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P0A110

- NDOB_PSEPU

UniProt

P0A110 - NDOB_PSEPU

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Protein
Naphthalene 1,2-dioxygenase subunit alpha
Gene
ndoB, nahA3, nahAC, ndoC2
Organism
Pseudomonas putida (Arthrobacter siderocapsulatus)
Status
Reviewed - Annotation score: 5 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

Binds 1 2Fe-2S cluster Inferred.
Binds 1 iron ion Inferred.

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi81 – 811Iron-sulfur (2Fe-2S)
Metal bindingi83 – 831Iron-sulfur (2Fe-2S); via pros nitrogen
Metal bindingi101 – 1011Iron-sulfur (2Fe-2S)
Metal bindingi104 – 1041Iron-sulfur (2Fe-2S); via pros nitrogen
Metal bindingi208 – 2081Iron
Metal bindingi213 – 2131Iron
Metal bindingi362 – 3621Iron

GO - Molecular functioni

  1. 2 iron, 2 sulfur cluster binding Source: UniProtKB-KW
  2. iron ion binding Source: InterPro
  3. naphthalene 1,2-dioxygenase activity Source: UniProtKB-EC
  4. protein binding Source: IntAct

GO - Biological processi

  1. aromatic compound catabolic process Source: UniProtKB-KW
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

BioCyciMetaCyc:MONOMER-12802.
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:ndoB
Synonyms:nahA3, nahAC, ndoC2
Encoded oniPlasmid pDTG11 Publication
Plasmid NAH71 Publication
Plasmid NPL11 Publication
OrganismiPseudomonas putida (Arthrobacter siderocapsulatus)
Taxonomic identifieri303 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 449449Naphthalene 1,2-dioxygenase subunit alpha
PRO_0000085053Add
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 (NdoR) and ferredoxin (NdoA), and ISP is composed of a large alpha subunit (NdoB) and a small beta subunit (NdoC).

Binary interactionsi

WithEntry#Exp.IntActNotes
ndoCP0A1127EBI-1029015,EBI-1029028

Protein-protein interaction databases

IntActiP0A110. 1 interaction.
MINTiMINT-257428.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni3 – 53
Helixi11 – 133
Beta strandi15 – 173
Helixi18 – 214
Helixi24 – 3310
Turni34 – 374
Beta strandi40 – 445
Helixi45 – 473
Beta strandi53 – 597
Beta strandi62 – 687
Beta strandi74 – 807
Turni82 – 843
Beta strandi91 – 955
Beta strandi97 – 1004
Turni102 – 1043
Beta strandi107 – 1093
Beta strandi114 – 1163
Helixi120 – 1234
Turni124 – 1263
Helixi130 – 1323
Beta strandi139 – 1446
Beta strandi147 – 1526
Helixi159 – 1635
Helixi166 – 1749
Turni175 – 1773
Beta strandi180 – 19314
Helixi196 – 2049
Helixi209 – 2124
Helixi214 – 2207
Helixi225 – 2306
Beta strandi238 – 2436
Beta strandi249 – 2535
Turni257 – 2604
Turni263 – 2653
Helixi266 – 28419
Helixi286 – 2927
Beta strandi294 – 3007
Turni301 – 3033
Beta strandi304 – 3074
Turni308 – 3114
Beta strandi312 – 3209
Beta strandi323 – 33311
Helixi338 – 35215
Helixi357 – 37216
Turni376 – 3805
Beta strandi382 – 3843
Turni387 – 3904
Beta strandi393 – 3953
Beta strandi397 – 3993
Beta strandi401 – 4088
Helixi411 – 42414
Helixi429 – 4357
Turni436 – 4383
Helixi439 – 4446

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1EG9X-ray1.60A1-449[»]
1NDOX-ray2.25A/C/E1-449[»]
1O7GX-ray1.70A1-449[»]
1O7HX-ray2.20A1-449[»]
1O7MX-ray1.75A1-449[»]
1O7NX-ray1.40A1-449[»]
1O7PX-ray1.95A1-449[»]
1O7WX-ray1.90A1-449[»]
1UUVX-ray1.65A1-449[»]
1UUWX-ray2.30A1-449[»]
ProteinModelPortaliP0A110.
SMRiP0A110. Positions 1-447.

Miscellaneous databases

EvolutionaryTraceiP0A110.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini39 – 13799Rieske
Add
BLAST

Sequence similaritiesi

Contains 1 Rieske domain.

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.

P0A110-1 [UniParc]FASTAAdd to Basket

« Hide

MNYNNKILVS ESGLSQKHLI HGDEELFQHE LKTIFARNWL FLTHDSLIPA    50
PGDYVTAKMG IDEVIVSRQN DGSIRAFLNV CRHRGKTLVS VEAGNAKGFV 100
CSYHGWGFGS NGELQSVPFE KDLYGESLNK KCLGLKEVAR VESFHGFIYG 150
CFDQEAPPLM DYLGDAAWYL EPMFKHSGGL ELVGPPGKVV IKANWKAPAE 200
NFVGDAYHVG WTHASSLRSG ESIFSSLAGN AALPPEGAGL QMTSKYGSGM 250
GVLWDGYSGV HSADLVPELM AFGGAKQERL NKEIGDVRAR IYRSHLNCTV 300
FPNNSMLTCS GVFKVWNPID ANTTEVWTYA IVEKDMPEDL KRRLADSVQR 350
TFGPAGFWES DDNDNMETAS QNGKKYQSRD SDLLSNLGFG EDVYGDAVYP 400
GVVGKSAIGE TSYRGFYRAY QAHVSSSNWA EFEHASSTWH TELTKTTDR 449
Length:449
Mass (Da):49,608
Last modified:March 1, 2005 - v1
Checksum:i1FD2F42296B4F7A8
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti4 – 41N → K in strain: G7.
Natural varianti12 – 121S → F in strain: ATCC 17484.
Natural varianti15 – 151S → T in strain: G7.
Natural varianti32 – 321K → R in strain: G7.
Natural varianti50 – 501A → S in strain: G7.
Natural varianti70 – 701N → S in strain: G7.
Natural varianti90 – 912SV → NA in strain: G7.
Natural varianti122 – 1221D → E in strain: G7.
Natural varianti173 – 1731M → I in strain: G7.
Natural varianti225 – 2251S → A in strain: G7.
Natural varianti225 – 2251S → C in strain: BS202.
Natural varianti232 – 2321A → V in strain: G7.
Natural varianti275 – 2751A → S in strain: G7.
Natural varianti391 – 3911E → K in strain: G7.
Natural varianti421 – 4211Q → R in strain: ATCC 17484.
Natural varianti434 – 4341H → D in strain: G7.

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M23914 Genomic DNA. Translation: AAB47591.1.
U49496 Genomic DNA. Translation: AAA92141.1.
M83949 Genomic DNA. Translation: AAA25902.1.
AF010471 Genomic DNA. Translation: AAB62707.1.
AF004284 Genomic DNA. Translation: AAB61373.1.
PIRiJN0644.
JS0071.
RefSeqiNP_863072.1. NC_004999.1.
YP_534822.1. NC_007926.1.

Genome annotation databases

GeneIDi1343187.
3974209.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M23914 Genomic DNA. Translation: AAB47591.1 .
U49496 Genomic DNA. Translation: AAA92141.1 .
M83949 Genomic DNA. Translation: AAA25902.1 .
AF010471 Genomic DNA. Translation: AAB62707.1 .
AF004284 Genomic DNA. Translation: AAB61373.1 .
PIRi JN0644.
JS0071.
RefSeqi NP_863072.1. NC_004999.1.
YP_534822.1. NC_007926.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1EG9 X-ray 1.60 A 1-449 [» ]
1NDO X-ray 2.25 A/C/E 1-449 [» ]
1O7G X-ray 1.70 A 1-449 [» ]
1O7H X-ray 2.20 A 1-449 [» ]
1O7M X-ray 1.75 A 1-449 [» ]
1O7N X-ray 1.40 A 1-449 [» ]
1O7P X-ray 1.95 A 1-449 [» ]
1O7W X-ray 1.90 A 1-449 [» ]
1UUV X-ray 1.65 A 1-449 [» ]
1UUW X-ray 2.30 A 1-449 [» ]
ProteinModelPortali P0A110.
SMRi P0A110. Positions 1-447.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

IntActi P0A110. 1 interaction.
MINTi MINT-257428.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

GeneIDi 1343187.
3974209.

Enzyme and pathway databases

UniPathwayi UPA00082 .
BioCyci MetaCyc:MONOMER-12802.

Miscellaneous databases

EvolutionaryTracei P0A110.

Family and domain databases

Gene3Di 2.102.10.10. 1 hit.
3.90.380.10. 1 hit.
InterProi IPR017941. Rieske_2Fe-2S.
IPR015881. Ring-hydroxy_dOase_2Fe2S_BS.
IPR015879. Ring_hydroxy_dOase_asu_C_dom.
IPR001663. Rng_hydr_dOase-A.
[Graphical view ]
Pfami PF00355. Rieske. 1 hit.
PF00848. Ring_hydroxyl_A. 1 hit.
[Graphical view ]
PRINTSi PR00090. RNGDIOXGNASE.
SUPFAMi SSF50022. SSF50022. 1 hit.
PROSITEi PS51296. RIESKE. 1 hit.
PS00570. RING_HYDROXYL_ALPHA. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Cloning, nucleotide sequence and characterization of genes encoding naphthalene dioxygenase of Pseudomonas putida strain NCIB9816."
    Kurkela S., Lehvaeslaiho H., Palva E.T., Teeri T.H.
    Gene 73:355-362(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: DSM 8368 / NCIMB 9816.
  2. "Cloning and sequencing of the genes encoding 2-nitrotoluene dioxygenase from Pseudomonas sp. JS42."
    Parales J.V., Kumar A., Parales R.E., Gibson D.T.
    Gene 181:57-61(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: NCIMB 9816-4.
    Plasmid: pDTG1
  3. "Sequences of genes encoding naphthalene dioxygenase in Pseudomonas putida strains G7 and NCIB 9816-4."
    Simon M.J., Osslund T.D., Saunders R., Ensley B.D., Suggs S., Harcourt A.A., Suen W.-C., Cruden D.L., Gibson D.T., Zylstra G.J.
    Gene 127:31-37(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 17485 / DSM 50208 / JCM 6158 / NCIMB 12092 / Stanier 111 / Biotype A.
    Plasmid: NAH7
  4. "Nucleotide sequences of genes encoding an upper pathway of naphthalene metabolism of NPL1 plasmid from Pseudomonas putida strain BS202."
    Bezborodnikov S.G., Boronin A.M., Tiedje J.M.
    Submitted (JUL-1997) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: BS202.
    Plasmid: NPL1
  5. "Naphthalene dioxygenase genes from Pseudomonas putida."
    Hamann C.
    Submitted (JUN-1997) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 17484 / DSM 50222 / NCIMB 10535 / Stanier 110 / Biotype B.
  6. "Structure of an aromatic-ring-hydroxylating dioxygenase-naphthalene 1,2-dioxygenase."
    Kauppi B., Lee K., Carredano E., Parales R.E., Gibson D.T., Eklund H., Ramaswamy S.
    Structure 6:571-586(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS).
    Strain: NCIMB 9816-4.

Entry informationi

Entry nameiNDOB_PSEPU
AccessioniPrimary (citable) accession number: P0A110
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: June 11, 2014
This is version 62 of the entry and version 1 of the sequence. [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

External Data

Dasty 3

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