Naphthalene dioxygenase large subunit - Rhodococcus sp. NCIMB12038

Preferred order of sections

Names and origin

Protein names

Submitted name:
Naphthalene dioxygenase large subunit EMBL AAD28100.1

Gene names

Name:

narAa EMBL AAD28100.1

Organism

Rhodococcus sp. NCIMB12038 EMBL AAD28100.1

Taxonomic identifier

92694 [NCBI]

Taxonomic lineage

Bacteria › Actinobacteria › Actinobacteridae › Actinomycetales › Corynebacterineae › Nocardiaceae › Rhodococcus

Protein attributes

Sequence length	470 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Sequence similarities

Contains 1 Rieske domain. RuleBase RU004493

Ontologies

Keywords
Ligand	2Fe-2S RuleBase RU004492 PDB 2B1X PDB 2B24 Iron Iron-sulfur Metal-binding
Molecular function	Dioxygenase EMBL AAD28100.1 Oxidoreductase
Technical term	3D-structure PDB 2B1X PDB 2B24
Gene Ontology (GO)
Biological process	aromatic compound catabolic process Inferred from electronic annotation. Source: InterPro
Molecular function	2 iron, 2 sulfur cluster binding Inferred from electronic annotation. Source: UniProtKB-KW iron ion binding Inferred from electronic annotation. Source: InterPro oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of two atoms of oxygen into one donor Inferred from electronic annotation. Source: InterPro 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...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Sites

Metal binding

88

1

Iron-sulfur (2Fe-2S) PDB 2B1X PDB 2B24

Metal binding

90

1

Iron-sulfur (2Fe-2S); via pros nitrogen PDB 2B1X PDB 2B24

Metal binding

91

1

Iron-sulfur (2Fe-2S); via amide nitrogen PDB 2B1X PDB 2B24

Metal binding

108

1

Iron-sulfur (2Fe-2S) PDB 2B1X PDB 2B24

Metal binding

111

1

Iron-sulfur (2Fe-2S); via pros nitrogen PDB 2B1X PDB 2B24

Metal binding

216

1

Iron; via tele nitrogen PDB 2B1X PDB 2B24

Metal binding

221

1

Iron; via tele nitrogen PDB 2B1X PDB 2B24

Metal binding

372

1

Iron PDB 2B1X PDB 2B24

Sequences

Sequence

Length

Mass (Da)

Tools

Q9X3R9 [UniParc].

Last modified November 1, 1999. Version 1.
Checksum: 7C8B2FEC3DA9BEAF
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FASTA

470

52,522

        10         20         30         40         50         60 
MLSNELRQTL QKGLHDVNSD WTVPAAIIND PEVHDVERER IFGHAWVFLA HESEIPERGD 

        70         80         90        100        110        120 
YVVRYISEDQ FIVCRDEGGE IRGHLNACRH RGMQVCRAEM GNTSHFRCPY HGWTYSNTGS 

       130        140        150        160        170        180 
LVGVPAGKDA YGNQLKKSDW NLRPMPNLAS YKGLIFGSLD PHADSLEDYL GDLKFYLDIV 

       190        200        210        220        230        240 
LDRSDAGLQV VGAPQRWVID ANWKLGADNF VGDAYHTMMT HRSMVELGLA PPDPQFALYG 

       250        260        270        280        290        300 
EHIHTGHGHG LGIIGPPPGM PLPEFMGLPE NIVEELERRL TPEQVEIFRP TAFIHGTVFP 

       310        320        330        340        350        360 
NLSIGNFLMG KDHLSAPTAF LTLRLWHPLG PDKMEVMSFF LVEKDAPDWF KDESYKSYLR 

       370        380        390        400        410        420 
TFGISGGFEQ DDAENWRSIT RVMGGQFAKT GELNYQMGRG VLEPDPNWTG PGEAYPLDYA 

       430        440        450        460        470 
EANQRNFLEY WMQLMLAESP LRDGNSNGSG TADASTPAAA KSKSPAKAEA

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References

[1]	"Purification and characterization of a novel naphthalene dioxygenase from Rhodococcus sp. strain NCIMB12038." Larkin M.J., Allen C.C., Kulakov L.A., Lipscomb D.A. J. Bacteriol. 181:6200-6204(1999) [PubMed: 10498739] [Abstract] Cited for: NUCLEOTIDE SEQUENCE. Strain: NCIMB12038 EMBL AAD28100.1.
[2]	"Analysis of the Rhodococcus sp. NCIMB12038 naphthalene degradation genes regions." Chen S., Kulakov L.A., Larkin M.J. Submitted (APR-1999) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE. Strain: NCIMB12038 EMBL AAD28100.1.
[3]	Allen C.C.R., Lipscomb D., Larkin M.J., Kulakov L.A. Submitted (MAY-1999) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE. Strain: NCIMB12038 EMBL AAD28100.1.
[4]	Chen S., Kulakov L.A., Larkin M.J. Submitted (OCT-2003) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE. Strain: NCIMB12038 EMBL AAD28100.1.
[5]	"Structure and increased thermostability of Rhodococcus sp. naphthalene 1,2-dioxygenase." Gakhar L., Malik Z.A., Allen C.C., Lipscomb D.A., Larkin M.J., Ramaswamy S. J. Bacteriol. 187:7222-7231(2005) [PubMed: 16237006] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) IN COMPLEX WITH IRON AND IRON-SULFUR (2FE-2S).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AF082663 Genomic DNA. Translation: AAD28100.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2B1X	X-ray	2.00	A/C/E	1-470	[»]
2B24	X-ray	3.00	A/C/E	1-470	[»]

ProteinModelPortal

Q9X3R9.

SMR

Q9X3R9. Positions 1-441.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Family and domain databases

InterPro

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

Gene3D

G3DSA:2.102.10.10. Rieske_reg. 1 hit.

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...

Entry information

Entry name

Q9X3R9_9NOCA

Accession

Primary (citable) accession number: Q9X3R9

Entry history

Integrated into UniProtKB/TrEMBL:	November 1, 1999
Last sequence update:	November 1, 1999
Last modified:	June 28, 2011
This is version 50 of the entry and version 1 of the sequence. [Complete history]

Entry status

Unreviewed (UniProtKB/TrEMBL)