Reviewed, UniProtKB/Swiss-Prot P25006 (NIR_ACHCY)

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

Organism

Achromobacter cycloclastes

Taxonomic identifier

223 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Betaproteobacteria › Burkholderiales › Alcaligenaceae › Achromobacter

Protein attributes

Sequence length	378 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 Cu+ ion. Binds 1 Cu2+ ion. FAD.
Pathway	Nitrogen metabolism; nitrate reduction (denitrification); dinitrogen from nitrate: step 2/4.
Subunit structure	Homotrimer.
Subcellular location	Periplasm.
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
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological process	nitrate assimilation Inferred from electronic annotation. Source: UniProtKB-KW oxidation reduction 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: UniProtKB-KW 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 – 38

38

Tat-type signal Ref.2

Chain

39 – 378

340

Copper-containing nitrite reductase

PRO_0000002986

Regions

Domain

39 – 213

175

Plastocyanin-like 1

Domain

214 – 378

165

Plastocyanin-like 2

Sites

Metal binding

133

1

Copper 1; type 1

Metal binding

138

1

Copper 2; type 2

Metal binding

173

1

Copper 2; type 2

Metal binding

174

1

Copper 1; type 1

Metal binding

183

1

Copper 1; type 1

Metal binding

188

1

Copper 1; type 1

Metal binding

344

1

Copper 2; type 2

Secondary structure

1

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378

Helix Strand Turn

Details...

Helix

47 – 49

3

Beta strand

52 – 54

3

Beta strand

71 – 73

3

Beta strand

76 – 89

14

Beta strand

96 – 102

7

Beta strand

105 – 107

3

Beta strand

110 – 114

5

Beta strand

118 – 125

8

Helix

143 – 149

7

Beta strand

156 – 163

8

Beta strand

168 – 173

6

Helix

180 – 185

6

Beta strand

189 – 195

7

Beta strand

211 – 221

11

Helix

237 – 249

13

Beta strand

254 – 258

5

Turn

262 – 265

4

Helix

267 – 269

3

Beta strand

271 – 274

4

Beta strand

278 – 288

11

Beta strand

292 – 295

4

Beta strand

299 – 303

5

Beta strand

313 – 317

5

Beta strand

325 – 332

8

Beta strand

337 – 345

9

Helix

346 – 350

5

Beta strand

355 – 362

8

Turn

366 – 368

3

Beta strand

369 – 376

8

Sequences

	Sequence		Length	Mass (Da)
	P25006-1 [UniParc]. Last modified November 1, 1997. Version 2. Checksum: A70B52B814090EA5	FASTA	378	40,771
	10 20 30 40 50 60 MTEQLQMTRR TMLAGAALAG AVAPLLHTAQ AHAAGAAAAA GAAPVDISTL PRVKVDLVKP 70 80 90 100 110 120 PFVHAHDQVA KTGPRVVEFT MTIEEKKLVI DREGTEIHAM TFNGSVPGPL MVVHENDYVE 130 140 150 160 170 180 LRLINPDTNT LLHNIDFHAA TGALGGGALT QVNPGEETTL RFKATKPGVF VYHCAPEGMV 190 200 210 220 230 240 PWHVTSGMNG AIMVLPRDGL KDEKGQPLTY DKIYYVGEQD FYVPKDEAGN YKKYETPGEA 250 260 270 280 290 300 YEDAVKAMRT LTPTHIVFNG AVGALTGDHA LTAAVGERVL VVHSQANRDT RPHLIGGHGD 310 320 330 340 350 360 YVWATGKFRN PPDLDQETWL IPGGTAGAAF YTFRQPGVYA YVNHNLIEAF ELGAAGHFKV 370 TGEWNDDLMT SVVKPASM

References

[1]	"Cloning, characterization, and expression of the nitric oxide-generating nitrite reductase and of the blue copper protein genes of Achromobacter cycloclastes." Chen J.-Y., Chang W.-C., Chang T., Chang W.-C., Liu M.-Y., Payne W.J., le Gall J. Biochem. Biophys. Res. Commun. 219:423-428(1996) [PubMed: 8605003] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 21921 / IAM 1013.
[2]	"Amino acid sequence of nitrite reductase: a copper protein from Achromobacter cycloclastes." Fenderson F.F., Kumar S., Adman E.T., Liu M.-Y., Payne W.J., le Gall J. Biochemistry 30:7180-7185(1991) [PubMed: 1830217] [Abstract] Cited for: PROTEIN SEQUENCE OF 39-378. Strain: ATCC 21921 / IAM 1013.
[3]	"The 2.3-A X-ray structure of nitrite reductase from Achromobacter cycloclastes." Godden J.W., Turley S., Teller D.C., Adman E.T., Liu M.-Y., Payne W.J., le Gall J. Science 253:438-442(1991) [PubMed: 1862344] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
[4]	"The structure of copper-nitrite reductase from Achromobacter cycloclastes at five pH values, with NO2-bound and with type II copper depleted." Adman E.T., Godden J.W., Turley S. J. Biol. Chem. 270:27458-27474(1995) [PubMed: 7499203] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

Z48635 Genomic DNA. Translation: CAA88564.1.

PIR

JC4648.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1KCB	X-ray	1.65	A	39-378	[»]
1NIA	X-ray	2.50	A/B/C	39-378	[»]
1NIB	X-ray	2.70	A/B/C	39-378	[»]
1NIC	X-ray	1.90	A	39-378	[»]
1NID	X-ray	2.20	A	39-378	[»]
1NIE	X-ray	1.90	A	39-378	[»]
1NIF	X-ray	1.70	A	39-378	[»]
1RZP	X-ray	1.90	A/B/C	39-373	[»]
1RZQ	X-ray	2.20	A/B/C	39-373	[»]
2AVF	X-ray	2.60	A/B/C/D/E/F	39-367	[»]
2BW4	X-ray	0.90	A	39-378	[»]
2BW5	X-ray	1.12	A	39-378	[»]
2BWD	X-ray	1.15	A	39-378	[»]
2BWI	X-ray	1.10	A	39-378	[»]
2NRD	X-ray	2.10	A	39-378	[»]

ModBase

Search...

Enzyme and pathway databases

BRENDA

1.7.2.1. 258578.

Family and domain databases

InterPro

IPR001117. Cu-oxidase.
IPR011707. Cu-oxidase_3.
IPR001287. Cu_NO2-reductase_N.
IPR008972. Cupredoxin.
IPR012746. Nitrite_red_Cu.
IPR006311. Tat.
IPR017909. Twin_arg_translocation_Tat.
[Graphical view]

Gene3D

G3DSA:2.60.40.420. Cupredoxin. 2 hits.

Pfam

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

PRINTS

PR00695. CUNO2RDTASE.

ProDom

PD001235. Copper_blue_sub. 1 hit.
[Graphical view] [Entries sharing at least one domain]

TIGRFAMs

TIGR02376. Cu_nitrite_red. 1 hit.
TIGR01409. TAT_signal_seq. 1 hit.

PROSITE

PS51318. TAT. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

NIR_ACHCY

Accession

Primary (citable) accession number: P25006

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 1, 1992
Last sequence update:	November 1, 1997
Last modified:	June 16, 2009
This is version 78 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)