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Protein

Periplasmic nitrate reductase

Gene

napA

Organism
Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337) (Ralstonia eutropha)
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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi48Iron-sulfur (4Fe-4S)UniRule annotationCombined sources1 Publication1
Metal bindingi51Iron-sulfur (4Fe-4S)UniRule annotationCombined sources1 Publication1
Metal bindingi55Iron-sulfur (4Fe-4S)UniRule annotationCombined sources1 Publication1
Metal bindingi83Iron-sulfur (4Fe-4S)UniRule annotationCombined sources1 Publication1
Binding sitei85Mo-bis(molybdopterin guanine dinucleotide)UniRule annotationCombined sources1 Publication1
Binding sitei152Mo-bis(molybdopterin guanine dinucleotide)UniRule annotationCombined sources1 Publication1
Binding sitei177Mo-bis(molybdopterin guanine dinucleotide)UniRule annotationCombined sources1 Publication1
Binding sitei181Mo-bis(molybdopterin guanine dinucleotide)UniRule annotationCombined sources1 Publication1
Binding sitei375Mo-bis(molybdopterin guanine dinucleotide); via amide nitrogenUniRule annotationCombined sources1 Publication1
Binding sitei379Mo-bis(molybdopterin guanine dinucleotide)UniRule annotationCombined sources1 Publication1
Binding sitei485Mo-bis(molybdopterin guanine dinucleotide); via amide nitrogenUniRule annotationCombined sources1 Publication1
Binding sitei534Mo-bis(molybdopterin guanine dinucleotide)UniRule annotationCombined sources1 Publication1
Binding sitei561Mo-bis(molybdopterin guanine dinucleotide)UniRule annotationCombined sources1 Publication1
Binding sitei797Substrate; via amide nitrogenUniRule annotation1
Binding sitei805Mo-bis(molybdopterin guanine dinucleotide)UniRule annotationCombined sources1 Publication1
Binding sitei822Mo-bis(molybdopterin guanine dinucleotide)UniRule annotationCombined sources1 Publication1

GO - Molecular functioni

GO - Biological processi

Keywordsi

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

Names & Taxonomyi

Protein namesi
Recommended name:
Periplasmic nitrate reductaseUniRule annotation (EC:1.9.6.1UniRule annotation)
Gene namesi
Name:napA1 PublicationUniRule annotation
Ordered Locus Names:PHG211
Encoded oniPlasmid megaplasmid pHG10 Publication
OrganismiCupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337) (Ralstonia eutropha)
Taxonomic identifieri381666 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesBurkholderiaceaeCupriavidus
Proteomesi
  • UP000008210 Componenti: Plasmid megaplasmid pHG1

Subcellular locationi

  • Periplasm UniRule annotation1 Publication

GO - Cellular componenti

Keywords - Cellular componenti

Periplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 29Tat-type signalUniRule annotation1 PublicationAdd BLAST29
ChainiPRO_000001916830 – 831Periplasmic nitrate reductaseUniRule annotationAdd BLAST802

Post-translational modificationi

Predicted to be exported by the Tat system (By similarity). The position of the signal peptide cleavage has been experimentally proven (PubMed:8376334).UniRule annotation1 Publication

Expressioni

Inductioni

Expressed independently of nitrate induction and anaerobiosis.

Interactioni

Subunit structurei

Component of the periplasmic nitrate reductase NapAB complex composed of NapA and NapB.UniRule annotation2 Publications

Structurei

Secondary structure

1831
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi40 – 47Combined sources8
Beta strandi56 – 62Combined sources7
Beta strandi65 – 71Combined sources7
Turni76 – 80Combined sources5
Helixi84 – 87Combined sources4
Helixi88 – 91Combined sources4
Beta strandi103 – 107Combined sources5
Beta strandi115 – 119Combined sources5
Helixi122 – 139Combined sources18
Helixi142 – 144Combined sources3
Beta strandi145 – 149Combined sources5
Helixi155 – 166Combined sources12
Turni167 – 169Combined sources3
Beta strandi174 – 176Combined sources3
Helixi177 – 180Combined sources4
Helixi183 – 193Combined sources11
Helixi202 – 206Combined sources5
Beta strandi209 – 215Combined sources7
Helixi218 – 221Combined sources4
Helixi223 – 235Combined sources13
Beta strandi240 – 248Combined sources9
Helixi250 – 253Combined sources4
Beta strandi256 – 260Combined sources5
Turni263 – 265Combined sources3
Helixi266 – 279Combined sources14
Helixi285 – 291Combined sources7
Beta strandi292 – 297Combined sources6
Helixi310 – 314Combined sources5
Beta strandi324 – 327Combined sources4
Helixi329 – 337Combined sources9
Helixi341 – 348Combined sources8
Helixi352 – 363Combined sources12
Beta strandi369 – 374Combined sources6
Helixi375 – 378Combined sources4
Helixi383 – 397Combined sources15
Beta strandi405 – 409Combined sources5
Turni414 – 419Combined sources6
Helixi420 – 423Combined sources4
Helixi439 – 448Combined sources10
Helixi464 – 472Combined sources9
Beta strandi478 – 483Combined sources6
Helixi486 – 489Combined sources4
Turni493 – 496Combined sources4
Helixi497 – 502Combined sources6
Beta strandi507 – 514Combined sources8
Helixi517 – 520Combined sources4
Beta strandi523 – 529Combined sources7
Helixi531 – 533Combined sources3
Beta strandi536 – 539Combined sources4
Beta strandi543 – 548Combined sources6
Helixi561 – 569Combined sources9
Helixi574 – 577Combined sources4
Helixi580 – 583Combined sources4
Helixi587 – 589Combined sources3
Helixi594 – 598Combined sources5
Beta strandi600 – 603Combined sources4
Helixi609 – 611Combined sources3
Helixi619 – 624Combined sources6
Helixi628 – 640Combined sources13
Turni641 – 644Combined sources4
Helixi650 – 655Combined sources6
Beta strandi659 – 662Combined sources4
Beta strandi670 – 674Combined sources5
Turni675 – 677Combined sources3
Beta strandi697 – 701Combined sources5
Beta strandi713 – 715Combined sources3
Beta strandi717 – 722Combined sources6
Helixi734 – 736Combined sources3
Helixi738 – 743Combined sources6
Beta strandi748 – 751Combined sources4
Helixi753 – 758Combined sources6
Beta strandi766 – 770Combined sources5
Beta strandi775 – 785Combined sources11
Beta strandi792 – 797Combined sources6
Helixi804 – 806Combined sources3
Turni814 – 816Combined sources3
Beta strandi824 – 830Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3ML1X-ray1.60A30-831[»]
3O5AX-ray1.72A30-831[»]
ProteinModelPortaliP39185
SMRiP39185
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini41 – 974Fe-4S Mo/W bis-MGD-typeUniRule annotationAdd BLAST57

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni214 – 221Mo-bis(molybdopterin guanine dinucleotide) bindingUniRule annotationCombined sources1 Publication8
Regioni245 – 249Mo-bis(molybdopterin guanine dinucleotide) bindingUniRule annotationCombined sources1 Publication5
Regioni264 – 266Mo-bis(molybdopterin guanine dinucleotide) bindingUniRule annotationCombined sources1 Publication3
Regioni511 – 512Mo-bis(molybdopterin guanine dinucleotide) bindingUniRule annotationCombined sources1 Publication2
Regioni721 – 730Mo-bis(molybdopterin guanine dinucleotide) bindingUniRule annotationCombined sources1 Publication10

Sequence similaritiesi

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

Keywords - Domaini

Signal

Phylogenomic databases

HOGENOMiHOG000031441
KOiK02567
OMAiTQHWRQQ

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.

P39185-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKISRRDFIK QTAITATASV AGVTLPAGAA NFVTDSEVTK LKWSKAPCRF
60 70 80 90 100
CGTGCGVTVA VKDNKVVATQ GDPQAEVNKG LNCVKGYFLS KIMYGQDRLT
110 120 130 140 150
RPLMRMKNGK YDKNGDFAPV TWDQAFDEME RQFKRVLKEK GPTAVGMFGS
160 170 180 190 200
GQWTVWEGYA AAKLYKAGFR SNNIDPNARH CMASAAAGFM RTFGMDEPMG
210 220 230 240 250
CYDDFEAADA FVLWGSNMAE MHPILWTRVT DRRLSHPKTR VVVLSTFTHR
260 270 280 290 300
CFDLADIGII FKPQTDLAML NYIANYIIRN NKVNKDFVNK HTVFKEGVTD
310 320 330 340 350
IGYGLRPDHP LQKAAKNASD PGAAKVITFD EFAKFVSKYD ADYVSKLSAV
360 370 380 390 400
PKAKLDQLAE LYADPNIKVM SLWTMGFNQH TRGTWANNMV YNLHLLTGKI
410 420 430 440 450
ATPGNSPFSL TGQPSACGTA REVGTFSHRL PADMVVTNPK HREEAERIWK
460 470 480 490 500
LPPGTIPDKP GYDAVLQNRM LKDGKLNAYW VQVNNNMQAA ANLMEEGLPG
510 520 530 540 550
YRNPANFIVV SDAYPTVTAL AADLVLPSAM WVEKEGAYGN AERRTQFWHQ
560 570 580 590 600
LVDAPGEARS DLWQLVEFAK RFKVEEVWPP ELIAKKPEYK GKTLYDVLYR
610 620 630 640 650
NGQVDKFPLK DVNAEYHNAE AKAFGFYLQK GLFEEYATFG RGHGHDLAPF
660 670 680 690 700
DAYHEARGLR WPVVNGKETR WRYREGSDPY VKAGTGFQFY GNPDGKAVIF
710 720 730 740 750
ALPYEPPAES PDKEYPYWLV TGRVLEHWHS GSMTRRVPEL YRSFPNAVVF
760 770 780 790 800
MHPEDAKALG LRRGVEVEVV SRRGRMRSRI ETRGRDAPPR GLVFVPWFDA
810 820 830
SQLINKVTLD ATCPISLQTD FKKCAVKIVK V
Length:831
Mass (Da):93,346
Last modified:September 27, 2004 - v2
Checksum:i34CE1CDE6677C42F
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti146 – 151GMFGSG → ACSAPA in CAA50507 (PubMed:8376334).Curated6

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X71385 Genomic DNA Translation: CAA50507.1
AY305378 Genomic DNA Translation: AAP85963.1
PIRiA48489
RefSeqiWP_011154126.1, NC_005241.1

Genome annotation databases

EnsemblBacteriaiAAP85963; AAP85963; PHG211
KEGGireh:PHG211
PATRICifig|381666.6.peg.159

Similar proteinsi

Entry informationi

Entry nameiNAPA_CUPNH
AccessioniPrimary (citable) accession number: P39185
Secondary accession number(s): Q7WXC3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: September 27, 2004
Last modified: March 28, 2018
This is version 141 of the entry and version 2 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, Plasmid, Reference proteome
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Main funding by: National Institutes of Health