Dissimilatory copper-containing nitrite reductase - Alcaligenes xylosoxydans xylosoxydans

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O68601 (O68601_ALCXX) Unreviewed, UniProtKB/TrEMBL

Last modified September 21, 2011. Version 75. History...

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

Third-party data

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

Names and origin

Protein names

Submitted name:
Dissimilatory copper-containing nitrite reductase EMBL AAC05831.1

Submitted name:
Nitrite Reductase (NiR) EMBL BAA33678.1

Gene names

Name:

nir EMBL AAC05831.1

Organism

Alcaligenes xylosoxydans xylosoxydans (Achromobacter xylosoxidans) EMBL AAC05831.1

Taxonomic identifier

85698 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Betaproteobacteria › Burkholderiales › Alcaligenaceae › Achromobacter

Protein attributes

Sequence length	360 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

Ontologies

Keywords
Domain	Signal EMBL BAA33678.1
Technical term	3D-structure PDB 2ZON PDB 2BP8 PDB 2VM4 PDB 2XXG PDB 2XXF PDB 2VM3 PDB 2BP0 PDB 2XWZ PDB 1NDT PDB 2JFC PDB 1GS8 PDB 1GS7 PDB 1OE3 PDB 1GS6 PDB 1HAW PDB 1HAU PDB 1OE2 PDB 1WAE PDB 1OE1 PDB 1WA0 PDB 2BO0 PDB 2VMJ PDB 1BQ5 PDB 1WA2 PDB 1WA1 PDB 2XX1 PDB 2XX0 PDB 2VN3 PDB 2VW7 PDB 2VW4 PDB 2VW6
Gene Ontology (GO)
Biological process	nitrogen compound metabolic process Inferred from electronic annotation. Source: InterPro
Molecular function	copper ion binding Inferred from electronic annotation. Source: InterPro nitrite reductase (NO-forming) activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

26 – 360

335

Nitrite Reductase EMBL BAA33678.1

Sites

Metal binding

113

Copper 1; via pros nitrogen{EI10,EI11, EI12,EI13,EI14,EI15,EI17,EI18,EI19,EI2, EI20,EI21,EI24,EI25,EI26,EI29,EI3,EI30,EI31,EI32,EI34,EI35,EI4,EI7,EI8}

Metal binding

118

Copper 2; via tele nitrogen{EI10,EI11, EI12,EI14,EI15,EI18,EI19,EI2,EI20,EI21, EI24,EI25,EI26,EI29,EI3,EI31,EI32,EI35,EI4,EI7,EI8}

Metal binding

118

Zinc 1; via tele nitrogen PDB 1GS7 PDB 2BO0 PDB 2VMJ PDB 2JL3

Metal binding

153

Copper 2; via tele nitrogen{EI10,EI11, EI12,EI14,EI15,EI18,EI2,EI20,EI21,EI24, EI25,EI26,EI29,EI3,EI31,EI32,EI35,EI4,EI7,EI8}

Metal binding

153

Zinc 1; via tele nitrogen PDB 1GS7 PDB 2BO0 PDB 2VMJ PDB 2JL3

Metal binding

154

Copper 1{EI10,EI11,EI12,EI13,EI14,EI15, EI17,EI18,EI19,EI2,EI20,EI21,EI24,EI25, EI26,EI29,EI3,EI30,EI31,EI32,EI34,EI35,EI4,EI7,EI8}

Metal binding

163

Copper 1; via pros nitrogen{EI10,EI11, EI12,EI13,EI14,EI15,EI17,EI18,EI19,EI2, EI20,EI21,EI24,EI25,EI26,EI29,EI3,EI30,EI31,EI32,EI34,EI35,EI4,EI7,EI8}

Metal binding

168

Copper 1{EI10,EI12,EI13,EI14,EI17,EI18, EI19,EI2,EI20,EI21,EI24,EI25,EI26,EI29,EI30,EI31,EI32,EI34,EI35,EI4,EI7}

Metal binding

189

Zinc 2; via tele nitrogen{EI19,EI21,EI23, EI25,EI26,EI29,EI3,EI30,EI34,EI35,EI4,EI7,EI8}

Metal binding

191

Zinc 2 PDB 2BP8 PDB 2VM4 PDB 2VM3 PDB 2BP0 PDB 1WAE PDB 1WA0 PDB 2VMJ PDB 1WA2 PDB 1WA1 PDB 2VN3 PDB 2VW7 PDB 2JL3 PDB 2JL0

Metal binding

324

Copper 2; via tele nitrogen{EI10,EI11, EI12,EI14,EI15,EI18,EI19,EI2,EI20,EI21, EI24,EI25,EI26,EI29,EI3,EI35,EI4,EI7,EI8}

Metal binding

324

Zinc 1; via tele nitrogen PDB 1GS7 PDB 2BO0 PDB 2VMJ PDB 2JL3

Sequences

Sequence

Length

Mass (Da)

Tools

O68601 [UniParc].

Last modified August 1, 1998. Version 1.
Checksum: 3748B5BD3BFF44E7
Show »

FASTA

360

38,939

        10         20         30         40         50         60 
MNALRPTLLA AALAFTMAAG TAWAQDADKL PHTKVTLVAP PQVHPHEQAT KSGPKVVEFT 

        70         80         90        100        110        120 
MTIEEKKMVI DDKGTTLQAM TFNGSMPGPT LVVHEGDYVQ LTLVNPATNA MPHNVDFHGA 

       130        140        150        160        170        180 
TGALGGAKLT NVNPGEQATL RFKADRSGTF VYHCAPEGMV PWHVVSGMSG TLMVLPRDGL 

       190        200        210        220        230        240 
KDPQGKPLHY DRAYTIGEFD LYIPKGPDGK YKDYATLAES YGDTVQVMRT LTPSHIVFNG 

       250        260        270        280        290        300 
KVGALTGANA LTAKVGETVL LIHSQANRDT RPHLIGGHGD WVWETGKFAN PPQRDLETWF 

       310        320        330        340        350        360 
IRGGSAGAAL YTFKQPGVYA YLNHNLIEAF ELGAAGHIKV EGKWNDDLMK QIKAPAPIPR

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References

[1]	"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: 19890332] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) OF 25-360 IN COMPLEX WITH COPPER.
[2]	"The covalent structure of the blue copper-containing nitrite reductase from Achromobacter xylosoxidans." Vandenberghe I.H., Meyer T.E., Cusanovich M.A., Van Beeumen J.J. Biochem. Biophys. Res. Commun. 247:734-740(1998) [PubMed: 9647763] [Abstract] Cited for: PROTEIN SEQUENCE.
[3]	"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: 12691751] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.04 ANGSTROMS) OF 26-360 IN COMPLEX WITH COPPER.
[4]	"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: 11829502] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) OF 25-360 IN COMPLEX WITH COPPER AND ZINC.
[5]	"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: 21469743] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.46 ANGSTROMS) OF 26-360.
[6]	"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: 9735294] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) OF 26-359 IN COMPLEX WITH COPPER.
[7]	"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 Biol. Crystallogr. 57:1110-1118(2001) [PubMed: 11468394] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) OF 25-360 IN COMPLEX WITH COPPER.
[8]	"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: 15927201] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.35 ANGSTROMS) OF 26-360 IN COMPLEX WITH COPPER AND ZINC.
[9]	"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: 18353369] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF 25-360 IN COMPLEX WITH COPPER AND ZINC.
[10]	"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: 18491346] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS) OF 25-360 IN COMPLEX WITH COPPER AND ZINC.
[11]	"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: 19053252] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) OF 26-360.
[12]	"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: 15610025] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) OF 25-360 IN COMPLEX WITH COPPER AND ZINC.
[13]	"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: 17503096] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS) OF 26-360 IN COMPLEX WITH COPPER.
[14]	"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: 9792907] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) OF 19-360 IN COMPLEX WITH COPPER.
[15]	"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: 15554622] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF 25-360 IN COMPLEX WITH COPPER AND ZINC.
[16]	"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: 18728313] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) OF 25-360 IN COMPLEX WITH COPPER AND ZINC.
[17]	"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: 10049725] [Abstract] Cited for: NUCLEOTIDE SEQUENCE. Strain: NCIMB11015 EMBL AAC05831.1.
[18]	"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: GIFU1051 EMBL BAA33678.1.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AF051831 Genomic DNA. Translation: AAC05831.1.
AB013078 Genomic DNA. Translation: BAA33678.1.

PIR

JE0215.
JG0170.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1BQ5	X-ray	2.05	A	19-360	[»]
1GS6	X-ray	2.20	X	25-360	[»]
1GS7	X-ray	1.85	A	25-360	[»]
1GS8	X-ray	1.90	A	25-360	[»]
1HAU	X-ray	1.90	A	25-360	[»]
1HAW	X-ray	1.90	A	25-360	[»]
1NDT	X-ray	2.10	A	26-359	[»]
1OE1	X-ray	1.04	A	26-360	[»]
1OE2	X-ray	1.12	A	26-360	[»]
1OE3	X-ray	1.15	A	26-360	[»]
1WA0	X-ray	1.60	X	25-360	[»]
1WA1	X-ray	1.65	X	25-360	[»]
1WA2	X-ray	1.72	X	25-360	[»]
1WAE	X-ray	1.95	A	25-360	[»]
2BO0	X-ray	1.35	A	26-360	[»]
2BP0	X-ray	1.90	A/B	25-360	[»]
2BP8	X-ray	1.90	A/B	25-360	[»]
2JFC	X-ray	2.40	A/B/C/D/E/F	26-360	[»]
2VM3	X-ray	1.80	A	25-360	[»]
2VM4	X-ray	1.90	A	25-360	[»]
2VMJ	X-ray	2.50	A	25-360	[»]
2VN3	X-ray	2.35	A	25-360	[»]
2VW4	X-ray	1.90	A/B	25-360	[»]
2VW6	X-ray	1.90	A/B	25-360	[»]
2VW7	X-ray	1.90	A/B	25-360	[»]
2XWZ	X-ray	2.34	A/B/C/D/E/F	26-360	[»]
2XX0	X-ray	1.46	A/B	26-360	[»]
2XX1	X-ray	3.00	A/B/C/D/E/F	26-360	[»]
2XXF	X-ray	1.50	A/B	26-360	[»]
2XXG	X-ray	1.60	A/C	26-360	[»]
2ZON	X-ray	1.70	A/B/C	25-360	[»]

ProteinModelPortal

O68601.

SMR

O68601. Positions 25-360.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Family and domain databases

InterPro

IPR001117. Cu-oxidase.
IPR011707. Cu-oxidase_3.
IPR008972. Cupredoxin.
IPR001287. NO2-reductase_Cu.
[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.

SUPFAM

SSF49503. Cupredoxin. 2 hits.

TIGRFAMs

TIGR02376. Cu_nitrite_red. 1 hit.

ProtoNet

Search...

Entry information

Entry name

O68601_ALCXX

Accession

Primary (citable) accession number: O68601

Entry history

Integrated into UniProtKB/TrEMBL:	August 1, 1998
Last sequence update:	August 1, 1998
Last modified:	September 21, 2011
This is version 75 of the entry and version 1 of the sequence. [Complete history]

Entry status

Unreviewed (UniProtKB/TrEMBL)

Preferred order of sections

Names and origin

Protein attributes

Ontologies

Sequence annotation (Features)

Molecule processing

Sites

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protocols and materials databases

Family and domain databases

Entry information