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P72181 (NIRS_PARPN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 3, 2013. Version 91. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Nitrite reductase
EC=1.7.2.1
Alternative name(s):
Cytochrome cd1
Cytochrome oxidase
Hydroxylamine reductase
EC=1.7.99.1
Gene names
Name:nirS
OrganismParacoccus pantotrophus (Thiosphaera pantotropha)
Taxonomic identifier82367 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Alphaproteobacteria › Rhodobacterales › Rhodobacteraceae › Paracoccus

Protein attributes

Sequence length596 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Catalytic activity

Nitric oxide + H2O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H+.

NH3 + H2O + acceptor = hydroxylamine + reduced acceptor.

Cofactor

Binds 2 heme groups per subunit.

Subunit structure

Homodimer.

Subcellular location

Periplasm.

Sequence similarities

Contains 1 cytochrome c domain.

Ontologies

Keywords
   Biological processElectron transport
Transport
   Cellular componentPeriplasm
   DomainSignal
   LigandHeme
Iron
Metal-binding
   Molecular functionOxidoreductase
   Technical term3D-structure
Gene Ontology (GO)
   Biological_processelectron transport chain

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentperiplasmic space

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionelectron carrier activity

Inferred from electronic annotation. Source: InterPro

heme binding

Inferred from electronic annotation. Source: InterPro

hydroxylamine reductase activity

Inferred from electronic annotation. Source: EC

metal 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 keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 2929
Chain30 – 596567Nitrite reductase
PRO_0000006575

Regions

Domain77 – 16286Cytochrome c
Region30 – 7647N-terminal tail
Region163 – 596434D1-heme domain

Sites

Metal binding461Iron (heme axial ligand)
Metal binding981Iron (heme axial ligand)
Metal binding2291Iron (heme D1 proximal ligand)
Binding site941Heme (covalent)
Binding site971Heme (covalent)

Experimental info

Sequence conflict281S → A in AAB17878. Ref.1
Sequence conflict761S → T in AAB17878. Ref.1
Sequence conflict1301G → A in AAB17878. Ref.1
Sequence conflict2141A → T in AAB17878. Ref.1

Secondary structure

1 ..................................................................................................................... 596
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P72181 [UniParc].

Last modified November 8, 2002. Version 2.
Checksum: ABAD0C871E8FB7F1

FASTA59665,383
        10         20         30         40         50         60 
MRQRTPFARP GLLASAALAL VLGPLAASAQ EQVAPPKDPA AALEDHKTRT DNRYEPSLDN 

        70         80         90        100        110        120 
LAQQDVAAPG APEGVSALSD AQYNEANKIY FERCAGCHGV LRKGATGKAL TPDLTRDLGF 

       130        140        150        160        170        180 
DYLQSFITYG SPAGMPNWGT SGELSAEQVD LMANYLLLDP AAPPEFGMKE MRESWKVHVA 

       190        200        210        220        230        240 
PEDRPTQQEN DWDLENLFSV TLRDAGQIAL IDGATYEIKS VLDTGYAVHI SRLSASGRYL 

       250        260        270        280        290        300 
FVIGRDGKVN MIDLWMKEPT TVAEIKIGSE ARSIETSKME GWEDKYAIAG AYWPPQYVIM 

       310        320        330        340        350        360 
DGETLEPKKI QSTRGMTYDE QEYHPEPRVA AILASHYRPE FIVNVKETGK ILLVDYTDLD 

       370        380        390        400        410        420 
NLKTTEISAE RFLHDGGLDG SHRYFITAAN ARNKLVVIDT KEGKLVAIED TGGQTPHPGR 

       430        440        450        460        470        480 
GANFVHPTFG PVWATSHMGD DSVALIGTDP EGHPDNAWKI LDSFPALGGG SLFIKTHPNS 

       490        500        510        520        530        540 
QYLYVDATLN PEAEISGSVA VFDIKAMTGD GSDPEFKTLP IAEWAGITEG QPRVVQGEFN 

       550        560        570        580        590 
KDGTEVWFSV WNGKDQESAL VVVDDKTLEL KHVIKDERLV TPTGKFNVYN TMTDTY

« Hide

References

[1]"Transcriptional analysis of the nirS gene, encoding cytochrome cd1 nitrite reductase, of Paracoccus pantotrophus LMD 92.63."
Saunders N.F.W., Ferguson S.J., Baker S.C.
Microbiology 146:509-516(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: LMD 92.63.
[2]"The cytochrome c domain of dimeric cytochrome cd(1) of Paracoccus pantotrophus can be produced at high levels as a monomeric holoprotein using an improved c-type cytochrome expression system in Escherichia coli."
Gordon E.H.J., Steensma E., Ferguson S.J.
Biochem. Biophys. Res. Commun. 281:788-794(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]"The anatomy of a bifunctional enzyme: structural basis for reduction of oxygen to water and synthesis of nitric oxide by cytochrome cd1."
Fueloep V., Moir J.W.B., Ferguson S.J., Hajdu J.
Cell 81:369-377(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS).
[4]"Cytochrome cd1 structure: unusual haem environments in a nitrite reductase and analysis of factors contributing to beta-propeller folds."
Baker S.C., Saunders N.F.W., Willis A.C., Ferguson S.J., Fueloep V., Hajdu J.
J. Mol. Biol. 269:440-455(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.2 ANGSTROMS).
[5]"Haem-ligand switching during catalysis in crystals of a nitrogen-cycle enzyme."
Williams P.A., Fueloep V., Garman E.F., Saunders N.F.W., Ferguson S.J., Hajdu J.
Nature 389:406-412(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
[6]"Proton-coupled structural changes upon binding of carbon monoxide to cytochrome cd1: a combined flash photolysis and X-ray crystallography study."
Sjoegren T., Svensson-Ek M., Hajdu J., Brzezinski P.
Biochemistry 39:10967-10974(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
[7]"X-ray crystallographic study of cyanide binding provides insights into the structure-function relationship for cytochrome cd1 nitrite reductase from Paracoccus pantotrophus."
Jafferji A., Allen J.W.A., Ferguson S.J., Fueloep V.
J. Biol. Chem. 275:25089-25094(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.59 ANGSTROMS).
[8]"Structure of the bound dioxygen species in the cytochrome oxidase reaction of cytochrome cd1 nitrite reductase."
Sjoegren T., Hajdu J.
J. Biol. Chem. 276:13072-13076(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.46 ANGSTROMS).
[9]"The structure of an alternative form of Paracoccus pantotrophus cytochrome cd1 nitrite reductase."
Sjoegren T., Hajdu J.
J. Biol. Chem. 276:29450-29455(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		U75413 Genomic DNA. Translation: AAB17878.1.
AJ401462 Genomic DNA. Translation: CAC03621.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1AOFX-ray2.00A/B30-596[»]
1AOMX-ray1.80A/B30-596[»]
1AOQX-ray1.80A/B30-596[»]
1DY7X-ray1.60A/B30-596[»]
1E2RX-ray1.59A/B30-596[»]
1GQ1X-ray1.40A/B30-596[»]
1H9XX-ray2.10A/B30-596[»]
1H9YX-ray2.40A/B30-596[»]
1HCMX-ray2.50A/B30-596[»]
1HJ3X-ray1.60A/B30-596[»]
1HJ4X-ray1.60A/B30-596[»]
1HJ5X-ray1.46A/B30-596[»]
1QKSX-ray1.28A/B30-596[»]
ProteinModelPortalP72181.
SMRP72181. Positions 38-596.
ModBaseSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Family and domain databases

Gene3D2.130.10.10. 1 hit.
2.140.10.20. 1 hit.
InterProIPR009056. Cyt_c_dom.
IPR011048. Cyt_cd1_nitrite_Rdtase_haem_C.
IPR003143. Cyt_d1_haem_dom.
IPR015943. WD40/YVTN_repeat-like_dom.
[Graphical view]
SUPFAMSSF51004. Cyt_cd1_haem_C. 1 hit.
SSF46626. Cytochrome_c. 1 hit.
PROSITEPS51007. CYTC. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP72181.

Entry information

Entry nameNIRS_PARPN
AccessionPrimary (citable) accession number: P72181
Secondary accession number(s): Q9FCQ0
Entry history
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 8, 2002
Last modified: April 3, 2013
This is version 91 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents