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Protein

Naphthalene 1,2-dioxygenase system, large oxygenase component

Gene

doxB

Organism
Pseudomonas sp. (strain C18)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Component of the naphthalene dioxygenase (NDO) multicomponent enzyme system which catalyzes the incorporation of both atoms of molecular oxygen into naphthalene to form cis-(1R,2S)-dihydroxy-1,2-dihydronaphthalene. The alpha subunit has a catalytic role in the holoenzyme.1 Publication

Miscellaneous

Encoded on an unnamed 75 kb plasmid.1 Publication

Catalytic activityi

Naphthalene + NADH + O2 = (1R,2S)-1,2-dihydronaphthalene-1,2-diol + NAD+.By similarity

Cofactori

Protein has several cofactor binding sites:
  • [2Fe-2S] cluster2 PublicationsNote: Binds 1 [2Fe-2S] cluster per subunit.2 Publications
  • Fe2+2 PublicationsNote: Binds 1 Fe2+ ion per subunit.2 Publications

Pathwayi: naphthalene degradation

This protein is involved in the pathway naphthalene degradation, which is part of Aromatic compound metabolism.1 Publication
View all proteins of this organism that are known to be involved in the pathway naphthalene degradation and in Aromatic compound metabolism.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi81Iron-sulfur (2Fe-2S)Combined sources2 Publications1
Metal bindingi83Iron-sulfur (2Fe-2S); via pros nitrogenCombined sources2 Publications1
Metal bindingi101Iron-sulfur (2Fe-2S)Combined sources2 Publications1
Metal bindingi104Iron-sulfur (2Fe-2S); via pros nitrogenCombined sources2 Publications1
Metal bindingi208IronCombined sources2 Publications1
Metal bindingi213IronCombined sources2 Publications1
Metal bindingi362IronCombined sources2 Publications1

GO - Molecular functioni

  • 2 iron, 2 sulfur cluster binding Source: UniProtKB
  • iron ion binding Source: UniProtKB
  • naphthalene 1,2-dioxygenase activity Source: UniProtKB

GO - Biological processi

Keywordsi

Molecular functionDioxygenase, Oxidoreductase
Biological processAromatic hydrocarbons catabolism
Ligand2Fe-2S, Iron, Iron-sulfur, Metal-binding, NAD

Enzyme and pathway databases

UniPathwayiUPA00082

Names & Taxonomyi

Protein namesi
Recommended name:
Naphthalene 1,2-dioxygenase system, large oxygenase componentBy similarity (EC:1.14.12.12By similarity)
Alternative name(s):
ISP NAPBy similarity
Naphthalene 1,2-dioxygenase ISP alphaBy similarity
Naphthalene 1,2-dioxygenase subunit alpha1 Publication
Short name:
ND subunit alphaBy similarity
Short name:
NDO subunit alphaBy similarity
Gene namesi
Name:doxB1 Publication
Encoded oniPlasmid unnamed1 Publication
OrganismiPseudomonas sp. (strain C18)
Taxonomic identifieri69011 [NCBI]
Taxonomic lineageiBacteriaProteobacteria

Pathology & Biotechi

Disruption phenotypei

Cells lacking this gene are unable to degrade naphthalene.1 Publication

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi352F → V: Changes the regioselectivity of the product for naphthalene, phenanthrene and biphenyl. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000850541 – 449Naphthalene 1,2-dioxygenase system, large oxygenase componentAdd BLAST449

Interactioni

Subunit structurei

The naphthalene dioxygenase (NDO) multicomponent enzyme system is composed of an electron transfer component and a dioxygenase component (iron sulfur protein (ISP)). The electron transfer component is composed of a ferredoxin reductase and a ferredoxin (DoxA), and the dioxygenase component is formed of a heterohexamer (trimer of heterodimers) of three large alpha subunits (DoxB) and three small beta subunits (DoxD).2 Publications1 Publication

Structurei

Secondary structure

1449
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni3 – 5Combined sources3
Helixi11 – 13Combined sources3
Beta strandi15 – 17Combined sources3
Helixi18 – 21Combined sources4
Helixi24 – 33Combined sources10
Turni34 – 37Combined sources4
Beta strandi40 – 44Combined sources5
Helixi45 – 47Combined sources3
Beta strandi53 – 59Combined sources7
Beta strandi62 – 68Combined sources7
Beta strandi74 – 80Combined sources7
Turni82 – 84Combined sources3
Beta strandi91 – 95Combined sources5
Beta strandi97 – 100Combined sources4
Turni102 – 104Combined sources3
Beta strandi107 – 109Combined sources3
Beta strandi114 – 116Combined sources3
Helixi120 – 123Combined sources4
Turni124 – 126Combined sources3
Helixi130 – 132Combined sources3
Beta strandi139 – 144Combined sources6
Beta strandi147 – 152Combined sources6
Helixi159 – 163Combined sources5
Helixi166 – 174Combined sources9
Turni175 – 177Combined sources3
Beta strandi180 – 193Combined sources14
Helixi196 – 204Combined sources9
Helixi209 – 212Combined sources4
Helixi214 – 220Combined sources7
Helixi225 – 230Combined sources6
Beta strandi238 – 243Combined sources6
Beta strandi249 – 253Combined sources5
Turni257 – 260Combined sources4
Turni263 – 265Combined sources3
Helixi266 – 284Combined sources19
Helixi286 – 292Combined sources7
Beta strandi294 – 300Combined sources7
Turni301 – 303Combined sources3
Beta strandi304 – 307Combined sources4
Turni308 – 311Combined sources4
Beta strandi312 – 320Combined sources9
Beta strandi323 – 333Combined sources11
Helixi338 – 352Combined sources15
Helixi357 – 372Combined sources16
Turni376 – 380Combined sources5
Beta strandi382 – 384Combined sources3
Turni387 – 390Combined sources4
Beta strandi393 – 395Combined sources3
Beta strandi397 – 399Combined sources3
Beta strandi401 – 410Combined sources10
Helixi411 – 424Combined sources14
Helixi429 – 434Combined sources6
Turni435 – 438Combined sources4
Helixi439 – 444Combined sources6

3D structure databases

ProteinModelPortaliP0A111
SMRiP0A111
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A111

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini39 – 137RieskePROSITE-ProRule annotationAdd BLAST99

Sequence similaritiesi

Family and domain databases

Gene3Di2.102.10.10, 1 hit
InterProiView protein in InterPro
IPR017941 Rieske_2Fe-2S
IPR036922 Rieske_2Fe-2S_sf
IPR015881 Ring-hydroxy_dOase_2Fe2S_BS
IPR015879 Ring_hydroxy_dOase_asu_C_dom
IPR001663 Rng_hydr_dOase-A
PfamiView protein in Pfam
PF00355 Rieske, 1 hit
PF00848 Ring_hydroxyl_A, 1 hit
PRINTSiPR00090 RNGDIOXGNASE
SUPFAMiSSF50022 SSF50022, 1 hit
PROSITEiView protein in PROSITE
PS51296 RIESKE, 1 hit
PS00570 RING_HYDROXYL_ALPHA, 1 hit

Sequencei

Sequence statusi: Complete.

P0A111-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNYNNKILVS ESGLSQKHLI HGDEELFQHE LKTIFARNWL FLTHDSLIPA
60 70 80 90 100
PGDYVTAKMG IDEVIVSRQN DGSIRAFLNV CRHRGKTLVS VEAGNAKGFV
110 120 130 140 150
CSYHGWGFGS NGELQSVPFE KDLYGESLNK KCLGLKEVAR VESFHGFIYG
160 170 180 190 200
CFDQEAPPLM DYLGDAAWYL EPMFKHSGGL ELVGPPGKVV IKANWKAPAE
210 220 230 240 250
NFVGDAYHVG WTHASSLRSG ESIFSSLAGN AALPPEGAGL QMTSKYGSGM
260 270 280 290 300
GVLWDGYSGV HSADLVPELM AFGGAKQERL NKEIGDVRAR IYRSHLNCTV
310 320 330 340 350
FPNNSMLTCS GVFKVWNPID ANTTEVWTYA IVEKDMPEDL KRRLADSVQR
360 370 380 390 400
TFGPAGFWES DDNDNMETAS QNGKKYQSRD SDLLSNLGFG EDVYGDAVYP
410 420 430 440
GVVGKSAIGE TSYRGFYRAY QAHVSSSNWA EFEHASSTWH TELTKTTDR
Length:449
Mass (Da):49,608
Last modified:March 1, 2005 - v1
Checksum:i1FD2F42296B4F7A8
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M60405 Genomic DNA Translation: AAA16125.1
PIRiS27632

Similar proteinsi

Entry informationi

Entry nameiNDOB_PSEU8
AccessioniPrimary (citable) accession number: P0A111
Secondary accession number(s): O07830
, O33461, P23094, Q52124
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 1, 2005
Last sequence update: March 1, 2005
Last modified: November 22, 2017
This is version 65 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

3D-structure, Plasmid

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

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