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P72181

- NIRS_PARPN

UniProt

P72181 - NIRS_PARPN

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Protein

Nitrite reductase

Gene

nirS

Organism
Paracoccus pantotrophus (Thiosphaera pantotropha)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Catalytic activityi

Nitric oxide + H2O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H+.
NH3 + H2O + acceptor = hydroxylamine + reduced acceptor.

Cofactori

Binds 2 heme groups per subunit.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi46 – 461Iron (heme axial ligand)
Binding sitei94 – 941Heme (covalent)
Binding sitei97 – 971Heme (covalent)
Metal bindingi98 – 981Iron (heme axial ligand)
Metal bindingi229 – 2291Iron (heme D1 proximal ligand)

GO - Molecular functioni

  1. electron carrier activity Source: InterPro
  2. heme binding Source: InterPro
  3. hydroxylamine reductase activity Source: UniProtKB-EC
  4. metal ion binding Source: UniProtKB-KW
  5. nitrite reductase (NO-forming) activity Source: UniProtKB-EC
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Electron transport, Transport

Keywords - Ligandi

Heme, Iron, Metal-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Nitrite reductase (EC:1.7.2.1)
Alternative name(s):
Cytochrome cd1
Cytochrome oxidase
Hydroxylamine reductase (EC:1.7.99.1)
Gene namesi
Name:nirS
OrganismiParacoccus pantotrophus (Thiosphaera pantotropha)
Taxonomic identifieri82367 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhodobacteralesRhodobacteraceaeParacoccus

Subcellular locationi

GO - Cellular componenti

  1. periplasmic space Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Periplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2929Add
BLAST
Chaini30 – 596567Nitrite reductasePRO_0000006575Add
BLAST

Interactioni

Subunit structurei

Homodimer.

Structurei

Secondary structure

1
596
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi39 – 413
Helixi42 – 454
Beta strandi50 – 556
Helixi61 – 633
Helixi80 – 9314
Helixi95 – 984
Beta strandi105 – 1073
Helixi112 – 1187
Helixi120 – 1278
Beta strandi132 – 1343
Turni136 – 1383
Beta strandi142 – 1443
Helixi146 – 15712
Helixi168 – 1747
Beta strandi176 – 1794
Helixi181 – 1833
Helixi194 – 1963
Beta strandi197 – 2026
Turni203 – 2064
Beta strandi207 – 2126
Turni213 – 2153
Beta strandi218 – 2236
Beta strandi228 – 2336
Beta strandi239 – 2446
Beta strandi247 – 2537
Beta strandi256 – 2583
Beta strandi261 – 2666
Beta strandi269 – 2768
Turni283 – 2853
Beta strandi286 – 2938
Beta strandi296 – 3016
Turni302 – 3043
Beta strandi307 – 3126
Turni318 – 3203
Beta strandi323 – 3253
Beta strandi329 – 3346
Beta strandi336 – 34510
Turni346 – 3494
Beta strandi350 – 3556
Beta strandi359 – 36810
Beta strandi371 – 3788
Beta strandi384 – 3896
Helixi390 – 3923
Beta strandi394 – 3996
Turni400 – 4034
Beta strandi404 – 4107
Beta strandi412 – 4165
Beta strandi422 – 4265
Turni427 – 4293
Beta strandi430 – 44718
Turni450 – 4523
Turni454 – 4563
Beta strandi459 – 4657
Beta strandi481 – 4866
Helixi493 – 4964
Beta strandi499 – 5035
Helixi504 – 5063
Beta strandi510 – 5123
Beta strandi516 – 5194
Helixi521 – 5255
Beta strandi533 – 5397
Beta strandi543 – 5519
Beta strandi559 – 5646
Turni565 – 5684
Beta strandi569 – 5746
Beta strandi581 – 5877
Helixi588 – 5925

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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[»]
ProteinModelPortaliP72181.
SMRiP72181. Positions 38-596.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP72181.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini77 – 16286Cytochrome cPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni30 – 7647N-terminal tailAdd
BLAST
Regioni163 – 596434D1-heme domainAdd
BLAST

Sequence similaritiesi

Contains 1 cytochrome c domain.PROSITE-ProRule annotation

Keywords - Domaini

Signal

Family and domain databases

Gene3Di1.10.760.10. 1 hit.
2.130.10.10. 1 hit.
2.140.10.20. 1 hit.
InterProiIPR009056. Cyt_c-like_dom.
IPR003143. Cyt_cd1_C.
IPR011048. Haem_d1.
IPR015943. WD40/YVTN_repeat-like_dom.
[Graphical view]
PfamiPF13442. Cytochrome_CBB3. 1 hit.
[Graphical view]
SUPFAMiSSF46626. SSF46626. 2 hits.
SSF51004. SSF51004. 1 hit.
PROSITEiPS51007. CYTC. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P72181-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MRQRTPFARP GLLASAALAL VLGPLAASAQ EQVAPPKDPA AALEDHKTRT
60 70 80 90 100
DNRYEPSLDN LAQQDVAAPG APEGVSALSD AQYNEANKIY FERCAGCHGV
110 120 130 140 150
LRKGATGKAL TPDLTRDLGF DYLQSFITYG SPAGMPNWGT SGELSAEQVD
160 170 180 190 200
LMANYLLLDP AAPPEFGMKE MRESWKVHVA PEDRPTQQEN DWDLENLFSV
210 220 230 240 250
TLRDAGQIAL IDGATYEIKS VLDTGYAVHI SRLSASGRYL FVIGRDGKVN
260 270 280 290 300
MIDLWMKEPT TVAEIKIGSE ARSIETSKME GWEDKYAIAG AYWPPQYVIM
310 320 330 340 350
DGETLEPKKI QSTRGMTYDE QEYHPEPRVA AILASHYRPE FIVNVKETGK
360 370 380 390 400
ILLVDYTDLD NLKTTEISAE RFLHDGGLDG SHRYFITAAN ARNKLVVIDT
410 420 430 440 450
KEGKLVAIED TGGQTPHPGR GANFVHPTFG PVWATSHMGD DSVALIGTDP
460 470 480 490 500
EGHPDNAWKI LDSFPALGGG SLFIKTHPNS QYLYVDATLN PEAEISGSVA
510 520 530 540 550
VFDIKAMTGD GSDPEFKTLP IAEWAGITEG QPRVVQGEFN KDGTEVWFSV
560 570 580 590
WNGKDQESAL VVVDDKTLEL KHVIKDERLV TPTGKFNVYN TMTDTY
Length:596
Mass (Da):65,383
Last modified:November 8, 2002 - v2
Checksum:iABAD0C871E8FB7F1
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti28 – 281S → A in AAB17878. (PubMed:10708389)Curated
Sequence conflicti76 – 761S → T in AAB17878. (PubMed:10708389)Curated
Sequence conflicti130 – 1301G → A in AAB17878. (PubMed:10708389)Curated
Sequence conflicti214 – 2141A → T in AAB17878. (PubMed:10708389)Curated

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U75413 Genomic DNA. Translation: AAB17878.1.
AJ401462 Genomic DNA. Translation: CAC03621.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U75413 Genomic DNA. Translation: AAB17878.1 .
AJ401462 Genomic DNA. Translation: CAC03621.1 .

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1AOF X-ray 2.00 A/B 30-596 [» ]
1AOM X-ray 1.80 A/B 30-596 [» ]
1AOQ X-ray 1.80 A/B 30-596 [» ]
1DY7 X-ray 1.60 A/B 30-596 [» ]
1E2R X-ray 1.59 A/B 30-596 [» ]
1GQ1 X-ray 1.40 A/B 30-596 [» ]
1H9X X-ray 2.10 A/B 30-596 [» ]
1H9Y X-ray 2.40 A/B 30-596 [» ]
1HCM X-ray 2.50 A/B 30-596 [» ]
1HJ3 X-ray 1.60 A/B 30-596 [» ]
1HJ4 X-ray 1.60 A/B 30-596 [» ]
1HJ5 X-ray 1.46 A/B 30-596 [» ]
1QKS X-ray 1.28 A/B 30-596 [» ]
ProteinModelPortali P72181.
SMRi P72181. Positions 38-596.
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Miscellaneous databases

EvolutionaryTracei P72181.

Family and domain databases

Gene3Di 1.10.760.10. 1 hit.
2.130.10.10. 1 hit.
2.140.10.20. 1 hit.
InterProi IPR009056. Cyt_c-like_dom.
IPR003143. Cyt_cd1_C.
IPR011048. Haem_d1.
IPR015943. WD40/YVTN_repeat-like_dom.
[Graphical view ]
Pfami PF13442. Cytochrome_CBB3. 1 hit.
[Graphical view ]
SUPFAMi SSF46626. SSF46626. 2 hits.
SSF51004. SSF51004. 1 hit.
PROSITEi PS51007. CYTC. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  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).

Entry informationi

Entry nameiNIRS_PARPN
AccessioniPrimary (citable) accession number: P72181
Secondary accession number(s): Q9FCQ0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 8, 2002
Last modified: October 29, 2014
This is version 97 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3