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Protein
Submitted name:

Copper-containing nitrite reductase

Gene

nir

Organism
Alcaligenes xylosoxydans xylosoxydans (Achromobacter xylosoxidans)
Status
Unreviewed-Annotation score: Annotation score: 2 out of 5-Experimental evidence at protein leveli

Functioni

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi113 – 1131Copper 1; via pros nitrogenCombined sources
Metal bindingi118 – 1181Copper 2; via tele nitrogenCombined sources
Metal bindingi118 – 1181Zinc 1; via tele nitrogenCombined sources
Metal bindingi153 – 1531Copper 2; via tele nitrogenCombined sources
Metal bindingi153 – 1531Zinc 1; via tele nitrogenCombined sources
Metal bindingi154 – 1541Copper 1Combined sources
Metal bindingi163 – 1631Copper 1; via pros nitrogenCombined sources
Metal bindingi168 – 1681Copper 1Combined sources
Metal bindingi189 – 1891Zinc 2; via tele nitrogenCombined sources
Metal bindingi191 – 1911Zinc 2Combined sources
Metal bindingi324 – 3241Copper 1; via tele nitrogenCombined sources
Metal bindingi324 – 3241Copper 2; via tele nitrogenCombined sources
Metal bindingi324 – 3241Zinc 1; via tele nitrogenCombined sources

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

OxidoreductaseImported

Keywords - Ligandi

CopperCombined sources, Metal-bindingCombined sources, ZincCombined sources

Enzyme and pathway databases

BRENDAi1.7.2.1. 238.

Names & Taxonomyi

Protein namesi
Submitted name:
Copper-containing nitrite reductaseImported (EC:1.7.2.1Imported)
Submitted name:
Dissimilatory copper-containing nitrite reductaseImported
Submitted name:
Nitrite Reductase (NiR)Imported
Gene namesi
Name:nirImported
Synonyms:nirKImported
ORF Names:ERS451415_02178Imported
OrganismiAlcaligenes xylosoxydans xylosoxydans (Achromobacter xylosoxidans)Imported
Taxonomic identifieri85698 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesAlcaligenaceaeAchromobacter
Proteomesi
  • UP000059657 Componenti: Chromosome 1

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2424Sequence analysisAdd
BLAST
Chaini25 – 360336Sequence analysisPRO_5007697050Add
BLAST

Interactioni

Protein-protein interaction databases

DIPiDIP-59300N.
STRINGi1003200.AXXA_20893.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1BQ5X-ray2.05A19-360[»]
1GS6X-ray2.20X25-360[»]
1GS7X-ray1.85A25-360[»]
1GS8X-ray1.90A25-360[»]
1HAUX-ray1.90A25-360[»]
1HAWX-ray1.90A25-360[»]
1NDTX-ray2.10A26-359[»]
1OE1X-ray1.04A26-360[»]
1OE2X-ray1.12A26-360[»]
1OE3X-ray1.15A26-360[»]
1WA0X-ray1.60X25-360[»]
1WA1X-ray1.65X25-360[»]
1WA2X-ray1.72X25-360[»]
1WAEX-ray1.95A25-360[»]
2BO0X-ray1.35A26-360[»]
2BP0X-ray1.90A/B25-360[»]
2BP8X-ray1.90A/B25-360[»]
2JFCX-ray2.40A/B/C/D/E/F26-360[»]
2VM3X-ray1.80A25-360[»]
2VM4X-ray1.90A25-360[»]
2VMJX-ray2.50A25-154[»]
A168-360[»]
2VN3X-ray2.35A25-360[»]
2VW4X-ray1.90A/B25-360[»]
2VW6X-ray1.90A/B25-360[»]
2VW7X-ray1.90A/B25-360[»]
2XWZX-ray2.34A/B/C/D/E/F26-360[»]
2XX0X-ray1.46A/B26-360[»]
2XX1X-ray3.00A/B/C/D/E/F26-360[»]
2XXFX-ray1.50A/B26-360[»]
2XXGX-ray1.60A/C26-360[»]
2ZONX-ray1.70A/B/C25-360[»]
4CSPX-ray1.70A/F26-360[»]
4CSZX-ray1.75A26-360[»]
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini69 – 177109Plastocyanin-likeInterPro annotationAdd
BLAST
Domaini193 – 344152Plastocyanin-likeInterPro annotationAdd
BLAST

Keywords - Domaini

SignalSequence analysis

Phylogenomic databases

eggNOGiENOG4105CEI. Bacteria.
COG2132. LUCA.

Family and domain databases

Gene3Di2.60.40.420. 2 hits.
InterProiIPR001117. Cu-oxidase.
IPR011707. Cu-oxidase_3.
IPR008972. Cupredoxin.
IPR001287. NO2-reductase_Cu.
[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.

Sequencei

Sequence statusi: Complete.

O68601-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNALRPTLLA AALAFTMAAG TAWAQDADKL PHTKVTLVAP PQVHPHEQAT
60 70 80 90 100
KSGPKVVEFT MTIEEKKMVI DDKGTTLQAM TFNGSMPGPT LVVHEGDYVQ
110 120 130 140 150
LTLVNPATNA MPHNVDFHGA TGALGGAKLT NVNPGEQATL RFKADRSGTF
160 170 180 190 200
VYHCAPEGMV PWHVVSGMSG TLMVLPRDGL KDPQGKPLHY DRAYTIGEFD
210 220 230 240 250
LYIPKGPDGK YKDYATLAES YGDTVQVMRT LTPSHIVFNG KVGALTGANA
260 270 280 290 300
LTAKVGETVL LIHSQANRDT RPHLIGGHGD WVWETGKFAN PPQRDLETWF
310 320 330 340 350
IRGGSAGAAL YTFKQPGVYA YLNHNLIEAF ELGAAGHIKV EGKWNDDLMK
360
QIKAPAPIPR
Length:360
Mass (Da):38,939
Last modified:August 1, 1998 - v1
Checksum:i3748B5BD3BFF44E7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF051831 Genomic DNA. Translation: AAC05831.1.
AB013078 Genomic DNA. Translation: BAA33678.1.
LN831029 Genomic DNA. Translation: CKH22667.1.
PIRiJE0215.
JG0170.
RefSeqiWP_006384283.1. NZ_LNCS01000026.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF051831 Genomic DNA. Translation: AAC05831.1.
AB013078 Genomic DNA. Translation: BAA33678.1.
LN831029 Genomic DNA. Translation: CKH22667.1.
PIRiJE0215.
JG0170.
RefSeqiWP_006384283.1. NZ_LNCS01000026.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1BQ5X-ray2.05A19-360[»]
1GS6X-ray2.20X25-360[»]
1GS7X-ray1.85A25-360[»]
1GS8X-ray1.90A25-360[»]
1HAUX-ray1.90A25-360[»]
1HAWX-ray1.90A25-360[»]
1NDTX-ray2.10A26-359[»]
1OE1X-ray1.04A26-360[»]
1OE2X-ray1.12A26-360[»]
1OE3X-ray1.15A26-360[»]
1WA0X-ray1.60X25-360[»]
1WA1X-ray1.65X25-360[»]
1WA2X-ray1.72X25-360[»]
1WAEX-ray1.95A25-360[»]
2BO0X-ray1.35A26-360[»]
2BP0X-ray1.90A/B25-360[»]
2BP8X-ray1.90A/B25-360[»]
2JFCX-ray2.40A/B/C/D/E/F26-360[»]
2VM3X-ray1.80A25-360[»]
2VM4X-ray1.90A25-360[»]
2VMJX-ray2.50A25-154[»]
A168-360[»]
2VN3X-ray2.35A25-360[»]
2VW4X-ray1.90A/B25-360[»]
2VW6X-ray1.90A/B25-360[»]
2VW7X-ray1.90A/B25-360[»]
2XWZX-ray2.34A/B/C/D/E/F26-360[»]
2XX0X-ray1.46A/B26-360[»]
2XX1X-ray3.00A/B/C/D/E/F26-360[»]
2XXFX-ray1.50A/B26-360[»]
2XXGX-ray1.60A/C26-360[»]
2ZONX-ray1.70A/B/C25-360[»]
4CSPX-ray1.70A/F26-360[»]
4CSZX-ray1.75A26-360[»]
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-59300N.
STRINGi1003200.AXXA_20893.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Phylogenomic databases

eggNOGiENOG4105CEI. Bacteria.
COG2132. LUCA.

Enzyme and pathway databases

BRENDAi1.7.2.1. 238.

Family and domain databases

Gene3Di2.60.40.420. 2 hits.
InterProiIPR001117. Cu-oxidase.
IPR011707. Cu-oxidase_3.
IPR008972. Cupredoxin.
IPR001287. NO2-reductase_Cu.
[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.
ProtoNetiSearch...

Publicationsi

  1. "Type 1 Cu structure of blue nitrite reductase from Alcaligenes xylosoxidans GIFU 1051 at 2.05 A resolution: comparison of blue and green nitrite reductases."
    Inoue T., Gotowda M., Deligeer, Kataoka K., Yamaguchi K., Suzuki S., Watanabe H., Gohow M., Kai Y.
    J. Biochem. 124:876-879(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) OF 19-360 IN COMPLEX WITH COPPER.
  2. "X-ray structure of a blue-copper nitrite reductase in two crystal forms. The nature of the copper sites, mode of substrate binding and recognition by redox partner."
    Dodd F.E., Van Beeumen J., Eady R.R., Hasnain S.S.
    J. Mol. Biol. 282:369-382(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) OF 26-359 IN COMPLEX WITH COPPER.
  3. "Cloning and Expression of Copper Nitrite Reductase Gene from Alcaligenes xylosoxidans GIFU1051."
    Kataoka K., Furusawa H., Yamaguchi K., Suzuki S.
    Submitted (APR-1998) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE.
    Strain: GIFU1051Imported.
  4. "Cloning, sequencing, and transcriptional studies of the gene encoding copper-containing nitrite reductase from Alcaligenes xylosoxidans NCIMB 11015."
    Suzuki E., Horikoshi N., Kohzuma T.
    Biochem. Biophys. Res. Commun. 255:427-431(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE.
    Strain: NCIMB11015Imported.
  5. "X-ray structure of a blue copper nitrite reductase at high pH and in copper-free form at 1.9 A resolution."
    Ellis M.J., Dodd F.E., Strange R.W., Prudencio M., Sawers G., Eady R.R., Hasnain S.S.
    Acta Crystallogr. D 57:1110-1118(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) OF 25-360 IN COMPLEX WITH COPPER.
  6. "Biochemical and crystallographic studies of the Met144Ala, Asp92Asn and His254Phe mutants of the nitrite reductase from Alcaligenes xylosoxidans provide insight into the enzyme mechanism."
    Ellis M.J., Prudencio M., Dodd F.E., Strange R.W., Sawers G., Eady R.R., Hasnain S.S.
    J. Mol. Biol. 316:51-64(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) OF 25-360 IN COMPLEX WITH COPPER AND ZINC.
  7. "Atomic resolution structures of native copper nitrite reductase from Alcaligenes xylosoxidans and the active site mutant Asp92Glu."
    Ellis M.J., Dodd F.E., Sawers G., Eady R.R., Hasnain S.S.
    J. Mol. Biol. 328:429-438(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.04 ANGSTROMS) OF 26-360 IN COMPLEX WITH COPPER.
  8. "Insights into redox partner interactions and substrate binding in nitrite reductase from Alcaligenes xylosoxidans: crystal structures of the Trp138His and His313Gln mutants."
    Barrett M.L., Harris R.L., Antonyuk S., Hough M.A., Ellis M.J., Sawers G., Eady R.R., Hasnain S.S.
    Biochemistry 43:16311-16319(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) OF 25-360 IN COMPLEX WITH COPPER AND ZINC.
  9. "Observation of an unprecedented Cu Bis-His site: crystal structure of the H129V mutant of nitrite reductase."
    Ellis M.J., Antonyuk S.V., Strange R.W., Sawers G., Eady R.R., Hasnain S.S.
    Inorg. Chem. 43:7591-7593(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF 25-360 IN COMPLEX WITH COPPER AND ZINC.
  10. "High resolution structural studies of mutants provide insights into catalysis and electron transfer processes in copper nitrite reductase."
    Hough M.A., Ellis M.J., Antonyuk S., Strange R.W., Sawers G., Eady R.R., Samar Hasnain S.
    J. Mol. Biol. 350:300-309(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.35 ANGSTROMS) OF 26-360 IN COMPLEX WITH COPPER AND ZINC.
  11. "The structure of the Met144Leu mutant of copper nitrite reductase from Alcaligenes xylosoxidans provides the first glimpse of a protein-protein complex with azurin II."
    Paraskevopoulos K., Hough M.A., Sawers R.G., Eady R.R., Hasnain S.S.
    J. Biol. Inorg. Chem. 12:789-796(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS) OF 26-360 IN COMPLEX WITH COPPER.
  12. "Identification of the proton channel to the active site type 2 Cu center of nitrite reductase: structural and enzymatic properties of the His254Phe and Asn90Ser mutants."
    Hough M.A., Eady R.R., Hasnain S.S.
    Biochemistry 47:13547-13553(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) OF 26-360 IN COMPLEX WITH COPPER AND ZINC.
  13. "The importance of the long type 1 copper-binding loop of nitrite reductase for structure and function."
    Sato K., Firbank S.J., Li C., Banfield M.J., Dennison C.
    Chemistry 14:5820-5828(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS) OF 25-360 IN COMPLEX WITH COPPER AND ZINC.
  14. "Crystallography with online optical and X-ray absorption spectroscopies demonstrates an ordered mechanism in copper nitrite reductase."
    Hough M.A., Antonyuk S.V., Strange R.W., Eady R.R., Hasnain S.S.
    J. Mol. Biol. 378:353-361(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF 25-360 IN COMPLEX WITH COPPER AND ZINC.
  15. "On-line optical and X-ray spectroscopies with crystallography: an integrated approach for determining metalloprotein structures in functionally well defined states."
    Ellis M.J., Buffey S.G., Hough M.A., Hasnain S.S.
    J. Synchrotron Radiat. 15:433-439(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) OF 25-360 IN COMPLEX WITH COPPER AND ZINC.
  16. "Structural basis of inter-protein electron transfer for nitrite reduction in denitrification."
    Nojiri M., Koteishi H., Nakagami T., Kobayashi K., Inoue T., Yamaguchi K., Suzuki S.
    Nature 462:117-120(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) OF 25-360 IN COMPLEX WITH COPPER.
  17. "Proton-coupled electron transfer in the catalytic cycle of Alcaligenes xylosoxidans copper-dependent nitrite reductase."
    Leferink N.G., Han C., Antonyuk S.V., Heyes D.J., Rigby S.E., Hough M.A., Eady R.R., Scrutton N.S., Hasnain S.S.
    Biochemistry 50:4121-4131(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.46 ANGSTROMS) OF 26-360 IN COMPLEX WITH COPPER AND ZINC.
  18. "Impact of residues remote from the catalytic centre on enzyme catalysis of copper nitrite reductase."
    Leferink N.G., Antonyuk S.V., Houwman J.A., Scrutton N.S., Eady R.R., Hasnain S.S.
    Nat. Commun. 5:4395-4395(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) OF 26-360 IN COMPLEX WITH COPPER AND ZINC.
  19. Murphy D.
    Submitted (MAR-2015) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE.
    Strain: NCTC10807Imported.

Entry informationi

Entry nameiO68601_ALCXX
AccessioniPrimary (citable) accession number: O68601
Entry historyi
Integrated into UniProtKB/TrEMBL: August 1, 1998
Last sequence update: August 1, 1998
Last modified: July 6, 2016
This is version 112 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

3D-structureCombined sources, Complete proteomeImported

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.