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P0A110

- NDOB_PSEPU

UniProt

P0A110 - NDOB_PSEPU

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Protein

Naphthalene 1,2-dioxygenase subunit alpha

Gene

ndoB

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

Protein has several cofactor binding sites:

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

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 alphaPRO_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

1
449
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni3 – 53Combined sources
Helixi11 – 133Combined sources
Beta strandi15 – 173Combined sources
Helixi18 – 214Combined sources
Helixi24 – 3310Combined sources
Turni34 – 374Combined sources
Beta strandi40 – 445Combined sources
Helixi45 – 473Combined sources
Beta strandi53 – 597Combined sources
Beta strandi62 – 687Combined sources
Beta strandi74 – 807Combined sources
Turni82 – 843Combined sources
Beta strandi91 – 955Combined sources
Beta strandi97 – 1004Combined sources
Turni102 – 1043Combined sources
Beta strandi107 – 1093Combined sources
Beta strandi114 – 1163Combined sources
Helixi120 – 1234Combined sources
Turni124 – 1263Combined sources
Helixi130 – 1323Combined sources
Beta strandi139 – 1446Combined sources
Beta strandi147 – 1526Combined sources
Helixi159 – 1635Combined sources
Helixi166 – 1749Combined sources
Turni175 – 1773Combined sources
Beta strandi180 – 19314Combined sources
Helixi196 – 2049Combined sources
Helixi209 – 2124Combined sources
Helixi214 – 2207Combined sources
Helixi225 – 2306Combined sources
Beta strandi238 – 2436Combined sources
Beta strandi249 – 2535Combined sources
Turni257 – 2604Combined sources
Turni263 – 2653Combined sources
Helixi266 – 28419Combined sources
Helixi286 – 2927Combined sources
Beta strandi294 – 3007Combined sources
Turni301 – 3033Combined sources
Beta strandi304 – 3074Combined sources
Turni308 – 3114Combined sources
Beta strandi312 – 3209Combined sources
Beta strandi323 – 33311Combined sources
Helixi338 – 35215Combined sources
Helixi357 – 37216Combined sources
Turni376 – 3805Combined sources
Beta strandi382 – 3843Combined sources
Turni387 – 3904Combined sources
Beta strandi393 – 3953Combined sources
Beta strandi397 – 3993Combined sources
Beta strandi401 – 4088Combined sources
Helixi411 – 42414Combined sources
Helixi429 – 4357Combined sources
Turni436 – 4383Combined sources
Helixi439 – 4446Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A110.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini39 – 13799RieskePROSITE-ProRule annotationAdd
BLAST

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.

P0A110-1 [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

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:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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:
PDBei
RCSB PDBi
PDBji
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: November 26, 2014
This is version 65 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