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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: -Protein inferred from homologyi

Functioni

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

Catalytic activityi

2 ferrocytochrome + nitrate + 2 H+ = 2 ferricytochrome + nitrite.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)DescriptionActionsGraphical viewLength
Metal bindingi51Iron-sulfur (4Fe-4S)UniRule annotation1
Metal bindingi54Iron-sulfur (4Fe-4S)UniRule annotation1
Metal bindingi58Iron-sulfur (4Fe-4S)UniRule annotation1
Metal bindingi86Iron-sulfur (4Fe-4S)UniRule annotation1
Binding sitei88Mo-bis(molybdopterin guanine dinucleotide)UniRule annotation1
Binding sitei155Mo-bis(molybdopterin guanine dinucleotide)UniRule annotation1
Binding sitei180Mo-bis(molybdopterin guanine dinucleotide)UniRule annotation1
Binding sitei184Mo-bis(molybdopterin guanine dinucleotide)UniRule annotation1
Binding sitei378Mo-bis(molybdopterin guanine dinucleotide); via amide nitrogenUniRule annotation1
Binding sitei382Mo-bis(molybdopterin guanine dinucleotide)UniRule annotation1
Binding sitei488Mo-bis(molybdopterin guanine dinucleotide); via amide nitrogenUniRule annotation1
Binding sitei537Mo-bis(molybdopterin guanine dinucleotide)UniRule annotation1
Binding sitei564Mo-bis(molybdopterin guanine dinucleotide)UniRule annotation1
Binding sitei800Substrate; via amide nitrogenUniRule annotation1
Binding sitei808Mo-bis(molybdopterin guanine dinucleotide)UniRule annotation1
Binding sitei825Mo-bis(molybdopterin guanine dinucleotide)UniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

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

Enzyme and pathway databases

BioCyciBDIA224911:G1G3J-7089-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Periplasmic nitrate reductaseUniRule annotation (EC:1.9.6.1UniRule 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
Proteomesi
  • UP000002526 Componenti: Chromosome

Subcellular locationi

  • Periplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Periplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 32Tat-type signalUniRule annotationAdd BLAST32
ChainiPRO_000004597933 – 837Periplasmic nitrate reductaseUniRule annotationAdd BLAST805

Post-translational modificationi

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

Interactioni

Subunit structurei

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

Protein-protein interaction databases

STRINGi224911.blr7038.

Structurei

3D structure databases

ProteinModelPortaliQ89EN5.
SMRiQ89EN5.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini44 – 1004Fe-4S Mo/W bis-MGD-typeUniRule annotationAdd BLAST57

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni217 – 224Mo-bis(molybdopterin guanine dinucleotide) bindingUniRule annotation8
Regioni248 – 252Mo-bis(molybdopterin guanine dinucleotide) bindingUniRule annotation5
Regioni267 – 269Mo-bis(molybdopterin guanine dinucleotide) bindingUniRule annotation3
Regioni514 – 515Mo-bis(molybdopterin guanine dinucleotide) bindingUniRule annotation2
Regioni724 – 733Mo-bis(molybdopterin guanine dinucleotide) bindingUniRule annotation10

Sequence similaritiesi

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

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG4107QIW. Bacteria.
COG0243. LUCA.
HOGENOMiHOG000031441.
InParanoidiQ89EN5.
KOiK02567.
OMAiANSMGTR.
OrthoDBiPOG091H060P.
PhylomeDBiQ89EN5.

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.
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.
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.

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)DescriptionActionsGraphical viewLength
Sequence conflicti282K → N in AAG31648 (PubMed:14663073).Curated1
Sequence conflicti307 – 308GL → RV in AAG31648 (PubMed:14663073).Curated2
Sequence conflicti326 – 331DSTDMS → RNDPRQD (PubMed:14663073).Curated6

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. NZ_CP011360.1.

Genome annotation databases

EnsemblBacteriaiBAC52303; BAC52303; BAC52303.
GeneIDi1048006.
KEGGibja:blr7038.
PATRICifig|224911.44.peg.7092.

Similar proteinsi

Entry informationi

Entry nameiNAPA_BRADU
AccessioniPrimary (citable) accession number: Q89EN5
Secondary accession number(s): Q9F5L3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 7, 2006
Last sequence update: June 1, 2003
Last modified: March 28, 2018
This is version 105 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome