bindingi181Copper 1; type 11
Metal bindingi186Copper 1; type 11
Metal bindingi342Copper 2; type 21 Publication1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Nitrate assimilation

Keywords - Ligandi

Copper, FAD, Flavoprotein, Metal-binding

Enzyme and pathway databases

BRENDAi1.7.2.1. 232.
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

Complete GO annotation...

Keywords - Cellular componenti

Periplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi171H → K: Loses nitrite-reducing activity. 1 Publication1
Mutagenesisi186M → E: Contains only a type II copper atom and fails to catalyze the reduction of nitrite. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 33Tat-type signalPROSITE-ProRule annotation1 PublicationAdd BLAST33
ChainiPRO_000000298734 – 376Copper-containing nitrite reductaseAdd BLAST343

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei34Pyrrolidone carboxylic acid1

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

1376
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi42 – 46Combined sources5
Beta strandi50 – 52Combined sources3
Beta strandi69 – 71Combined sources3
Beta strandi74 – 87Combined sources14
Beta strandi94 – 100Combined sources7
Beta strandi103 – 105Combined sources3
Beta strandi109 – 112Combined sources4
Beta strandi116 – 123Combined sources8
Helixi141 – 147Combined sources7
Beta strandi154 – 161Combined sources8
Beta strandi166 – 171Combined sources6
Helixi178 – 183Combined sources6
Beta strandi187 – 193Combined sources7
Beta strandi209 – 219Combined sources11
Helixi235 – 238Combined sources4
Helixi239 – 246Combined sources8
Turni247 – 249Combined sources3
Beta strandi252 – 256Combined sources5
Turni260 – 263Combined sources4
Helixi265 – 267Combined sources3
Beta strandi269 – 272Combined sources4
Beta strandi276 – 286Combined sources11
Beta strandi290 – 293Combined sources4
Beta strandi297 – 301Combined sources5
Beta strandi306 – 308Combined sources3
Beta strandi311 – 316Combined sources6
Beta strandi323 – 330Combined sources8
Beta strandi335 – 343Combined sources9
Helixi344 – 348Combined sources5
Beta strandi353 – 360Combined sources8
Turni364 – 366Combined sources3
Beta strandi367 – 375Combined sources9

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
4YSCX-ray2.03A/B/C40-376[»]
4YSEX-ray1.20A/B/C40-376[»]
5D4HX-ray1.30A/B/C40-376[»]
5D4IX-ray1.60A/B/C40-376[»]
5D4JX-ray2.00A/B/C40-376[»]
5F7AX-ray1.54A/B/C40-376[»]
5F7BX-ray1.56A/B/C40-376[»]
ProteinModelPortaliP38501.
SMRiP38501.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP38501.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini34 – 211Plastocyanin-like 1Add BLAST178
Domaini212 – 376Plastocyanin-like 2Add BLAST165

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

        10         20         30         40         50
MAEQMQISRR TILAGAALAG ALAPVLATTS AWGQGAVRKA TAAEIAALPR
60 70 80 90 100
QKVELVDPPF VHAHSQVAEG GPKVVEFTMV IEEKKIVIDD AGTEVHAMAF
110 120 130 140 150
NGTVPGPLMV VHQDDYLELT LINPETNTLM HNIDFHAATG ALGGGGLTEI
160 170 180 190 200
NPGEKTILRF KATKPGVFVY HCAPPGMVPW HVVSGMNGAI MVLPREGLHD
210 220 230 240 250
GKGKALTYDK IYYVGEQDFY VPRDENGKYK KYEAPGDAYE DTVKVMRTLT
260 270 280 290 300
PTHVVFNGAV GALTGDKAMT AAVGEKVLIV HSQANRDTRP HLIGGHGDYV
310 320 330 340 350
WATGKFNTPP DVDQETWFIP GGAAGAAFYT FQQPGIYAYV NHNLIEAFEL
360 370
GAAAHFKVTG EWNDDLMTSV LAPSGT
Length:376
Mass (Da):40,332
Last modified:October 1, 1994 - v1
Checksum:i0AD918988301BF29
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D13155 Genomic DNA. Translation: BAA02440.1.
PIRiI39582.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D13155 Genomic DNA. Translation: BAA02440.1.
PIRiI39582.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
4YSCX-ray2.03A/B/C40-376[»]
4YSEX-ray1.20A/B/C40-376[»]
5D4HX-ray1.30A/B/C40-376[»]
5D4IX-ray1.60A/B/C40-376[»]
5D4JX-ray2.00A/B/C40-376[»]
5F7AX-ray1.54A/B/C40-376[»]
5F7BX-ray1.56A/B/C40-376[»]
ProteinModelPortaliP38501.
SMRiP38501.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

UniPathwayiUPA00652; UER00707.
BRENDAi1.7.2.1. 232.
SABIO-RKP38501.

Miscellaneous databases

EvolutionaryTraceiP38501.

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]
ProtoNetiSearch...

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: November 2, 2016
This is version 110 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

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.