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Protein

Naphthalene 1,2-dioxygenase subunit alpha

Gene

ndoB

Organism
Pseudomonas putida (Arthrobacter siderocapsulatus)
Status
Reviewed-Annotation score: 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: 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)1
Metal bindingi83Iron-sulfur (2Fe-2S); via pros nitrogen1
Metal bindingi101Iron-sulfur (2Fe-2S)1
Metal bindingi104Iron-sulfur (2Fe-2S); via pros nitrogen1
Metal bindingi208Iron1
Metal bindingi213Iron1
Metal bindingi362Iron1

GO - Molecular functioni

GO - Biological processi

Keywordsi

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

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-12802.
BRENDAi1.14.12.12. 5092.
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)DescriptionActionsGraphical viewLength
ChainiPRO_00000850531 – 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 (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 interactor.
MINTiMINT-257428.

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 – 408Combined sources8
Helixi411 – 424Combined sources14
Helixi429 – 435Combined sources7
Turni436 – 438Combined sources3
Helixi439 – 444Combined sources6

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP0A110.

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.
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.

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)DescriptionActionsGraphical viewLength
Natural varianti4N → K in strain: G7. 1
Natural varianti12S → F in strain: ATCC 17484. 1
Natural varianti15S → T in strain: G7. 1
Natural varianti32K → R in strain: G7. 1
Natural varianti50A → S in strain: G7. 1
Natural varianti70N → S in strain: G7. 1
Natural varianti90 – 91SV → NA in strain: G7. 2
Natural varianti122D → E in strain: G7. 1
Natural varianti173M → I in strain: G7. 1
Natural varianti225S → A in strain: G7. 1
Natural varianti225S → C in strain: BS202. 1
Natural varianti232A → V in strain: G7. 1
Natural varianti275A → S in strain: G7. 1
Natural varianti391E → K in strain: G7. 1
Natural varianti421Q → R in strain: ATCC 17484. 1
Natural varianti434H → D in strain: G7. 1

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.
WP_011117400.1. NC_004999.1.
WP_011475377.1. NC_007926.1.
YP_534822.1. NC_007926.1.

Genome annotation databases

GeneIDi1343187.
3974209.

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.

Entry informationi

Entry nameiNDOB_PSEPU
AccessioniPrimary (citable) accession number: P0A110
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: June 7, 2017
This is version 85 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