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Protein

Naphthalene 1,2-dioxygenase subunit alpha

Gene

doxB

Organism
Pseudomonas sp. (strain C18)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-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-naphthalene dihydrodiol.

Catalytic activityi

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

Cofactori

Protein has several cofactor binding sites:
  • [2Fe-2S] clusterBy similarityNote: Binds 1 [2Fe-2S] cluster.By similarity
  • Fe cationBy similarityNote: Binds 1 Fe cation.By similarity

Pathwayi: naphthalene degradation

This protein is involved in the pathway naphthalene degradation, which is part of Aromatic compound metabolism.
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)PROSITE-ProRule annotation1
Metal bindingi83Iron-sulfur (2Fe-2S); via pros nitrogenPROSITE-ProRule annotation1
Metal bindingi101Iron-sulfur (2Fe-2S)PROSITE-ProRule annotation1
Metal bindingi104Iron-sulfur (2Fe-2S); via pros nitrogenPROSITE-ProRule annotation1
Metal bindingi208IronBy similarity1
Metal bindingi213IronBy similarity1
Metal bindingi362IronBy similarity1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Dioxygenase, Oxidoreductase

Keywords - Biological processi

Aromatic hydrocarbons catabolism

Keywords - Ligandi

2Fe-2S, Iron, Iron-sulfur, Metal-binding, NAD

Enzyme and pathway databases

UniPathwayiUPA00082.

Names & Taxonomyi

Protein namesi
Recommended name:
Naphthalene 1,2-dioxygenase subunit alpha (EC:1.14.12.12)
Alternative name(s):
Naphthalene 1,2-dioxygenase ISP alpha
Gene namesi
Name:doxB
Encoded oniPlasmid unnamed1 Publication
OrganismiPseudomonas sp. (strain C18)
Taxonomic identifieri69011 [NCBI]
Taxonomic lineageiBacteriaProteobacteria

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000850541 – 449Naphthalene 1,2-dioxygenase subunit alphaAdd BLAST449

Interactioni

Subunit structurei

Naphthalene dioxygenase (NDO) multicomponent enzyme system is composed of an electron transfer component and an iron sulfur protein (ISP). The electron transfer component is composed of ferredoxin reductase and ferredoxin (DoxA), and ISP is composed of a large alpha subunit (DoxB) and a small beta subunit (DoxD) (Probable).Curated

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

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2HMJX-ray1.50A1-449[»]
2HMKX-ray1.65A1-449[»]
2HMLX-ray1.80A1-449[»]
2HMMX-ray1.60A1-449[»]
2HMNX-ray1.70A1-449[»]
2HMOX-ray1.60A1-449[»]
4HJLX-ray1.50A1-446[»]
4HKVX-ray1.65A1-449[»]
4HM0X-ray1.80A1-449[»]
4HM1X-ray1.50A1-449[»]
4HM2X-ray1.60A1-449[»]
4HM3X-ray1.50A1-449[»]
4HM4X-ray1.50A1-449[»]
4HM5X-ray1.50A1-449[»]
4HM6X-ray1.50A1-449[»]
4HM7X-ray1.50A1-449[»]
4HM8X-ray1.30A1-449[»]
ProteinModelPortaliP0A111.
SMRiP0A111.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A111.

Family & Domainsi

Domains and Repeats

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

Sequence similaritiesi

Contains 1 Rieske domain.PROSITE-ProRule annotation

Family and domain databases

Gene3Di2.102.10.10. 1 hit.
3.90.380.10. 1 hit.
InterProiIPR017941. Rieske_2Fe-2S.
IPR015881. Ring-hydroxy_dOase_2Fe2S_BS.
IPR015879. Ring_hydroxy_dOase_asu_C_dom.
IPR001663. Rng_hydr_dOase-A.
[Graphical view]
PfamiPF00355. Rieske. 1 hit.
PF00848. Ring_hydroxyl_A. 1 hit.
[Graphical view]
PRINTSiPR00090. RNGDIOXGNASE.
SUPFAMiSSF50022. SSF50022. 1 hit.
PROSITEiPS51296. RIESKE. 1 hit.
PS00570. RING_HYDROXYL_ALPHA. 1 hit.
[Graphical view]

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.

Cross-referencesi

Sequence databases

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

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2HMJX-ray1.50A1-449[»]
2HMKX-ray1.65A1-449[»]
2HMLX-ray1.80A1-449[»]
2HMMX-ray1.60A1-449[»]
2HMNX-ray1.70A1-449[»]
2HMOX-ray1.60A1-449[»]
4HJLX-ray1.50A1-446[»]
4HKVX-ray1.65A1-449[»]
4HM0X-ray1.80A1-449[»]
4HM1X-ray1.50A1-449[»]
4HM2X-ray1.60A1-449[»]
4HM3X-ray1.50A1-449[»]
4HM4X-ray1.50A1-449[»]
4HM5X-ray1.50A1-449[»]
4HM6X-ray1.50A1-449[»]
4HM7X-ray1.50A1-449[»]
4HM8X-ray1.30A1-449[»]
ProteinModelPortaliP0A111.
SMRiP0A111.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

UniPathwayiUPA00082.

Miscellaneous databases

EvolutionaryTraceiP0A111.

Family and domain databases

Gene3Di2.102.10.10. 1 hit.
3.90.380.10. 1 hit.
InterProiIPR017941. Rieske_2Fe-2S.
IPR015881. Ring-hydroxy_dOase_2Fe2S_BS.
IPR015879. Ring_hydroxy_dOase_asu_C_dom.
IPR001663. Rng_hydr_dOase-A.
[Graphical view]
PfamiPF00355. Rieske. 1 hit.
PF00848. Ring_hydroxyl_A. 1 hit.
[Graphical view]
PRINTSiPR00090. RNGDIOXGNASE.
SUPFAMiSSF50022. SSF50022. 1 hit.
PROSITEiPS51296. RIESKE. 1 hit.
PS00570. RING_HYDROXYL_ALPHA. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiNDOB_PSEU8
AccessioniPrimary (citable) accession number: P0A111
Secondary accession number(s): O07830
, O33461, P23094, Q52124
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 1, 2005
Last sequence update: March 1, 2005
Last modified: November 2, 2016
This is version 60 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Encoded on an unnamed 75 kb plasmid.1 Publication

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

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.