P0A110 (NDOB_PSEPU) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Naphthalene 1,2-dioxygenase subunit alpha
EC=1.14.12.12

Alternative name(s):
Naphthalene 1,2-dioxygenase ISP alpha

Gene names

Name:	ndoB
Synonyms:	nahA3, nahAC, ndoC2

Encoded on

Plasmid pDTG1 Ref.2
Plasmid NAH7 Ref.3
Plasmid NPL1 Ref.4

Organism

Pseudomonas putida (Arthrobacter siderocapsulatus)

Taxonomic identifier

303 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Pseudomonadales › Pseudomonadaceae › Pseudomonas › Pseudomonas putida group

Protein attributes

Sequence length	449 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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 activity	Naphthalene + NADH + O2 = (1R,2S)-1,2-dihydronaphthalene-1,2-diol + NAD+.
Cofactor	Binds 1 2Fe-2S cluster Probable. Binds 1 iron ion Probable.
Pathway	Aromatic compound metabolism; naphthalene degradation.
Subunit structure	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).
Sequence similarities	Belongs to the bacterial ring-hydroxylating dioxygenase alpha subunit family. Contains 1 Rieske domain.

Ontologies

Keywords
Biological process	Aromatic hydrocarbons catabolism
Ligand	2Fe-2S Iron Iron-sulfur Metal-binding NAD
Molecular function	Dioxygenase Oxidoreductase
Technical term	3D-structure Plasmid
Gene Ontology (GO)
Biological_process	aromatic compound catabolic process Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	2 iron, 2 sulfur cluster binding Inferred from electronic annotation. Source: UniProtKB-KW iron ion binding Inferred from electronic annotation. Source: InterPro naphthalene 1,2-dioxygenase activity Inferred from electronic annotation. Source: EC oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
ndoC	P0A112	7	EBI-1029015,EBI-1029028

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 449

449

Naphthalene 1,2-dioxygenase subunit alpha

PRO_0000085053

Regions

Domain

39 – 137

99

Rieske

Sites

Metal binding

81

1

Iron-sulfur (2Fe-2S)

Metal binding

83

1

Iron-sulfur (2Fe-2S); via pros nitrogen

Metal binding

101

1

Iron-sulfur (2Fe-2S)

Metal binding

104

1

Iron-sulfur (2Fe-2S); via pros nitrogen

Metal binding

208

1

Iron

Metal binding

213

1

Iron

Metal binding

362

1

Iron

Natural variations

Natural variant

4

1

N → K in strain: G7.

Natural variant

12

1

S → F in strain: ATCC 17484.

Natural variant

15

1

S → T in strain: G7.

Natural variant

32

1

K → R in strain: G7.

Natural variant

50

1

A → S in strain: G7.

Natural variant

70

1

N → S in strain: G7.

Natural variant

90 – 91

2

SV → NA in strain: G7.

Natural variant

122

1

D → E in strain: G7.

Natural variant

173

1

M → I in strain: G7.

Natural variant

225

1

S → A in strain: G7.

Natural variant

225

1

S → C in strain: BS202.

Natural variant

232

1

A → V in strain: G7.

Natural variant

275

1

A → S in strain: G7.

Natural variant

391

1

E → K in strain: G7.

Natural variant

421

1

Q → R in strain: ATCC 17484.

Natural variant

434

1

H → D in strain: G7.

Secondary structure

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449

Helix Strand Turn

Details...

Turn

3 – 5

3

Helix

11 – 13

3

Beta strand

15 – 17

3

Helix

18 – 21

4

Helix

24 – 33

10

Turn

34 – 37

4

Beta strand

40 – 44

5

Helix

45 – 47

3

Beta strand

53 – 59

7

Beta strand

62 – 68

7

Beta strand

74 – 80

7

Turn

82 – 84

3

Beta strand

91 – 95

5

Beta strand

97 – 100

4

Turn

102 – 104

3

Beta strand

107 – 109

3

Beta strand

114 – 116

3

Helix

120 – 123

4

Turn

124 – 126

3

Helix

130 – 132

3

Beta strand

139 – 144

6

Beta strand

147 – 152

6

Helix

159 – 163

5

Helix

166 – 174

9

Turn

175 – 177

3

Beta strand

180 – 193

14

Helix

196 – 204

9

Helix

209 – 212

4

Helix

214 – 220

7

Helix

225 – 230

6

Beta strand

238 – 243

6

Beta strand

249 – 253

5

Turn

257 – 260

4

Turn

263 – 265

3

Helix

266 – 284

19

Helix

286 – 292

7

Beta strand

294 – 300

7

Turn

301 – 303

3

Beta strand

304 – 307

4

Turn

308 – 311

4

Beta strand

312 – 320

9

Beta strand

323 – 333

11

Helix

338 – 352

15

Helix

357 – 372

16

Turn

376 – 380

5

Beta strand

382 – 384

3

Turn

387 – 390

4

Beta strand

393 – 395

3

Beta strand

397 – 399

3

Beta strand

401 – 408

8

Helix

411 – 424

14

Helix

429 – 435

7

Turn

436 – 438

3

Helix

439 – 444

6

Sequences

	Sequence		Length	Mass (Da)
	P0A110 [UniParc]. Last modified March 1, 2005. Version 1. Checksum: 1FD2F42296B4F7A8	FASTA	449	49,608
	10 20 30 40 50 60 MNYNNKILVS ESGLSQKHLI HGDEELFQHE LKTIFARNWL FLTHDSLIPA PGDYVTAKMG 70 80 90 100 110 120 IDEVIVSRQN DGSIRAFLNV CRHRGKTLVS VEAGNAKGFV CSYHGWGFGS NGELQSVPFE 130 140 150 160 170 180 KDLYGESLNK KCLGLKEVAR VESFHGFIYG CFDQEAPPLM DYLGDAAWYL EPMFKHSGGL 190 200 210 220 230 240 ELVGPPGKVV IKANWKAPAE NFVGDAYHVG WTHASSLRSG ESIFSSLAGN AALPPEGAGL 250 260 270 280 290 300 QMTSKYGSGM GVLWDGYSGV HSADLVPELM AFGGAKQERL NKEIGDVRAR IYRSHLNCTV 310 320 330 340 350 360 FPNNSMLTCS GVFKVWNPID ANTTEVWTYA IVEKDMPEDL KRRLADSVQR TFGPAGFWES 370 380 390 400 410 420 DDNDNMETAS QNGKKYQSRD SDLLSNLGFG EDVYGDAVYP GVVGKSAIGE TSYRGFYRAY 430 440 QAHVSSSNWA EFEHASSTWH TELTKTTDR

References

[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.
[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.
[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.
[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.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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.

PIR

JN0644.
JS0071.

RefSeq

NP_863072.1. NC_004999.1.
YP_534822.1. NC_007926.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

P0A110.

SMR

P0A110. Positions 1-447.

ModBase

Search...

Protein-protein interaction databases

IntAct

P0A110. 1 interaction.

MINT

MINT-257428.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

1343187.
3974209.

Phylogenomic databases

ProtClustDB

CLSK644467.

Enzyme and pathway databases

BioCyc

MetaCyc:MONOMER-12802.

UniPathway

UPA00082.

Family and domain databases

Gene3D

2.102.10.10. 1 hit.

InterPro

IPR017941. Rieske_2Fe-2S.
IPR015881. Ring-hydroxy_dOase_2Fe2S_BS.
IPR015879. Ring_hydroxy_dOase_asu_C_dom.
IPR001663. Rng_hydr_dOase-A.
[Graphical view]

Pfam

PF00355. Rieske. 1 hit.
PF00848. Ring_hydroxyl_A. 1 hit.
[Graphical view]

PRINTS

PR00090. RNGDIOXGNASE.

SUPFAM

SSF50022. Rieske_dom. 1 hit.

PROSITE

PS51296. RIESKE. 1 hit.
PS00570. RING_HYDROXYL_ALPHA. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P0A110.

Entry information

Entry name

NDOB_PSEPU

Accession

Primary (citable) accession number: P0A110
Secondary accession number(s): O07830 , O33461, P23094, Q52124

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 1, 2005
Last sequence update:	March 1, 2005
Last modified:	April 3, 2013
This is version 58 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program