Q53239 (NIR_RHOS5) Reviewed, UniProtKB/Swiss-Prot

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
Ordered Locus Names:	Rsph17025_1595

Organism

Rhodobacter sphaeroides (strain ATCC 17025 / ATH 2.4.3) [Complete proteome] [HAMAP]

Taxonomic identifier

349102 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Alphaproteobacteria › Rhodobacterales › Rhodobacteraceae › Rhodobacter › Rhodobacter sphaeroides

Protein attributes

Sequence length	374 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 By similarity.
Subcellular location	Periplasm By similarity.
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 not 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 Complete proteome
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 – 31

31

Tat-type signal Potential

Chain

32 – 374

343

Copper-containing nitrite reductase

PRO_0000002992

Regions

Domain

93 – 189

97

Plastocyanin-like 1

Domain

254 – 355

102

Plastocyanin-like 2

Sites

Metal binding

126

1

Copper 1; type 1 By similarity

Metal binding

131

1

Copper 2; type 2 By similarity

Metal binding

166

1

Copper 2; type 2 By similarity

Metal binding

167

1

Copper 1; type 1 By similarity

Metal binding

177

1

Copper 1; type 1 By similarity

Metal binding

182

1

Copper 1; type 1 By similarity

Metal binding

338

1

Copper 2; type 2 By similarity

Experimental info

Sequence conflict

27

1

E → Q in AAB05767. Ref.1

Sequence conflict

230

1

D → T in AAB05767. Ref.1

Sequence conflict

281

1

N → K in AAB05767. Ref.1

Sequence conflict

319

1

S → T in AAB05767. Ref.1

Sequence conflict

351

1

H → S in AAB05767. Ref.1

Sequence conflict

367 – 368

2

VA → WP in AAB05767. Ref.1

Secondary structure

1

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374

Helix Strand Turn

Details...

Beta strand

46 – 48

3

Beta strand

65 – 67

3

Beta strand

70 – 85

16

Beta strand

88 – 95

8

Beta strand

98 – 100

3

Beta strand

103 – 107

5

Beta strand

111 – 118

8

Helix

136 – 142

7

Beta strand

149 – 156

8

Beta strand

161 – 166

6

Helix

173 – 179

7

Beta strand

183 – 189

7

Beta strand

205 – 215

11

Beta strand

223 – 225

3

Helix

231 – 242

12

Turn

243 – 245

3

Beta strand

248 – 252

5

Turn

256 – 259

4

Helix

261 – 263

3

Beta strand

265 – 268

4

Beta strand

272 – 282

11

Beta strand

286 – 289

4

Beta strand

293 – 297

5

Beta strand

307 – 312

6

Beta strand

319 – 326

8

Beta strand

331 – 339

9

Helix

340 – 344

5

Beta strand

349 – 356

8

Turn

360 – 362

3

Beta strand

363 – 371

9

Sequences

	Sequence		Length	Mass (Da)
	Q53239 [UniParc]. Last modified October 23, 2007. Version 2. Checksum: BD0FACA94A991F3B	FASTA	374	40,232
	10 20 30 40 50 60 MFTRRAALVG AAALASAPLV IRTAGAEEAP AQLASAAPVD LSNLPRVKHT LVPPPFAHAH 70 80 90 100 110 120 EQVAASGPVI NEFEMRIIEK EVQLDEDAYL QAMTFDGSIP GPLMIVHEGD YVELTLINPP 130 140 150 160 170 180 ENTMPHNIDF HAATGALGGG GLTLINPGEK VVLRFKATRA GAFVYHCAPG GPMIPWHVVS 190 200 210 220 230 240 GMAGCIMVLP RDGLKDHEGK PVRYDTVYYI GESDHYIPKD EDGTYMRFSD PSEGYEDMVA 250 260 270 280 290 300 VMDTLIPSHI VFNGAVGALT GEGALKAKVG DNVLFVHSQP NRDSRPHLIG GHGDLVWETG 310 320 330 340 350 360 KFHNAPERDL ETWFIRGGSA GAALYKFLQP GVYAYVNHNL IEAVHKGATA HVLVEGEWDN 370 DLMEQVVAPV GLTG

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Characterization and regulation of the gene encoding nitrite reductase in Rhodobacter sphaeroides 2.4.3." Tosques I.E., Kwiatkowski A.V., Shi J., Shapleigh J.P. J. Bacteriol. 179:1090-1095(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Complete sequence of chromosome of Rhodobacter sphaeroides ATCC 17025." US DOE Joint Genome Institute Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S., Chertkov O., Brettin T., Bruce D., Han C., Schmutz J., Larimer F., Land M. , Hauser L., Kyrpides N., Kim E., Richardson P., Mackenzie C., Choudhary M., Donohue T.J., Kaplan S. Submitted (APR-2007) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 17025 / ATH 2.4.3.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U62291 Genomic DNA. Translation: AAB05767.1.
CP000661 Genomic DNA. Translation: ABP70488.1.

RefSeq

YP_001167793.1. NC_009428.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1MZY	X-ray	1.46	A	39-371	[»]
1MZZ	X-ray	2.00	A/B/C	39-371	[»]
1N70	X-ray	1.60	A	41-374	[»]
1ZV2	X-ray	1.74	A	44-371	[»]
2A3T	X-ray	1.85	A	44-371	[»]
2DWS	X-ray	1.85	A	44-371	[»]
2DWT	X-ray	1.90	A	44-372	[»]
2DY2	X-ray	2.26	A	44-372	[»]

ProteinModelPortal

Q53239.

SMR

Q53239. Positions 44-372.

ModBase

Search...

Protein-protein interaction databases

STRING

349102.Rsph17025_1595.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

ABP70488; ABP70488; Rsph17025_1595.

GeneID

5082406.

KEGG

rsq:Rsph17025_1595.

PATRIC

23161440. VBIRhoSph94549_1644.

Organism-specific databases

CMR

Search...

Phylogenomic databases

eggNOG

COG2132.

HOGENOM

HOG000217143.

KO

K00368.

OMA

HIVFNGA.

ProtClustDB

CLSK891937.

Enzyme and pathway databases

BioCyc

RSPH349102:GHE1-2922-MONOMER.

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

Q53239.

Entry information

Entry name

NIR_RHOS5

Accession

Primary (citable) accession number: Q53239
Secondary accession number(s): A4WSX4

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	October 23, 2007
Last modified:	May 1, 2013
This is version 93 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program