P81445 (NIR_ALCXX) 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

Organism

Alcaligenes xylosoxydans xylosoxydans (Achromobacter xylosoxidans)

Taxonomic identifier

85698 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Betaproteobacteria › Burkholderiales › Alcaligenaceae › Achromobacter

Protein attributes

Sequence length	330 AA.
Sequence status	Complete.
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. Binds 1 Cu+ ion. The Cu+ ion is bound within a single monomer. FAD.
Pathway	Nitrogen metabolism; nitrate reduction (denitrification); dinitrogen from nitrate: step 2/4.
Subunit structure	Homotrimer.
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.
Sequence similarities	Belongs to the multicopper oxidase family. Contains 2 plastocyanin-like domains.

Ontologies

Keywords
Biological process	Nitrate assimilation
Cellular component	Periplasm
Domain	Repeat
Ligand	Copper FAD Flavoprotein Metal-binding
Molecular function	Oxidoreductase
Technical term	3D-structure
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
	Chain	1 – 330	330	Copper-containing nitrite reductase		PRO_0000085586
Regions
	Domain	1 – 165	165	Plastocyanin-like 1
	Domain	166 – 330	165	Plastocyanin-like 2
Sites
	Metal binding	85	1	Copper 1; type 1
	Metal binding	90	1	Copper 2; type 2
	Metal binding	125	1	Copper 2; type 2
	Metal binding	126	1	Copper 1; type 1
	Metal binding	135	1	Copper 1; type 1
	Metal binding	140	1	Copper 1; type 1
	Metal binding	296	1	Copper 2; type 2

Sequences

	Sequence		Length	Mass (Da)
	P81445 [UniParc]. Last modified November 1, 1998. Version 1. Checksum: E2C38C3A2CEBFCE8	FASTA	330	34,413
	10 20 30 40 50 60 GLPRVAVDLV APPLVHPHSQ VAAGAPKVVQ FRMSIEEKKM VADDDGTTAQ AMTFNGSVPG 70 80 90 100 110 120 PTLVVHEGDY IELTLVNPAT NSMPHNVDFH AATGALGGAG LTQVVPGQEA VLRFKADRSG 130 140 150 160 170 180 TFVYHCAPAG MVPWHVVSGM NGALMVLPRD GLRDAAGAAL AYDRVYTIGE SDLYVPKAAD 190 200 210 220 230 240 GNYSDYPALA SAYADTVAVM RTLTPSHAVF NGAVGALTGA NALTAAVGES VLIIHSQANR 250 260 270 280 290 300 DSRPHLIGGH GDWVWTTGKF ANPPQLNMET WFIPGGSAAA ALYTFKQPGT YAYLSHNLIE 310 320 330 AMELGAAAQA SVEGQWDDDL MTSVAAPGPA

References

[1]	"Structures of a blue-copper nitrite reductase and its substrate-bound complex." Dodd F.E., Hasnain S.S., Abraham Z.H.L., Eady R.R., Smith B.E. Acta Crystallogr. D 53:406-418(1997) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS). Strain: LMG 1865 / NCIMB 11015 / Iwasaki.
[2]	"Purification and characterization of the dissimilatory nitrite reductase from Alcaligenes xylosoxidans subsp. xylosoxidans (N.C.I.M.B. 11015): evidence for the presence of both type 1 and type 2 copper centres." Abraham Z.H.L., Lowe D.J., Smith B.E. Biochem. J. 295:587-593(1993) [PubMed] [Europe PMC] [Abstract] Cited for: CHARACTERIZATION. Strain: LMG 1865 / NCIMB 11015 / Iwasaki.

Cross-references

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1NDR	X-ray	3.00	A/B/C	1-330	[»]
1NDS	X-ray	2.80	A/B/C	1-330	[»]

ProteinModelPortal

P81445.

SMR

P81445. Positions 2-329.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Enzyme and pathway databases

SABIO-RK

P81445.

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.
[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.

ProtoNet

Search...

Other

EvolutionaryTrace

P81445.

Entry information

Entry name

NIR_ALCXX

Accession

Primary (citable) accession number: P81445

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 11, 2002
Last sequence update:	November 1, 1998
Last modified:	April 3, 2013
This is version 68 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program