Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Copper-containing nitrite reductase

Gene

nirK

Organism
Achromobacter cycloclastes
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:
  • Cu+Note: Binds 1 Cu+ ion.
  • Cu2+Note: Binds 1 Cu2+ ion.
  • FAD

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. Nitrous-oxide reductase (nosZ)
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 bindingi133Copper 1; type 11
Metal bindingi138Copper 2; type 21
Metal bindingi173Copper 2; type 21
Metal bindingi174Copper 1; type 11
Metal bindingi183Copper 1; type 11
Metal bindingi188Copper 1; type 11
Metal bindingi344Copper 2; type 21

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. 69.
SABIO-RKP25006.
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
OrganismiAchromobacter cycloclastes
Taxonomic identifieri223 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesAlcaligenaceaeAchromobacter

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Periplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 38Tat-type signalPROSITE-ProRule annotation1 PublicationAdd BLAST38
ChainiPRO_000000298639 – 378Copper-containing nitrite reductaseAdd BLAST340

Post-translational modificationi

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

Interactioni

Subunit structurei

Homotrimer.

Structurei

Secondary structure

1378
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi47 – 49Combined sources3
Beta strandi52 – 54Combined sources3
Beta strandi71 – 73Combined sources3
Beta strandi76 – 89Combined sources14
Beta strandi96 – 102Combined sources7
Beta strandi105 – 107Combined sources3
Beta strandi111 – 114Combined sources4
Beta strandi118 – 125Combined sources8
Beta strandi135 – 140Combined sources6
Helixi143 – 149Combined sources7
Beta strandi156 – 163Combined sources8
Beta strandi168 – 173Combined sources6
Turni177 – 179Combined sources3
Helixi180 – 185Combined sources6
Beta strandi189 – 195Combined sources7
Beta strandi211 – 221Combined sources11
Beta strandi227 – 229Combined sources3
Helixi237 – 249Combined sources13
Beta strandi254 – 258Combined sources5
Turni262 – 265Combined sources4
Helixi267 – 269Combined sources3
Beta strandi271 – 274Combined sources4
Beta strandi278 – 288Combined sources11
Beta strandi292 – 295Combined sources4
Beta strandi299 – 303Combined sources5
Beta strandi313 – 317Combined sources5
Beta strandi325 – 332Combined sources8
Beta strandi337 – 345Combined sources9
Helixi346 – 350Combined sources5
Beta strandi355 – 362Combined sources8
Turni366 – 368Combined sources3
Beta strandi369 – 371Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1KCBX-ray1.65A39-378[»]
1NIAX-ray2.50A/B/C39-378[»]
1NIBX-ray2.70A/B/C39-378[»]
1NICX-ray1.90A39-378[»]
1NIDX-ray2.20A39-378[»]
1NIEX-ray1.90A39-378[»]
1NIFX-ray1.70A39-378[»]
1RZPX-ray1.90A/B/C39-373[»]
1RZQX-ray2.20A/B/C39-373[»]
2AVFX-ray2.60A/B/C/D/E/F39-367[»]
2BW4X-ray0.90A39-378[»]
2BW5X-ray1.12A39-378[»]
2BWDX-ray1.15A39-378[»]
2BWIX-ray1.10A39-378[»]
2NRDX-ray2.10A39-378[»]
2Y1AX-ray1.95A39-378[»]
5AKRX-ray0.87A1-378[»]
5I6KX-ray1.07A45-378[»]
5I6LX-ray1.08A46-377[»]
5I6MX-ray1.09A46-377[»]
5I6NX-ray1.22A46-377[»]
5I6OX-ray1.45A46-377[»]
5I6PX-ray1.56A46-377[»]
ProteinModelPortaliP25006.
SMRiP25006.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP25006.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini39 – 213Plastocyanin-like 1Add BLAST175
Domaini214 – 378Plastocyanin-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

Phylogenomic databases

KOiK00368.

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.

P25006-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTEQLQMTRR TMLAGAALAG AVAPLLHTAQ AHAAGAAAAA GAAPVDISTL
60 70 80 90 100
PRVKVDLVKP PFVHAHDQVA KTGPRVVEFT MTIEEKKLVI DREGTEIHAM
110 120 130 140 150
TFNGSVPGPL MVVHENDYVE LRLINPDTNT LLHNIDFHAA TGALGGGALT
160 170 180 190 200
QVNPGEETTL RFKATKPGVF VYHCAPEGMV PWHVTSGMNG AIMVLPRDGL
210 220 230 240 250
KDEKGQPLTY DKIYYVGEQD FYVPKDEAGN YKKYETPGEA YEDAVKAMRT
260 270 280 290 300
LTPTHIVFNG AVGALTGDHA LTAAVGERVL VVHSQANRDT RPHLIGGHGD
310 320 330 340 350
YVWATGKFRN PPDLDQETWL IPGGTAGAAF YTFRQPGVYA YVNHNLIEAF
360 370
ELGAAGHFKV TGEWNDDLMT SVVKPASM
Length:378
Mass (Da):40,771
Last modified:November 1, 1997 - v2
Checksum:iA70B52B814090EA5
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z48635 Genomic DNA. Translation: CAA88564.1.
PIRiJC4648.

Genome annotation databases

KEGGiag:CAA88564.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z48635 Genomic DNA. Translation: CAA88564.1.
PIRiJC4648.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1KCBX-ray1.65A39-378[»]
1NIAX-ray2.50A/B/C39-378[»]
1NIBX-ray2.70A/B/C39-378[»]
1NICX-ray1.90A39-378[»]
1NIDX-ray2.20A39-378[»]
1NIEX-ray1.90A39-378[»]
1NIFX-ray1.70A39-378[»]
1RZPX-ray1.90A/B/C39-373[»]
1RZQX-ray2.20A/B/C39-373[»]
2AVFX-ray2.60A/B/C/D/E/F39-367[»]
2BW4X-ray0.90A39-378[»]
2BW5X-ray1.12A39-378[»]
2BWDX-ray1.15A39-378[»]
2BWIX-ray1.10A39-378[»]
2NRDX-ray2.10A39-378[»]
2Y1AX-ray1.95A39-378[»]
5AKRX-ray0.87A1-378[»]
5I6KX-ray1.07A45-378[»]
5I6LX-ray1.08A46-377[»]
5I6MX-ray1.09A46-377[»]
5I6NX-ray1.22A46-377[»]
5I6OX-ray1.45A46-377[»]
5I6PX-ray1.56A46-377[»]
ProteinModelPortaliP25006.
SMRiP25006.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

KEGGiag:CAA88564.

Phylogenomic databases

KOiK00368.

Enzyme and pathway databases

UniPathwayiUPA00652; UER00707.
BRENDAi1.7.2.1. 69.
SABIO-RKP25006.

Miscellaneous databases

EvolutionaryTraceiP25006.

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_ACHCY
AccessioniPrimary (citable) accession number: P25006
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 1, 1992
Last sequence update: November 1, 1997
Last modified: November 2, 2016
This is version 110 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, 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.