Copper-containing nitrite reductase precursor

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P38501 (NIR_ALCFA) Reviewed, UniProtKB/Swiss-Prot

Last modified April 3, 2013. Version 97. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Copper-containing nitrite reductase
EC=1.7.2.1

Alternative name(s):
Cu-NIR

Gene names

Name:	nirK
Synonyms:	nir

Organism

Alcaligenes faecalis

Taxonomic identifier

511 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Betaproteobacteria › Burkholderiales › Alcaligenaceae › Alcaligenes

Protein attributes

Sequence length	376 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Catalytic activity	Nitric oxide + H₂O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H⁺.
Cofactor	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.
Pathway	Nitrogen metabolism; nitrate reduction (denitrification); dinitrogen from nitrate: step 2/4.
Subunit structure	Homotrimer.
Subcellular location	Periplasm.
Induction	Under anaerobic growth conditions and by nitrite.
Domain	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.
Post-translational modification	Predicted to be exported by the Tat system. The position of the signal peptide cleavage has been experimentally proven.
Sequence similarities	Belongs to the multicopper oxidase family. Contains 2 plastocyanin-like domains.

Ontologies

Keywords
Biological process	Nitrate assimilation
Cellular component	Periplasm
Domain	Repeat Signal
Ligand	Copper FAD Flavoprotein Metal-binding
Molecular function	Oxidoreductase
PTM	Pyrrolidone carboxylic acid
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological_process	denitrification pathway Inferred from electronic annotation. Source: UniProtKB-UniPathway nitrate assimilation Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	periplasmic space Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	copper ion binding Inferred from electronic annotation. Source: InterPro nitrite reductase (NO-forming) activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Signal peptide

1 – 33

Tat-type signal Ref.1

Chain

34 – 376

343

Copper-containing nitrite reductase

PRO_0000002987

Regions

Domain

34 – 211

178

Plastocyanin-like 1

Domain

212 – 376

165

Plastocyanin-like 2

Sites

Metal binding

131

Copper 1; type 1 Ref.2

Metal binding

136

Copper 2; type 2

Metal binding

171

Copper 2; type 2

Metal binding

172

Copper 1; type 1

Metal binding

181

Copper 1; type 1

Metal binding

186

Copper 1; type 1

Metal binding

342

Copper 2; type 2 Ref.2

Amino acid modifications

Modified residue

Pyrrolidone carboxylic acid

Experimental info

Mutagenesis

171

H → K: Loses nitrite-reducing activity.

Mutagenesis

186

M → E: Contains only a type II copper atom and fails to catalyze the reduction of nitrite.

Secondary structure

376

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P38501 [UniParc].

Last modified October 1, 1994. Version 1.
Checksum: 0AD918988301BF29
Show »

FASTA

376

40,332

        10         20         30         40         50         60 
MAEQMQISRR TILAGAALAG ALAPVLATTS AWGQGAVRKA TAAEIAALPR QKVELVDPPF 

        70         80         90        100        110        120 
VHAHSQVAEG GPKVVEFTMV IEEKKIVIDD AGTEVHAMAF NGTVPGPLMV VHQDDYLELT 

       130        140        150        160        170        180 
LINPETNTLM HNIDFHAATG ALGGGGLTEI NPGEKTILRF KATKPGVFVY HCAPPGMVPW 

       190        200        210        220        230        240 
HVVSGMNGAI MVLPREGLHD GKGKALTYDK IYYVGEQDFY VPRDENGKYK KYEAPGDAYE 

       250        260        270        280        290        300 
DTVKVMRTLT PTHVVFNGAV GALTGDKAMT AAVGEKVLIV HSQANRDTRP HLIGGHGDYV 

       310        320        330        340        350        360 
WATGKFNTPP DVDQETWFIP GGAAGAAFYT FQQPGIYAYV NHNLIEAFEL GAAAHFKVTG 

       370 
EWNDDLMTSV LAPSGT

« Hide

References

[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).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

D13155 Genomic DNA. Translation: BAA02440.1.

PIR

I39582.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

P38501.

SMR

P38501. Positions 40-376.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Enzyme and pathway databases

SABIO-RK

P38501.

UniPathway

UPA00652; UER00707.

Family and domain databases

Gene3D

2.60.40.420. 2 hits.

InterPro

IPR001117. Cu-oxidase.
IPR011707. Cu-oxidase_3.
IPR008972. Cupredoxin.
IPR001287. NO2-reductase_Cu.
IPR006311. TAT_signal.
[Graphical view]

Pfam

PF00394. Cu-oxidase. 1 hit.
PF07732. Cu-oxidase_3. 1 hit.
[Graphical view]

PRINTS

PR00695. CUNO2RDTASE.

SUPFAM

SSF49503. Cupredoxin. 2 hits.

TIGRFAMs

TIGR02376. Cu_nitrite_red. 1 hit.

PROSITE

PS51318. TAT. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P38501.

Entry information

Entry name

NIR_ALCFA

Accession

Primary (citable) accession number: P38501

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1994
Last sequence update:	October 1, 1994
Last modified:	April 3, 2013
This is version 97 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Amino acid modifications

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protocols and materials databases

Enzyme and pathway databases

Family and domain databases

Other

Entry information

Relevant documents