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Protein

Periplasmic nitrate reductase

Gene

napA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Catalytic subunit of the periplasmic nitrate reductase complex NapAB. Receives electrons from NapB and catalyzes the reduction of nitrate to nitrite.UniRule annotation1 Publication

Catalytic activityi

2 ferrocytochrome + nitrate + 2 H+ = 2 ferricytochrome + nitrite.UniRule annotation1 Publication

Cofactori

Protein has several cofactor binding sites:
  • [4Fe-4S] clusterUniRule annotation1 PublicationNote: Binds 1 [4Fe-4S] cluster.UniRule annotation1 Publication
  • Mo-bis(molybdopterin guanine dinucleotide)UniRule annotation1 PublicationNote: Binds 1 molybdenum-bis(molybdopterin guanine dinucleotide) (Mo-bis-MGD) cofactor per subunit.UniRule annotation1 Publication

Enzyme regulationi

Interaction in the cytoplasm with the NapD chaperone prevents premature export.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi46Iron-sulfur (4Fe-4S)UniRule annotationCombined sources1 Publication1
Metal bindingi49Iron-sulfur (4Fe-4S)UniRule annotationCombined sources1 Publication1
Metal bindingi53Iron-sulfur (4Fe-4S)UniRule annotationCombined sources1 Publication1
Metal bindingi81Iron-sulfur (4Fe-4S)UniRule annotationCombined sources1 Publication1
Binding sitei83Mo-bis(molybdopterin guanine dinucleotide)UniRule annotationCombined sources1 Publication1
Binding sitei150Mo-bis(molybdopterin guanine dinucleotide)UniRule annotationCombined sources1 Publication1
Binding sitei175Mo-bis(molybdopterin guanine dinucleotide)UniRule annotationCombined sources1 Publication1
Binding sitei179Mo-bis(molybdopterin guanine dinucleotide)UniRule annotationCombined sources1 Publication1
Binding sitei372Mo-bis(molybdopterin guanine dinucleotide); via amide nitrogenUniRule annotationCombined sources1 Publication1
Binding sitei376Mo-bis(molybdopterin guanine dinucleotide)UniRule annotationCombined sources1 Publication1
Binding sitei482Mo-bis(molybdopterin guanine dinucleotide); via amide nitrogenUniRule annotationCombined sources1 Publication1
Binding sitei531Mo-bis(molybdopterin guanine dinucleotide)UniRule annotationCombined sources1 Publication1
Binding sitei558Mo-bis(molybdopterin guanine dinucleotide)UniRule annotationCombined sources1 Publication1
Binding sitei794Substrate; via amide nitrogenUniRule annotationBy similarity1
Binding sitei802Mo-bis(molybdopterin guanine dinucleotide)UniRule annotationCombined sources1 Publication1
Binding sitei819Mo-bis(molybdopterin guanine dinucleotide)UniRule annotationCombined sources1 Publication1

GO - Molecular functioni

  • 4 iron, 4 sulfur cluster binding Source: EcoCyc
  • molybdenum ion binding Source: EcoCyc
  • molybdopterin cofactor binding Source: InterPro
  • NADH dehydrogenase activity Source: GO_Central
  • nitrate reductase (cytochrome) activity Source: UniProtKB-EC
  • nitrate reductase activity Source: CACAO

GO - Biological processi

  • anaerobic respiration Source: EcoliWiki
  • nitrate assimilation Source: UniProtKB-KW

Keywordsi

Molecular functionOxidoreductase
Biological processElectron transport, Nitrate assimilation, Transport
Ligand4Fe-4S, Iron, Iron-sulfur, Metal-binding, Molybdenum

Enzyme and pathway databases

BioCyciEcoCyc:NAPA-MONOMER
MetaCyc:NAPA-MONOMER
BRENDAi1.9.6.1 2165

Names & Taxonomyi

Protein namesi
Recommended name:
Periplasmic nitrate reductaseUniRule annotationCurated (EC:1.9.6.1UniRule annotation1 Publication)
Gene namesi
Name:napAUniRule annotation
Synonyms:yojC, yojD, yojE
Ordered Locus Names:b2206, JW2194
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG12067 napA

Subcellular locationi

  • Periplasm UniRule annotation1 Publication

GO - Cellular componenti

  • outer membrane-bounded periplasmic space Source: CACAO
  • periplasmic space Source: EcoCyc

Keywords - Cellular componenti

Periplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi6R → Q: Impairs interaction with NapD. Lack of nitrate reductase activity. Tat transport is blocked. 1 Publication1
Mutagenesisi10K → Q: Impairs interaction with NapD. Slight decrease in nitrate reductase activity. Minor defect in Tat transport. 1 Publication1
Mutagenesisi17A → L: Impairs interaction with NapD. 1 Publication1
Mutagenesisi17A → Q: Impairs interaction with NapD. Decrease in nitrate reductase activity. Defect in Tat transport. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 36Tat-type signal1 PublicationAdd BLAST36
ChainiPRO_000001917037 – 828Periplasmic nitrate reductaseAdd BLAST792

Post-translational modificationi

Exported by the Tat system (PubMed:17218314). The position of the signal peptide cleavage has been experimentally proven (PubMed:10234835).2 Publications

Proteomic databases

PaxDbiP33937
PRIDEiP33937

Interactioni

Subunit structurei

Component of the periplasmic nitrate reductase NapAB complex composed of NapA and NapB (PubMed:10234835, PubMed:17130127). Before export to the periplasm, the NapA twin-arginine signal sequence interacts with NapD and NapF (PubMed:17074894, PubMed:17901208, PubMed:22329966, PubMed:24314029, Ref. 13).7 Publications

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi4262221, 162 interactors
DIPiDIP-10304N
IntActiP33937, 14 interactors
MINTiP33937
STRINGi316385.ECDH10B_2363

Structurei

Secondary structure

1828
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi6 – 21Combined sources16
Beta strandi26 – 29Combined sources4
Beta strandi40 – 45Combined sources6
Beta strandi47 – 49Combined sources3
Beta strandi54 – 60Combined sources7
Beta strandi63 – 69Combined sources7
Turni74 – 78Combined sources5
Helixi82 – 85Combined sources4
Helixi86 – 89Combined sources4
Beta strandi101 – 109Combined sources9
Beta strandi114 – 117Combined sources4
Helixi120 – 137Combined sources18
Helixi140 – 142Combined sources3
Beta strandi143 – 147Combined sources5
Helixi153 – 164Combined sources12
Turni165 – 167Combined sources3
Beta strandi172 – 174Combined sources3
Helixi175 – 177Combined sources3
Turni178 – 180Combined sources3
Helixi181 – 190Combined sources10
Helixi200 – 205Combined sources6
Beta strandi207 – 213Combined sources7
Helixi216 – 219Combined sources4
Helixi221 – 232Combined sources12
Beta strandi238 – 246Combined sources9
Helixi248 – 252Combined sources5
Beta strandi254 – 258Combined sources5
Turni261 – 263Combined sources3
Helixi264 – 277Combined sources14
Helixi283 – 289Combined sources7
Beta strandi290 – 295Combined sources6
Helixi308 – 311Combined sources4
Beta strandi321 – 323Combined sources3
Helixi326 – 334Combined sources9
Helixi338 – 345Combined sources8
Helixi349 – 360Combined sources12
Beta strandi366 – 371Combined sources6
Helixi372 – 375Combined sources4
Helixi380 – 394Combined sources15
Beta strandi402 – 406Combined sources5
Turni411 – 416Combined sources6
Helixi417 – 420Combined sources4
Helixi436 – 446Combined sources11
Helixi461 – 469Combined sources9
Beta strandi475 – 480Combined sources6
Helixi483 – 486Combined sources4
Turni490 – 493Combined sources4
Helixi494 – 499Combined sources6
Beta strandi504 – 511Combined sources8
Helixi514 – 517Combined sources4
Beta strandi519 – 525Combined sources7
Helixi528 – 530Combined sources3
Beta strandi533 – 536Combined sources4
Beta strandi540 – 545Combined sources6
Helixi558 – 565Combined sources8
Helixi566 – 568Combined sources3
Helixi571 – 574Combined sources4
Helixi577 – 580Combined sources4
Helixi584 – 586Combined sources3
Helixi591 – 595Combined sources5
Turni599 – 602Combined sources4
Helixi606 – 608Combined sources3
Helixi616 – 621Combined sources6
Helixi625 – 637Combined sources13
Turni638 – 641Combined sources4
Helixi647 – 650Combined sources4
Beta strandi656 – 658Combined sources3
Beta strandi667 – 671Combined sources5
Turni672 – 674Combined sources3
Beta strandi694 – 698Combined sources5
Beta strandi710 – 712Combined sources3
Beta strandi714 – 719Combined sources6
Helixi731 – 733Combined sources3
Helixi735 – 738Combined sources4
Beta strandi745 – 747Combined sources3
Helixi750 – 754Combined sources5
Turni755 – 757Combined sources3
Beta strandi763 – 768Combined sources6
Beta strandi771 – 782Combined sources12
Beta strandi789 – 793Combined sources5
Helixi801 – 803Combined sources3
Turni811 – 813Combined sources3
Beta strandi821 – 826Combined sources6

3D structure databases

ProteinModelPortaliP33937
SMRiP33937
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP33937

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini39 – 954Fe-4S Mo/W bis-MGD-typeUniRule annotationAdd BLAST57

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni212 – 219Mo-bis(molybdopterin guanine dinucleotide) bindingUniRule annotationCombined sources1 Publication8
Regioni243 – 247Mo-bis(molybdopterin guanine dinucleotide) bindingUniRule annotationCombined sources1 Publication5
Regioni262 – 264Mo-bis(molybdopterin guanine dinucleotide) bindingUniRule annotationCombined sources1 Publication3
Regioni508 – 509Mo-bis(molybdopterin guanine dinucleotide) bindingUniRule annotationCombined sources1 Publication2
Regioni718 – 727Mo-bis(molybdopterin guanine dinucleotide) bindingUniRule annotationCombined sources1 Publication10

Domaini

The twin-arginine signal peptide of NapA is structured in its unbound form and undergoes a small but significant conformational change upon interaction with NapD.1 Publication

Sequence similaritiesi

Belongs to the prokaryotic molybdopterin-containing oxidoreductase family. NasA/NapA/NarB subfamily.UniRule annotationCurated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG4107QIW Bacteria
COG0243 LUCA
HOGENOMiHOG000031441
InParanoidiP33937
KOiK02567
OMAiANSMGTR
PhylomeDBiP33937

Family and domain databases

HAMAPiMF_01630 Nitrate_reduct_NapA, 1 hit
InterProiView protein in InterPro
IPR009010 Asp_de-COase-like_dom_sf
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
PANTHERiPTHR11615:SF123 PTHR11615:SF123, 1 hit
PfamiView protein in Pfam
PF04879 Molybdop_Fe4S4, 1 hit
PF00384 Molybdopterin, 1 hit
PF01568 Molydop_binding, 1 hit
SMARTiView protein in SMART
SM00926 Molybdop_Fe4S4, 1 hit
SUPFAMiSSF50692 SSF50692, 1 hit
TIGRFAMsiTIGR01706 NAPA, 1 hit
TIGR01409 TAT_signal_seq, 1 hit
PROSITEiView protein in PROSITE
PS51669 4FE4S_MOW_BIS_MGD, 1 hit
PS00551 MOLYBDOPTERIN_PROK_1, 1 hit
PS51318 TAT, 1 hit

Sequencei

Sequence statusi: Complete.

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

P33937-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKLSRRSFMK ANAVAAAAAA AGLSVPGVAR AVVGQQEAIK WDKAPCRFCG
60 70 80 90 100
TGCGVLVGTQ QGRVVACQGD PDAPVNRGLN CIKGYFLPKI MYGKDRLTQP
110 120 130 140 150
LLRMKNGKYD KEGEFTPITW DQAFDVMEEK FKTALKEKGP ESIGMFGSGQ
160 170 180 190 200
WTIWEGYAAS KLFKAGFRSN NIDPNARHCM ASAVVGFMRT FGMDEPMGCY
210 220 230 240 250
DDIEQADAFV LWGANMAEMH PILWSRITNR RLSNQNVTVA VLSTYQHRSF
260 270 280 290 300
ELADNGIIFT PQSDLVILNY IANYIIQNNA INQDFFSKHV NLRKGATDIG
310 320 330 340 350
YGLRPTHPLE KAAKNPGSDA SEPMSFEDYK AFVAEYTLEK TAEMTGVPKD
360 370 380 390 400
QLEQLAQLYA DPNKKVISYW TMGFNQHTRG VWANNLVYNL HLLTGKISQP
410 420 430 440 450
GCGPFSLTGQ PSACGTAREV GTFAHRLPAD MVVTNEKHRD ICEKKWNIPS
460 470 480 490 500
GTIPAKIGLH AVAQDRALKD GKLNVYWTMC TNNMQAGPNI NEERMPGWRD
510 520 530 540 550
PRNFIIVSDP YPTVSALAAD LILPTAMWVE KEGAYGNAER RTQFWRQQVQ
560 570 580 590 600
APGEAKSDLW QLVQFSRRFK TEEVWPEDLL AKKPELRGKT LYEVLYATPE
610 620 630 640 650
VSKFPVSELA EDQLNDESRE LGFYLQKGLF EEYAWFGRGH GHDLAPFDDY
660 670 680 690 700
HKARGLRWPV VNGKETQWRY SEGNDPYVKA GEGYKFYGKP DGKAVIFALP
710 720 730 740 750
FEPAAEAPDE EYDLWLSTGR VLEHWHTGSM TRRVPELHRA FPEAVLFIHP
760 770 780 790 800
LDAKARDLRR GDKVKVVSRR GEVISIVETR GRNRPPQGLV YMPFFDAAQL
810 820
VNKLTLDATD PLSKETDFKK CAVKLEKV
Length:828
Mass (Da):93,042
Last modified:November 1, 1997 - v3
Checksum:iCE2D7AB000FEAFCA
GO

Sequence cautioni

The sequence AAA16399 differs from that shown. Reason: Frameshift at positions 19 and 27.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti98T → R in AAA16399 (Ref. 1) Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00008 Genomic DNA Translation: AAA16399.1 Frameshift.
U00096 Genomic DNA Translation: AAC75266.1
AP009048 Genomic DNA Translation: BAA15989.2
PIRiD64990
RefSeqiNP_416710.1, NC_000913.3
WP_000778061.1, NZ_LN832404.1

Genome annotation databases

EnsemblBacteriaiAAC75266; AAC75266; b2206
BAA15989; BAA15989; BAA15989
GeneIDi947093
KEGGiecj:JW2194
eco:b2206
PATRICifig|1411691.4.peg.30

Similar proteinsi

Entry informationi

Entry nameiNAPA_ECOLI
AccessioniPrimary (citable) accession number: P33937
Secondary accession number(s): P78087
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: November 1, 1997
Last modified: July 18, 2018
This is version 168 of the entry and version 3 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

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