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Q53176

- NAPA_RHOS4

UniProt

Q53176 - NAPA_RHOS4

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Protein

Periplasmic nitrate reductase

Gene

napA

Organism
Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli

Functioni

Catalytic subunit of the periplasmic nitrate reductase (NAP). Only expressed at high levels during aerobic growth. NapAB complex receives electrons from the membrane-anchored tetraheme protein NapC, thus allowing electron flow between membrane and periplasm. Essential function for nitrate assimilation and may have a role in anaerobic metabolism.

Catalytic activityi

Nitrite + acceptor = nitrate + reduced acceptor.UniRule annotation

Cofactori

Binds 1 4Fe-4S cluster.UniRule annotation
Binds 1 molybdenum-bis(molybdopterin guanine dinucleotide) (Mo-bis-MGD) cofactor per subunit.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi48 – 481Iron-sulfur (4Fe-4S)UniRule annotation
Metal bindingi51 – 511Iron-sulfur (4Fe-4S)UniRule annotation
Metal bindingi55 – 551Iron-sulfur (4Fe-4S)UniRule annotation
Metal bindingi83 – 831Iron-sulfur (4Fe-4S)UniRule annotation

GO - Molecular functioni

  1. 4 iron, 4 sulfur cluster binding Source: UniProtKB-HAMAP
  2. electron carrier activity Source: UniProtKB-HAMAP
  3. iron ion binding Source: UniProtKB-HAMAP
  4. molybdenum ion binding Source: InterPro
  5. nitrate reductase activity Source: UniProtKB-HAMAP

GO - Biological processi

  1. Mo-molybdopterin cofactor biosynthetic process Source: UniProtKB-HAMAP
  2. nitrate assimilation Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Electron transport, Nitrate assimilation, Transport

Keywords - Ligandi

4Fe-4S, Iron, Iron-sulfur, Metal-binding, Molybdenum

Enzyme and pathway databases

BioCyciRSPH272943:GJAS-4224-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Periplasmic nitrate reductaseUniRule annotation (EC:1.7.99.4UniRule annotation)
Gene namesi
Name:napAUniRule annotation
Ordered Locus Names:RHOS4_40230
ORF Names:RSP_4116
Encoded oniPlasmid pRS241c1 Publication
OrganismiRhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)
Taxonomic identifieri272943 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhodobacteralesRhodobacteraceaeRhodobacter
ProteomesiUP000002703: Plasmid pRS241c

Subcellular locationi

GO - Cellular componenti

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

Keywords - Cellular componenti

Periplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2929Tat-type signalUniRule annotationAdd
BLAST
Chaini30 – 831802Periplasmic nitrate reductasePRO_0000019171Add
BLAST

Post-translational modificationi

Predicted to be exported by the Tat system. The position of the signal peptide cleavage has not been experimentally proven.

Expressioni

Inductioni

Nitrate reductase activity can be induced by nitrate and not repressed by ammonium or oxygen.

Interactioni

Subunit structurei

Interacts with NapB.1 PublicationUniRule annotation

Protein-protein interaction databases

IntActiQ53176. 1 interaction.
STRINGi272943.RSP_4116.

Structurei

Secondary structure

1
831
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi42 – 476
Beta strandi56 – 627
Beta strandi65 – 717
Turni76 – 783
Helixi84 – 874
Helixi88 – 914
Beta strandi103 – 1053
Beta strandi107 – 1093
Helixi122 – 13918
Helixi142 – 1443
Beta strandi145 – 1495
Helixi155 – 16612
Beta strandi174 – 1763
Helixi178 – 1814
Helixi183 – 19311
Helixi204 – 2074
Beta strandi209 – 2157
Helixi218 – 2214
Helixi223 – 23513
Beta strandi240 – 2489
Helixi250 – 2534
Beta strandi256 – 2605
Turni263 – 2653
Helixi266 – 27914
Helixi285 – 2917
Beta strandi292 – 2965
Helixi310 – 3134
Helixi329 – 3379
Helixi341 – 3488
Helixi352 – 36110
Beta strandi369 – 3746
Helixi375 – 3784
Helixi383 – 39715
Beta strandi405 – 4095
Turni414 – 4196
Helixi420 – 4234
Turni431 – 4333
Beta strandi434 – 4374
Helixi439 – 44810
Helixi464 – 4729
Beta strandi478 – 4836
Helixi486 – 4894
Turni491 – 4977
Helixi498 – 5025
Beta strandi507 – 5148
Helixi517 – 5204
Beta strandi522 – 5287
Helixi531 – 5333
Beta strandi536 – 5394
Beta strandi543 – 5486
Helixi561 – 5699
Helixi574 – 5774
Helixi580 – 5856
Beta strandi587 – 5915
Turni594 – 5996
Beta strandi601 – 6055
Beta strandi607 – 6126
Beta strandi614 – 6174
Helixi619 – 6224
Beta strandi623 – 6264
Helixi628 – 63710
Beta strandi640 – 6445
Helixi652 – 6554
Beta strandi659 – 6613
Beta strandi670 – 6756
Beta strandi692 – 6943
Beta strandi697 – 7015
Beta strandi713 – 7153
Beta strandi717 – 7226
Helixi734 – 7363
Helixi738 – 7436
Beta strandi748 – 7503
Helixi753 – 7586
Beta strandi766 – 7705
Beta strandi775 – 78713
Beta strandi792 – 7965
Beta strandi800 – 8023
Helixi804 – 8063
Turni814 – 8163
Beta strandi825 – 8295

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1OGYX-ray3.20A/C/E/G/I/K/M/O30-831[»]
ProteinModelPortaliQ53176.
SMRiQ53176. Positions 41-829.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ53176.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini41 – 97574Fe-4S Mo/W bis-MGD-typeUniRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the prokaryotic molybdopterin-containing oxidoreductase family. NasA/NapA/NarB subfamily.UniRule annotation
Contains 1 4Fe-4S Mo/W bis-MGD-type domain.UniRule annotation

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiCOG0243.
HOGENOMiHOG000031441.
KOiK02567.
OMAiHQLVEAP.
OrthoDBiEOG6CVV7G.
PhylomeDBiQ53176.

Family and domain databases

HAMAPiMF_01630. Nitrate_reduct.
InterProiIPR009010. Asp_de-COase-like_dom.
IPR006657. MoPterin_dinucl-bd_dom.
IPR006656. Mopterin_OxRdtase.
IPR006963. Mopterin_OxRdtase_4Fe-4S_dom.
IPR027467. MopterinOxRdtase_cofactor_BS.
IPR010051. Periplasm_NO3_reductase_lsu.
IPR006311. TAT_signal.
IPR019546. TAT_signal_bac_arc.
[Graphical view]
PfamiPF04879. Molybdop_Fe4S4. 1 hit.
PF00384. Molybdopterin. 1 hit.
PF01568. Molydop_binding. 1 hit.
[Graphical view]
SMARTiSM00926. Molybdop_Fe4S4. 1 hit.
[Graphical view]
SUPFAMiSSF50692. SSF50692. 1 hit.
TIGRFAMsiTIGR01706. NAPA. 1 hit.
TIGR01409. TAT_signal_seq. 1 hit.
PROSITEiPS51669. 4FE4S_MOW_BIS_MGD. 1 hit.
PS00551. MOLYBDOPTERIN_PROK_1. 1 hit.
PS51318. TAT. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

Q53176-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MTLTRRDLIK AQAAATAAAA AGLPVSALAQ PVTGGAEALR IRWSKAPCRF
60 70 80 90 100
CGTGCGVMVG TRDGQVVATH GDTQAEVNRG LNCVKGYFLS KIMYGEDRLT
110 120 130 140 150
TPLLRMKDGV YHKEGEFAPV SWDEAFDVMA AQAKRVLKEK GPKAVGMFGS
160 170 180 190 200
GQWTIWEGYA ASKLMRAGFR SNNLDPNARH CMASAATAFM RTFGMDEPMG
210 220 230 240 250
CYDDFEAADA FVLWGSNMAE MHPILWSRLT DRRLSHEHVR VAVLSTFTHR
260 270 280 290 300
SMDLADTPII FRPGTDLAIL NYIAHHIIST GRVNRDFVDR HTNFALGATD
310 320 330 340 350
IGYGLRPEHQ LQLAAKGAAD AGAMTPTDFE TFAALVSEYT LEKAAEISGV
360 370 380 390 400
EPALLEELAE LYADPDRKVM SLWTMGFNQH VRGVWANHMV YNLHLLTGKI
410 420 430 440 450
SEPGNSPFSL TGQPSACGTA REVGTFAHRL PADMVVTNPE HRAHAEEIWK
460 470 480 490 500
LPAGLLPDWV GAHAVEQDRK LHDGEINFYW VQVNNNMQAA PNIDQETYPG
510 520 530 540 550
YRNPENFIVV SDAYPTVTGR CADLVLPAAM WVEKEGAYGN AERRTHFWHQ
560 570 580 590 600
LVEAPGEARS DLWQLMEFSK RFTTDEVWPE EILSAAPAYR GKTLFEVLFA
610 620 630 640 650
NGSVDRFPAS DVNPDHANHE AALFGFYPQK GLFEEYAAFG RGHGHDLAPF
660 670 680 690 700
DTYHEVRGLR WPVVEGEETR WRYREGFDPY VKPGEGLRFY GKPDGRAVIL
710 720 730 740 750
GVPYEPPAES PDEEFGFWLV TGRVLEHWHS GSMTLRVPEL YKAFPGAVCF
760 770 780 790 800
MHPEDARSRG LNRGSEVRVI SRRGEIRTRL ETRGRNRMPR GVVFVPWFDA
810 820 830
SQLINKVTLD ANDPISRQTD FKKCAVKIEA V
Length:831
Mass (Da):92,637
Last modified:January 24, 2006 - v2
Checksum:i74B35640749CC906
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti135 – 1351R → L in CAA86827. (PubMed:8730872)Curated
Sequence conflicti141 – 1411G → A(PubMed:8730872)Curated
Sequence conflicti143 – 1431K → E(PubMed:8730872)Curated
Sequence conflicti252 – 2521M → S in CAA86827. (PubMed:8730872)Curated
Sequence conflicti255 – 2551A → S in CAA86827. (PubMed:8730872)Curated
Sequence conflicti267 – 2671L → R in CAA86827. (PubMed:8730872)Curated
Sequence conflicti369 – 3691V → W in CAA86827. (PubMed:8730872)Curated
Sequence conflicti415 – 4151S → F in CAA86827. (PubMed:8730872)Curated
Sequence conflicti521 – 5211C → A in CAA86827. (PubMed:8730872)Curated
Sequence conflicti660 – 6601R → H in CAA86827. (PubMed:8730872)Curated
Sequence conflicti737 – 7371V → W in CAA86827. (PubMed:8730872)Curated

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
Z46806 Genomic DNA. Translation: CAA86827.1.
CP000146 Genomic DNA. Translation: ABA81591.1.
RefSeqiYP_345332.1. NC_007489.1.

Genome annotation databases

EnsemblBacteriaiABA81591; ABA81591; RSP_4116.
GeneIDi3711832.
KEGGirsp:RSP_4116.
PATRICi23149531. VBIRhoSph57909_0178.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
Z46806 Genomic DNA. Translation: CAA86827.1 .
CP000146 Genomic DNA. Translation: ABA81591.1 .
RefSeqi YP_345332.1. NC_007489.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1OGY X-ray 3.20 A/C/E/G/I/K/M/O 30-831 [» ]
ProteinModelPortali Q53176.
SMRi Q53176. Positions 41-829.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

IntActi Q53176. 1 interaction.
STRINGi 272943.RSP_4116.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ABA81591 ; ABA81591 ; RSP_4116 .
GeneIDi 3711832.
KEGGi rsp:RSP_4116.
PATRICi 23149531. VBIRhoSph57909_0178.

Phylogenomic databases

eggNOGi COG0243.
HOGENOMi HOG000031441.
KOi K02567.
OMAi HQLVEAP.
OrthoDBi EOG6CVV7G.
PhylomeDBi Q53176.

Enzyme and pathway databases

BioCyci RSPH272943:GJAS-4224-MONOMER.

Miscellaneous databases

EvolutionaryTracei Q53176.

Family and domain databases

HAMAPi MF_01630. Nitrate_reduct.
InterProi IPR009010. Asp_de-COase-like_dom.
IPR006657. MoPterin_dinucl-bd_dom.
IPR006656. Mopterin_OxRdtase.
IPR006963. Mopterin_OxRdtase_4Fe-4S_dom.
IPR027467. MopterinOxRdtase_cofactor_BS.
IPR010051. Periplasm_NO3_reductase_lsu.
IPR006311. TAT_signal.
IPR019546. TAT_signal_bac_arc.
[Graphical view ]
Pfami PF04879. Molybdop_Fe4S4. 1 hit.
PF00384. Molybdopterin. 1 hit.
PF01568. Molydop_binding. 1 hit.
[Graphical view ]
SMARTi SM00926. Molybdop_Fe4S4. 1 hit.
[Graphical view ]
SUPFAMi SSF50692. SSF50692. 1 hit.
TIGRFAMsi TIGR01706. NAPA. 1 hit.
TIGR01409. TAT_signal_seq. 1 hit.
PROSITEi PS51669. 4FE4S_MOW_BIS_MGD. 1 hit.
PS00551. MOLYBDOPTERIN_PROK_1. 1 hit.
PS51318. TAT. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Isolation of periplasmic nitrate reductase genes from Rhodobacter sphaeroides DSM 158: structural and functional differences among prokaryotic nitrate reductases."
    Reyes F., Roldan M.D., Klipp W., Castillo F., Moreno-Vivian C.
    Mol. Microbiol. 19:1307-1318(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Complete sequence of plasmid C of Rhodobacter sphaeroides 2.4.1."
    Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina T., Hammon N., Israni S., Pitluck S., Richardson P., Mackenzie C., Choudhary M., Larimer F., Hauser L.J., Land M., Donohue T.J., Kaplan S.
    Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158.
    Plasmid: pRS241c
  3. "Structural and redox plasticity in the heterodimeric periplasmic nitrate reductase."
    Arnoux P., Sabaty M., Alric J., Frangioni B., Guigliarelli B., Adriano J.-M., Pignol D.
    Nat. Struct. Biol. 10:928-934(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.2 ANGSTROMS) IN COMPLEX WITH NAPB.

Entry informationi

Entry nameiNAPA_RHOS4
AccessioniPrimary (citable) accession number: Q53176
Secondary accession number(s): Q3IV43
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: January 24, 2006
Last modified: October 29, 2014
This is version 115 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, Complete proteome, Plasmid, Reference proteome

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