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Protein

Periplasmic nitrate reductase

Gene

napA

Organism
Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Protein inferred from homologyi

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.UniRule annotation

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)UniRule annotationNote: Binds 1 molybdenum-bis(molybdopterin guanine dinucleotide) (Mo-bis-MGD) cofactor per subunit.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi51 – 511Iron-sulfur (4Fe-4S)UniRule annotation
Metal bindingi54 – 541Iron-sulfur (4Fe-4S)UniRule annotation
Metal bindingi58 – 581Iron-sulfur (4Fe-4S)UniRule annotation
Metal bindingi86 – 861Iron-sulfur (4Fe-4S)UniRule annotation

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

Enzyme and pathway databases

BioCyciBJAP224911:GJEJ-7091-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:blr7038
OrganismiBradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110)
Taxonomic identifieri224911 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBradyrhizobiaceaeBradyrhizobium
ProteomesiUP000002526 Componenti: Chromosome

Subcellular locationi

  • Periplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Periplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 3232Tat-type signalUniRule annotationAdd
BLAST
Chaini33 – 837805Periplasmic nitrate reductasePRO_0000045979Add
BLAST

Post-translational modificationi

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

Interactioni

Subunit structurei

Interacts with NapB.UniRule annotation

Protein-protein interaction databases

STRINGi224911.blr7038.

Structurei

3D structure databases

ProteinModelPortaliQ89EN5.
SMRiQ89EN5. Positions 44-832.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini44 – 100574Fe-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.
InParanoidiQ89EN5.
KOiK02567.
OrthoDBiEOG6CVV7G.
PhylomeDBiQ89EN5.

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.
[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.
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.

Q89EN5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTSPKLDRRQ MLKLEAAAIA AAAAGLPVPA LAANLATERE VSELKWDKAA
60 70 80 90 100
CRFCGTGCSV MVATKENRVV ATHGDIKAEV NRGLNCVKGY FLSKIMYGHD
110 120 130 140 150
RLTQPMLRKA NGKYDKNGDF TPVSWTEAFD IMEVKWKEAM KKRGPNGVAM
160 170 180 190 200
FGSGQWTIWE GYAASKLFKA GFRTNNIDPN ARHCMASAVA GMMRTFGIDE
210 220 230 240 250
PPGCYDDIEA TDAFVLWGSN MAEMHPILWT RLTDRRLSAP HVRVAVLSTF
260 270 280 290 300
EHRSFDLADI GMVFKPQTDL YLLNAIANHI IKTGRVNKDF VAAHTVFRRG
310 320 330 340 350
QTDIGYGLRP EHPLQKKATG AAKANDSTDM SYDEYVKFVS EYTLEKAAEM
360 370 380 390 400
SGVPLNRLEA LAELYADPKT KVVSFWTMGF NQHTRGVWCN NLVYNIHLLT
410 420 430 440 450
GKISSPGNSP FSLTGQPSAC GTAREVGTFS HRLPADMVVT NKEHRTKAEH
460 470 480 490 500
IWQLPEGTIP DKPGAHAVLQ SRMLKDGLIN AYWVQVNNNL QAGPNANEET
510 520 530 540 550
YPGFRNPDNF IVVSDAYPSV TALAADLILP TAMWVEKEGA YGNAERRTQF
560 570 580 590 600
WHQLVPAPGE SKSDLWQLME FSKRFKIEEV WPEELIAKKP EVRGKTLFDV
610 620 630 640 650
LYKNGQVDKF PVSDIEQGYL NDESKAFGFY VHKGLFEEYA SFGRGHGHDL
660 670 680 690 700
APFDAYHKER GLRWPVVNGQ ETRWRFREGS DPYVKQGTDV QFYGYPDGKA
710 720 730 740 750
RIFALPYEPA AESPDGEYPF WLSTGRVLEH WHSGTMTRRV PELYKAFPEA
760 770 780 790 800
VCFMHPDDAQ EAKIRRGDEV KVVSRRGFIR VRVETRGRDR PPRGLVFVPW
810 820 830
FDESKLINKV TLDATDPISL QTDFKKCAVR IERVNVS
Length:837
Mass (Da):94,215
Last modified:June 1, 2003 - v1
Checksum:i0F5976FF14FDD5CE
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti282 – 2821K → N in AAG31648 (PubMed:14663073).Curated
Sequence conflicti307 – 3082GL → RV in AAG31648 (PubMed:14663073).Curated
Sequence conflicti326 – 3316DSTDMS → RNDPRQD (PubMed:14663073).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000040 Genomic DNA. Translation: BAC52303.1.
AF314590 Genomic DNA. Translation: AAG31648.2.
RefSeqiNP_773678.1. NC_004463.1.
WP_011089775.1. NC_004463.1.

Genome annotation databases

EnsemblBacteriaiBAC52303; BAC52303; BAC52303.
GeneIDi1048006.
KEGGibja:blr7038.
PATRICi21197969. VBIBraJap65052_7217.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000040 Genomic DNA. Translation: BAC52303.1.
AF314590 Genomic DNA. Translation: AAG31648.2.
RefSeqiNP_773678.1. NC_004463.1.
WP_011089775.1. NC_004463.1.

3D structure databases

ProteinModelPortaliQ89EN5.
SMRiQ89EN5. Positions 44-832.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224911.blr7038.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAC52303; BAC52303; BAC52303.
GeneIDi1048006.
KEGGibja:blr7038.
PATRICi21197969. VBIBraJap65052_7217.

Phylogenomic databases

eggNOGiCOG0243.
HOGENOMiHOG000031441.
InParanoidiQ89EN5.
KOiK02567.
OrthoDBiEOG6CVV7G.
PhylomeDBiQ89EN5.

Enzyme and pathway databases

BioCyciBJAP224911:GJEJ-7091-MONOMER.

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.
[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.
PROSITEiPS51669. 4FE4S_MOW_BIS_MGD. 1 hit.
PS00551. MOLYBDOPTERIN_PROK_1. 1 hit.
PS51318. TAT. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110.
  2. "The Bradyrhizobium japonicum napEDABC genes encoding the periplasmic nitrate reductase are essential for nitrate respiration."
    Delgado M., Bonnard N., Tresierra-Ayala A., Bedmar E.J., Muller P.
    Microbiology 149:3395-3403(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: USDA 110spc4.

Entry informationi

Entry nameiNAPA_BRADU
AccessioniPrimary (citable) accession number: Q89EN5
Secondary accession number(s): Q9F5L3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 7, 2006
Last sequence update: June 1, 2003
Last modified: May 27, 2015
This is version 89 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.