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Protein

Naphthalene 1,2-dioxygenase subunit beta

Gene

doxD

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. The beta subunit may be responsible for the substrate specificity of the enzyme.

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.

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Dioxygenase, Oxidoreductase

Keywords - Biological processi

Aromatic hydrocarbons catabolism

Keywords - Ligandi

NAD

Enzyme and pathway databases

UniPathwayiUPA00082.

Names & Taxonomyi

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

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 194194Naphthalene 1,2-dioxygenase subunit betaPRO_0000085073Add
BLAST

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

1
194
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni5 – 73Combined sources
Helixi13 – 2311Combined sources
Helixi28 – 4619Combined sources
Helixi50 – 578Combined sources
Beta strandi58 – 6912Combined sources
Beta strandi84 – 907Combined sources
Helixi92 – 10312Combined sources
Helixi108 – 1103Combined sources
Beta strandi115 – 12713Combined sources
Beta strandi134 – 14714Combined sources
Turni148 – 1503Combined sources
Beta strandi151 – 16515Combined sources
Helixi167 – 1693Combined sources
Beta strandi171 – 1799Combined sources
Beta strandi183 – 1853Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2HMJX-ray1.50B1-194[»]
2HMKX-ray1.65B1-194[»]
2HMLX-ray1.80B1-194[»]
2HMMX-ray1.60B1-194[»]
2HMNX-ray1.70B1-194[»]
2HMOX-ray1.60B1-194[»]
4HJLX-ray1.50B3-194[»]
4HKVX-ray1.65B1-194[»]
4HM0X-ray1.80B1-194[»]
4HM1X-ray1.50B1-194[»]
4HM2X-ray1.60B1-194[»]
4HM3X-ray1.50B1-194[»]
4HM4X-ray1.50B1-194[»]
4HM5X-ray1.50B1-194[»]
4HM6X-ray1.50B1-194[»]
4HM7X-ray1.50B1-194[»]
4HM8X-ray1.30B1-194[»]
ProteinModelPortaliP0A113.
SMRiP0A113. Positions 2-194.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A113.

Family & Domainsi

Sequence similaritiesi

Family and domain databases

Gene3Di3.10.450.50. 1 hit.
InterProiIPR032710. NTF2-like_dom.
IPR000391. Rng_hydr_dOase-bsu.
[Graphical view]
PfamiPF00866. Ring_hydroxyl_B. 1 hit.
[Graphical view]
SUPFAMiSSF54427. SSF54427. 1 hit.

Sequencei

Sequence statusi: Complete.

P0A113-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MMINIQEDKL VSAHDAEEIL RFFNCHDSAL QQEATTLLTQ EAHLLDIQAY
60 70 80 90 100
RAWLEHCVGS EVQYQVISRE LRAASERRYK LNEAMNVYNE NFQQLKVRVE
110 120 130 140 150
HQLDPQNWGN SPKLRFTRFI TNVQAAMDVN DKELLHIRSN VILHRARRGN
160 170 180 190
QVDVFYAARE DKWKRGEGGV RKLVQRFVDY PERILQTHNL MVFL
Length:194
Mass (Da):22,935
Last modified:March 1, 2005 - v1
Checksum:i168D2E1535E66416
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M60405 Genomic DNA. Translation: AAA16127.1.
PIRiS27634.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M60405 Genomic DNA. Translation: AAA16127.1.
PIRiS27634.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2HMJX-ray1.50B1-194[»]
2HMKX-ray1.65B1-194[»]
2HMLX-ray1.80B1-194[»]
2HMMX-ray1.60B1-194[»]
2HMNX-ray1.70B1-194[»]
2HMOX-ray1.60B1-194[»]
4HJLX-ray1.50B3-194[»]
4HKVX-ray1.65B1-194[»]
4HM0X-ray1.80B1-194[»]
4HM1X-ray1.50B1-194[»]
4HM2X-ray1.60B1-194[»]
4HM3X-ray1.50B1-194[»]
4HM4X-ray1.50B1-194[»]
4HM5X-ray1.50B1-194[»]
4HM6X-ray1.50B1-194[»]
4HM7X-ray1.50B1-194[»]
4HM8X-ray1.30B1-194[»]
ProteinModelPortaliP0A113.
SMRiP0A113. Positions 2-194.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

UniPathwayiUPA00082.

Miscellaneous databases

EvolutionaryTraceiP0A113.

Family and domain databases

Gene3Di3.10.450.50. 1 hit.
InterProiIPR032710. NTF2-like_dom.
IPR000391. Rng_hydr_dOase-bsu.
[Graphical view]
PfamiPF00866. Ring_hydroxyl_B. 1 hit.
[Graphical view]
SUPFAMiSSF54427. SSF54427. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "Metabolism of dibenzothiophene and naphthalene in Pseudomonas strains: complete DNA sequence of an upper naphthalene catabolic pathway."
    Denome S.A., Stanley D.C., Olson E.S., Young K.D.
    J. Bacteriol. 175:6890-6901(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: C18.
    Plasmid: unnamed

Entry informationi

Entry nameiNDOC_PSEU8
AccessioniPrimary (citable) accession number: P0A113
Secondary accession number(s): P23095, Q52125
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 1, 2005
Last sequence update: March 1, 2005
Last modified: January 20, 2016
This is version 49 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.