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Protein

Periplasmic nitrate reductase

Gene

napA

Organism
Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)
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 annotation1 Publication)
Gene namesi
Name:napAUniRule annotation
Ordered Locus Names:RHOS4_40230
ORF Names:RSP_4116
Encoded oniPlasmid pRS241c1 Publication
OrganismiRhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)
Taxonomic identifieri272943 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhodobacteralesRhodobacteraceaeRhodobacter
Proteomesi
  • UP000002703 Componenti: Plasmid pRS241c

Subcellular locationi

  • Periplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Periplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 29Tat-type signalUniRule annotationAdd BLAST29
ChainiPRO_000001917130 – 831Periplasmic nitrate reductaseUniRule annotationAdd BLAST802

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

Expressioni

Inductioni

Nitrate reductase activity can be induced by nitrate and not repressed by ammonium or oxygen.

Interactioni

Subunit structurei

Component of the periplasmic nitrate reductase NapAB complex composed of NapA and NapB.UniRule annotation1 Publication

Protein-protein interaction databases

IntActiQ53176, 1 interactor

Structurei

Secondary structure

1831
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi42 – 47Combined sources6
Beta strandi56 – 62Combined sources7
Beta strandi65 – 71Combined sources7
Turni76 – 78Combined sources3
Helixi84 – 87Combined sources4
Helixi88 – 91Combined sources4
Beta strandi103 – 105Combined sources3
Beta strandi107 – 109Combined sources3
Helixi122 – 139Combined sources18
Helixi142 – 144Combined sources3
Beta strandi145 – 149Combined sources5
Helixi155 – 166Combined sources12
Beta strandi174 – 176Combined sources3
Helixi178 – 181Combined sources4
Helixi183 – 193Combined sources11
Helixi204 – 207Combined sources4
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 – 296Combined sources5
Helixi310 – 313Combined sources4
Helixi329 – 337Combined sources9
Helixi341 – 348Combined sources8
Helixi352 – 361Combined sources10
Beta strandi369 – 374Combined sources6
Helixi375 – 378Combined sources4
Helixi383 – 397Combined sources15
Beta strandi405 – 409Combined sources5
Turni414 – 419Combined sources6
Helixi420 – 423Combined sources4
Turni431 – 433Combined sources3
Beta strandi434 – 437Combined sources4
Helixi439 – 448Combined sources10
Helixi464 – 472Combined sources9
Beta strandi478 – 483Combined sources6
Helixi486 – 489Combined sources4
Turni491 – 497Combined sources7
Helixi498 – 502Combined sources5
Beta strandi507 – 514Combined sources8
Helixi517 – 520Combined sources4
Beta strandi522 – 528Combined sources7
Helixi531 – 533Combined sources3
Beta strandi536 – 539Combined sources4
Beta strandi543 – 548Combined sources6
Helixi561 – 569Combined sources9
Helixi574 – 577Combined sources4
Helixi580 – 585Combined sources6
Beta strandi587 – 591Combined sources5
Turni594 – 599Combined sources6
Beta strandi601 – 605Combined sources5
Beta strandi607 – 612Combined sources6
Beta strandi614 – 617Combined sources4
Helixi619 – 622Combined sources4
Beta strandi623 – 626Combined sources4
Helixi628 – 637Combined sources10
Beta strandi640 – 644Combined sources5
Helixi652 – 655Combined sources4
Beta strandi659 – 661Combined sources3
Beta strandi670 – 675Combined sources6
Beta strandi692 – 694Combined sources3
Beta strandi697 – 701Combined sources5
Beta strandi713 – 715Combined sources3
Beta strandi717 – 722Combined sources6
Helixi734 – 736Combined sources3
Helixi738 – 743Combined sources6
Beta strandi748 – 750Combined sources3
Helixi753 – 758Combined sources6
Beta strandi766 – 770Combined sources5
Beta strandi775 – 787Combined sources13
Beta strandi792 – 796Combined sources5
Beta strandi800 – 802Combined sources3
Helixi804 – 806Combined sources3
Turni814 – 816Combined sources3
Beta strandi825 – 829Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1OGYX-ray3.20A/C/E/G/I/K/M/O30-831[»]
ProteinModelPortaliQ53176
SMRiQ53176
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ53176

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 annotationBy similarity5
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
OrthoDBiPOG091H060P
PhylomeDBiQ53176

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.

Q53176-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTLTRRDLIK AQAAATAAAA AGLPVSALAQ PVTGGAEALR IRWSKAPCRF
60 70 80 90 100
CGTGCGVMVG TRDGQVVATH GDTQAEVNRG LNCVKGYFLS KIMYGEDRLT
110 120 130 140 150
TPLLRMKDGV YHKEGEFAPV SWDEAFDVMA AQAKRVLKEK GPKAVGMFGS
160 170 180 190 200
GQWTIWEGYA ASKLMRAGFR SNNLDPNARH CMASAATAFM RTFGMDEPMG
210 220 230 240 250
CYDDFEAADA FVLWGSNMAE MHPILWSRLT DRRLSHEHVR VAVLSTFTHR
260 270 280 290 300
SMDLADTPII FRPGTDLAIL NYIAHHIIST GRVNRDFVDR HTNFALGATD
310 320 330 340 350
IGYGLRPEHQ LQLAAKGAAD AGAMTPTDFE TFAALVSEYT LEKAAEISGV
360 370 380 390 400
EPALLEELAE LYADPDRKVM SLWTMGFNQH VRGVWANHMV YNLHLLTGKI
410 420 430 440 450
SEPGNSPFSL TGQPSACGTA REVGTFAHRL PADMVVTNPE HRAHAEEIWK
460 470 480 490 500
LPAGLLPDWV GAHAVEQDRK LHDGEINFYW VQVNNNMQAA PNIDQETYPG
510 520 530 540 550
YRNPENFIVV SDAYPTVTGR CADLVLPAAM WVEKEGAYGN AERRTHFWHQ
560 570 580 590 600
LVEAPGEARS DLWQLMEFSK RFTTDEVWPE EILSAAPAYR GKTLFEVLFA
610 620 630 640 650
NGSVDRFPAS DVNPDHANHE AALFGFYPQK GLFEEYAAFG RGHGHDLAPF
660 670 680 690 700
DTYHEVRGLR WPVVEGEETR WRYREGFDPY VKPGEGLRFY GKPDGRAVIL
710 720 730 740 750
GVPYEPPAES PDEEFGFWLV TGRVLEHWHS GSMTLRVPEL YKAFPGAVCF
760 770 780 790 800
MHPEDARSRG LNRGSEVRVI SRRGEIRTRL ETRGRNRMPR GVVFVPWFDA
810 820 830
SQLINKVTLD ANDPISRQTD FKKCAVKIEA V
Length:831
Mass (Da):92,637
Last modified:January 24, 2006 - v2
Checksum:i74B35640749CC906
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti135R → L in CAA86827 (PubMed:8730872).Curated1
Sequence conflicti141G → A (PubMed:8730872).Curated1
Sequence conflicti143K → E (PubMed:8730872).Curated1
Sequence conflicti252M → S in CAA86827 (PubMed:8730872).Curated1
Sequence conflicti255A → S in CAA86827 (PubMed:8730872).Curated1
Sequence conflicti267L → R in CAA86827 (PubMed:8730872).Curated1
Sequence conflicti369V → W in CAA86827 (PubMed:8730872).Curated1
Sequence conflicti415S → F in CAA86827 (PubMed:8730872).Curated1
Sequence conflicti521C → A in CAA86827 (PubMed:8730872).Curated1
Sequence conflicti660R → H in CAA86827 (PubMed:8730872).Curated1
Sequence conflicti737V → W in CAA86827 (PubMed:8730872).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z46806 Genomic DNA Translation: CAA86827.1
CP000146 Genomic DNA Translation: ABA81591.1
RefSeqiWP_011331398.1, NZ_AKVW01000005.1
YP_345332.1, NC_007489.1

Genome annotation databases

EnsemblBacteriaiABA81591; ABA81591; RSP_4116
GeneIDi3711832
KEGGirsp:RSP_4116
PATRICifig|272943.9.peg.178

Similar proteinsi

Entry informationi

Entry nameiNAPA_RHOS4
AccessioniPrimary (citable) accession number: Q53176
Secondary accession number(s): Q3IV43
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: January 24, 2006
Last modified: March 28, 2018
This is version 135 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, 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
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