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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: 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

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi48Iron-sulfur (4Fe-4S)UniRule annotation1
Metal bindingi51Iron-sulfur (4Fe-4S)UniRule annotation1
Metal bindingi55Iron-sulfur (4Fe-4S)UniRule annotation1
Metal bindingi83Iron-sulfur (4Fe-4S)UniRule annotation1

GO - Molecular functioni

GO - Biological processi

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

Names & Taxonomyi

Protein namesi
Recommended name:
Periplasmic nitrate reductaseUniRule annotation (EC:1.7.99.4UniRule annotation)
Gene namesi
Name:napAUniRule 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

GO - Cellular componenti

Complete GO annotation...

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 reductaseAdd BLAST802

Post-translational modificationi

Predicted to be exported by the Tat system. The position of the signal peptide cleavage has been experimentally proven.

Expressioni

Inductioni

Expressed independently of nitrate induction and anaerobiosis.

Interactioni

Subunit structurei

Interacts with NapB.UniRule annotation

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

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

HOGENOMiHOG000031441.
KOiK02567.
OMAiRIFALPY.

Family and domain databases

HAMAPiMF_01630. Nitrate_reduct. 1 hit.
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.

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.
GeneIDi2656653.
KEGGireh:PHG211.
PATRICi35228976. VBIRalEut6770_0159.

Cross-referencesi

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.

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...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAP85963; AAP85963; PHG211.
GeneIDi2656653.
KEGGireh:PHG211.
PATRICi35228976. VBIRalEut6770_0159.

Phylogenomic databases

HOGENOMiHOG000031441.
KOiK02567.
OMAiRIFALPY.

Family and domain databases

HAMAPiMF_01630. Nitrate_reduct. 1 hit.
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]
ProtoNetiSearch...

Entry informationi

Entry nameiNAPA_CUPNH
AccessioniPrimary (citable) accession number: P39185
Secondary accession number(s): Q7WXC3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: September 27, 2004
Last modified: November 2, 2016
This is version 133 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, Direct protein sequencing, 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.