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Protein

Periplasmic nitrate reductase

Gene

napA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 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 (By similarity).By similarity

Catalytic activityi

Nitrite + acceptor = nitrate + reduced acceptor.

Cofactori

Protein has several cofactor binding sites:

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi46Iron-sulfur (4Fe-4S)By similarity1
Metal bindingi49Iron-sulfur (4Fe-4S)By similarity1
Metal bindingi53Iron-sulfur (4Fe-4S)By similarity1
Metal bindingi81Iron-sulfur (4Fe-4S)By similarity1

GO - Molecular functioni

  • 4 iron, 4 sulfur cluster binding Source: EcoCyc
  • electron carrier activity Source: UniProtKB-HAMAP
  • iron ion binding Source: UniProtKB-HAMAP
  • molybdenum ion binding Source: EcoCyc
  • nitrate reductase activity Source: CACAO

GO - Biological processi

  • anaerobic respiration Source: EcoliWiki
  • Mo-molybdopterin cofactor biosynthetic process Source: UniProtKB-HAMAP
  • 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

BioCyciEcoCyc:NAPA-MONOMER.
ECOL316407:JW2194-MONOMER.
MetaCyc:NAPA-MONOMER.
BRENDAi1.9.6.1. 2165.

Names & Taxonomyi

Protein namesi
Recommended name:
Periplasmic nitrate reductase (EC:1.7.99.4)
Gene namesi
Name:napA
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 1 Publication

GO - Cellular componenti

  • outer membrane-bounded periplasmic space Source: CACAO
  • periplasmic space Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Periplasm

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. The position of the signal peptide cleavage has been experimentally proven.

Proteomic databases

PaxDbiP33937.
PRIDEiP33937.

Interactioni

Subunit structurei

Interacts with NapB.By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
napDP0A9I58EBI-554952,EBI-554985

Protein-protein interaction databases

BioGridi4262221. 119 interactors.
DIPiDIP-10304N.
IntActiP33937. 12 interactors.
MINTiMINT-1243254.
STRINGi511145.b2206.

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

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2NYAX-ray2.50A/F37-828[»]
2PQ4NMR-B1-35[»]
ProteinModelPortaliP33937.
SMRiP33937.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP33937.

Family & Domainsi

Domains and Repeats

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

Sequence similaritiesi

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG4107QIW. Bacteria.
COG0243. LUCA.
HOGENOMiHOG000031441.
InParanoidiP33937.
KOiK02567.
OMAiEEYDLWM.
PhylomeDBiP33937.

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.

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.
PATRICi32119771. VBIEscCol129921_2295.

Cross-referencesi

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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2NYAX-ray2.50A/F37-828[»]
2PQ4NMR-B1-35[»]
ProteinModelPortaliP33937.
SMRiP33937.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262221. 119 interactors.
DIPiDIP-10304N.
IntActiP33937. 12 interactors.
MINTiMINT-1243254.
STRINGi511145.b2206.

Proteomic databases

PaxDbiP33937.
PRIDEiP33937.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75266; AAC75266; b2206.
BAA15989; BAA15989; BAA15989.
GeneIDi947093.
KEGGiecj:JW2194.
eco:b2206.
PATRICi32119771. VBIEscCol129921_2295.

Organism-specific databases

EchoBASEiEB1994.
EcoGeneiEG12067. napA.

Phylogenomic databases

eggNOGiENOG4107QIW. Bacteria.
COG0243. LUCA.
HOGENOMiHOG000031441.
InParanoidiP33937.
KOiK02567.
OMAiEEYDLWM.
PhylomeDBiP33937.

Enzyme and pathway databases

BioCyciEcoCyc:NAPA-MONOMER.
ECOL316407:JW2194-MONOMER.
MetaCyc:NAPA-MONOMER.
BRENDAi1.9.6.1. 2165.

Miscellaneous databases

EvolutionaryTraceiP33937.
PROiP33937.

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_ECOLI
AccessioniPrimary (citable) accession number: P33937
Secondary accession number(s): P78087
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: November 1, 1997
Last modified: November 2, 2016
This is version 158 of the entry and version 3 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, 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

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.