EzCatDB: T00024
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DB codeT00024
RLCP classification10.21021.100.10205 : Electron transfer
10.21001.100.10900 : Electron transfer
CATH domainDomain 13.90.380.10 : Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1Catalytic domain
Domain 22.102.10.10 : Rieske Iron-sulfur ProteinCatalytic domain
Domain 33.10.450.50 : Nuclear Transport Factor 2; Chain
E.C.1.14.12.12
CSA1ndo
MACiEM0130

CATH domainRelated DB codes (homologues)
2.102.10.10 : Rieske Iron-sulfur ProteinM00222
3.10.450.50 : Nuclear Transport Factor 2; ChainS00176,S00545,S00177

Enzyme Name
UniProtKBKEGG

P0A110P0A111P0A112P0A113
Protein nameNaphthalene 1,2-dioxygenase subunit alphaNaphthalene 1,2-dioxygenase subunit alphaNaphthalene 1,2-dioxygenase subunit betaNaphthalene 1,2-dioxygenase subunit betanaphthalene 1,2-dioxygenase
naphthalene dioxygenase
naphthalene oxygenase
SynonymsEC 1.14.12.12
Naphthalene 1,2-dioxygenase ISP alpha
EC 1.14.12.12
Naphthalene 1,2-dioxygenase ISP alpha
EC 1.14.12.12
Naphthalene 1,2-dioxygenase ISP beta
EC 1.14.12.12
Naphthalene 1,2-dioxygenase ISP beta
RefSeqNP_863072.1 (Protein)
NC_004999.1 (DNA/RNA sequence)
YP_534822.1 (Protein)
NC_007926.1 (DNA/RNA sequence)

NP_863073.1 (Protein)
NC_004999.1 (DNA/RNA sequence)
YP_534823.1 (Protein)
NC_007926.1 (DNA/RNA sequence)

PfamPF00355 (Rieske)
PF00848 (Ring_hydroxyl_A)
[Graphical view]
PF00355 (Rieske)
PF00848 (Ring_hydroxyl_A)
[Graphical view]
PF00866 (Ring_hydroxyl_B)
[Graphical view]
PF00866 (Ring_hydroxyl_B)
[Graphical view]

KEGG pathways
MAP codePathways
MAP006241- and 2-Methylnaphthalene degradation
MAP00626Naphthalene and anthracene degradation
MAP00628Fluorene degradation
MAP00642Ethylbenzene degradation

UniProtKB:Accession NumberP0A110P0A111P0A112P0A113
Entry nameNDOB_PSEPUNDOB_PSEU8NDOC_PSEPUNDOC_PSEU8
ActivityNaphthalene + NADH + O(2) = (1R,2S)-1,2- dihydronaphthalene-1,2-diol + NAD(+).Naphthalene + NADH + O(2) = (1R,2S)-1,2- dihydronaphthalene-1,2-diol + NAD(+).Naphthalene + NADH + O(2) = (1R,2S)-1,2- dihydronaphthalene-1,2-diol + NAD(+).Naphthalene + NADH + O(2) = (1R,2S)-1,2- dihydronaphthalene-1,2-diol + NAD(+).
SubunitNaphthalene 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).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 and ferredoxin (doxA), and ISP is composed of a large alpha subunit (doxB) and a small beta subunit (doxD) (Probable).The 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 hexamer of three large alpha subunits (ndoB) and three small beta subunits (ndoC).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 and ferredoxin (doxA), and ISP is composed of a large alpha subunit (doxB) and a small beta subunit (doxD) (Probable).
Subcellular location



CofactorBinds 1 2Fe-2S cluster (Probable).,Binds 1 iron ion (Probable).Binds 1 2Fe-2S cluster (By similarity).,Binds 1 iron ion (By similarity).Binds 1 2Fe-2S cluster (Probable).,Binds 1 iron ion (Probable).Binds 1 2Fe-2S cluster (By similarity).,Binds 1 iron ion (By similarity).

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idL00023C00023C00829C00004C00007C00080C04314C00003
Compound[2Fe-2S]IronNaphthaleneNADHO2H+(1R,2S)-1,2-dihydronaphthalene-1,2-diolNAD+
Typeheavy metal,sulfide groupheavy metalaromatic ring (only carbon atom)amide group,amine group,nucleotideothersothersaromatic ring (only carbon atom),carbohydrateamide group,amine group,nucleotide
ChEBI33739
18248
82664
16482
16908
15379
26689
27140
15378
44343
15846
PubChem
23925
931
439153
977
1038
440294
5893
                
1eg9A01UnboundBound:_FEAnalogue:INDUnboundUnbound UnboundUnbound
1ndoA01UnboundBound:_FEUnboundUnboundUnbound UnboundUnbound
1ndoC01UnboundBound:_FEUnboundUnboundUnbound UnboundUnbound
1ndoE01UnboundBound:_FEUnboundUnboundUnbound UnboundUnbound
1o7gA01UnboundBound:_FEBound:NPYUnboundUnbound UnboundUnbound
1o7hA01UnboundBound:_FEUnboundUnboundUnbound UnboundUnbound
1o7mA01UnboundBound:_FEUnboundUnboundBound:OXY UnboundUnbound
1o7nA01UnboundBound:_FEAnalogue:INDUnboundBound:OXY UnboundUnbound
1o7pA01UnboundBound:_FEUnboundUnboundUnbound Bound:NDHUnbound
1o7wA01UnboundBound:_FEUnboundUnboundUnbound UnboundUnbound
1uuvA01UnboundBound:_FEAnalogue:INDUnboundAnalogue:_NO UnboundUnbound
1uuwA01UnboundBound:_FEUnboundUnboundAnalogue:_NO UnboundUnbound
1eg9A02Bound:FESUnboundUnboundUnboundUnbound UnboundUnbound
1ndoA02Bound:FESUnboundUnboundUnboundUnbound UnboundUnbound
1ndoC02Bound:FESUnboundUnboundUnboundUnbound UnboundUnbound
1ndoE02Bound:FESUnboundUnboundUnboundUnbound UnboundUnbound
1o7gA02Bound:FESUnboundUnboundUnboundUnbound UnboundUnbound
1o7hA02Bound:FESUnboundUnboundUnboundUnbound UnboundUnbound
1o7mA02Bound:FESUnboundUnboundUnboundUnbound UnboundUnbound
1o7nA02Bound:FESUnboundUnboundUnboundUnbound UnboundUnbound
1o7pA02Bound:FESUnboundUnboundUnboundUnbound UnboundUnbound
1o7wA02Bound:FESUnboundUnboundUnboundUnbound UnboundUnbound
1uuvA02Bound:FESUnboundUnboundUnboundUnbound UnboundUnbound
1uuwA02Bound:FESUnboundUnboundUnboundUnbound UnboundUnbound
1eg9BUnboundUnboundUnboundUnboundUnbound UnboundUnbound
1ndoBUnboundUnboundUnboundUnboundUnbound UnboundUnbound
1ndoDUnboundUnboundUnboundUnboundUnbound UnboundUnbound
1ndoFUnboundUnboundUnboundUnboundUnbound UnboundUnbound
1o7gBUnboundUnboundUnboundUnboundUnbound UnboundUnbound
1o7hBUnboundUnboundUnboundUnboundUnbound UnboundUnbound
1o7mBUnboundUnboundUnboundUnboundUnbound UnboundUnbound
1o7nBUnboundUnboundUnboundUnboundUnbound UnboundUnbound
1o7pBUnboundUnboundUnboundUnboundUnbound UnboundUnbound
1o7wBUnboundUnboundUnboundUnboundUnbound UnboundUnbound
1uuvBUnboundUnboundUnboundUnboundUnbound UnboundUnbound
1uuwBUnboundUnboundUnboundUnboundUnbound UnboundUnbound

Active-site residues
resource
Swiss-prot;P0A110, P0A111 & literature [4], [7], [9], [11], [17], [18]
pdbCatalytic residuesCofactor-binding residues
          
1eg9A01ASP 205;HIS 208
HIS 208;HIS 213;ASP 362(Iron binding)
1ndoA01ASP 205;HIS 208
HIS 208;HIS 213;ASP 362(Iron binding)
1ndoC01ASP 205;HIS 208
HIS 208;HIS 213;ASP 362(Iron binding)
1ndoE01ASP 205;HIS 208
HIS 208;HIS 213;ASP 362(Iron binding)
1o7gA01ASP 205;HIS 208
HIS 208;HIS 213;ASP 362(Iron binding)
1o7hA01ASP 205;HIS 208
HIS 208;HIS 213;ASP 362(Iron binding)
1o7mA01ASP 205;HIS 208
HIS 208;HIS 213;ASP 362(Iron binding)
1o7nA01ASP 205;HIS 208
HIS 208;HIS 213;ASP 362(Iron binding)
1o7pA01ASP 205;HIS 208
HIS 208;HIS 213;ASP 362(Iron binding)
1o7wA01ASP 205;HIS 208
HIS 208;HIS 213;ASP 362(Iron binding)
1uuvA01ASP 205;HIS 208
HIS 208;HIS 213;ASP 362(Iron binding)
1uuwA01ASP 205;HIS 208
HIS 208;HIS 213;ASP 362(Iron binding)
1eg9A02HIS 104
CYS  81;HIS  83;CYS 101;HIS 104(2Fe-2S cluster binding)
1ndoA02HIS 104
CYS  81;HIS  83;CYS 101;HIS 104(2Fe-2S cluster binding)
1ndoC02HIS 104
CYS  81;HIS  83;CYS 101;HIS 104(2Fe-2S cluster binding)
1ndoE02HIS 104
CYS  81;HIS  83;CYS 101;HIS 104(2Fe-2S cluster binding)
1o7gA02HIS 104
CYS  81;HIS  83;CYS 101;HIS 104(2Fe-2S cluster binding)
1o7hA02HIS 104
CYS  81;HIS  83;CYS 101;HIS 104(2Fe-2S cluster binding)
1o7mA02HIS 104
CYS  81;HIS  83;CYS 101;HIS 104(2Fe-2S cluster binding)
1o7nA02HIS 104
CYS  81;HIS  83;CYS 101;HIS 104(2Fe-2S cluster binding)
1o7pA02HIS 104
CYS  81;HIS  83;CYS 101;HIS 104(2Fe-2S cluster binding)
1o7wA02HIS 104
CYS  81;HIS  83;CYS 101;HIS 104(2Fe-2S cluster binding)
1uuvA02HIS 104
CYS  81;HIS  83;CYS 101;HIS 104(2Fe-2S cluster binding)
1uuwA02HIS 104
CYS  81;HIS  83;CYS 101;HIS 104(2Fe-2S cluster binding)
1eg9B 
 
1ndoB 
 
1ndoD 
 
1ndoF 
 
1o7gB 
 
1o7hB 
 
1o7mB 
 
1o7nB 
 
1o7pB 
 
1o7wB 
 
1uuvB 
 
1uuwB 
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[3]SCHEME I, p.30257-30260
[4]p.575-582
[5]p.11068-11070
[7]Fig.1, p.1835-1836
[9]Fig.2
[11]Scheme 1, p.706-709
[14]Scheme 2, p.1952
[17]Fig.1, P.7065-7066
[18]p.272-274
[19]Fig.2
[20]Fig
[21]Scheme 2, Scheme 3, Fig.7, Fig.9, p.443-451
[22]


references
[1]
PubMed ID7858982
JournalBioorg Med Chem
Year1994
Volume2
Pages727-34
AuthorsWhited GM, Downie JC, Hudlicky T, Fearnley SP, Dudding TC, Olivo HF, Parker D
TitleOxidation of 2-methoxynaphthalene by toluene, naphthalene and biphenyl dioxygenases:structure and absolute stereochemistry of metabolites.
[2]
PubMed ID8899998
JournalAppl Environ Microbiol
Year1996
Volume62
Pages4073-80
AuthorsResnick SM, Gibson DT
TitleRegio- and stereospecific oxidation of fluorene, dibenzofuran, and dibenzothiophene by naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816-4.
[3]
PubMed ID9374510
JournalJ Biol Chem
Year1997
Volume272
Pages30254-60
AuthorsDi Gennaro P, Sello G, Bianchi D, D'Amico P
TitleSpecificity of substrate recognition by Pseudomonas fluorescens N3 dioxygenase. The role of the oxidation potential and molecular geometry.
[4]
CommentsX-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS)
Medline ID98298434
PubMed ID9634695
JournalStructure
Year1998
Volume6
Pages571-86
AuthorsKauppi B, Lee K, Carredano E, Parales RE, Gibson DT, Eklund H, Ramaswamy S
TitleStructure of an aromatic-ring-hydroxylating dioxygenase-naphthalene 1,2-dioxygenase.
Related PDB1ndo
Related UniProtKBP0A110,P0A111,P23094,P23095
[5]
PubMed ID10390817
JournalAppl Microbiol Biotechnol
Year1999
Volume51
Pages592-7
AuthorsBarriault D, Sylvestre M
TitleFunctionality of biphenyl 2,3-dioxygenase components in naphthalene 1,2-dioxygenase.
[6]
PubMed ID10460161
JournalBiochemistry
Year1999
Volume38
Pages11062-72
AuthorsCoulter ED, Moon N, Batie CJ, Dunham WR, Ballou DP
TitleElectron paramagnetic resonance measurements of the ferrous mononuclear site of phthalate dioxygenase substituted with alternate divalent metal ions: direct evidence for ligation of two histidines in the copper(II)-reconstituted protein.
[7]
PubMed ID10074076
JournalJ Bacteriol
Year1999
Volume181
Pages1831-7
AuthorsParales RE, Parales JV, Gibson DT
TitleAspartate 205 in the catalytic domain of naphthalene dioxygenase is essential for activity.
[8]
PubMed ID10713518
JournalActa Crystallogr D Biol Crystallogr
Year2000
Volume56
Pages313-21
AuthorsCarredano E, Kauppi B, Choudhury D, Ramaswamy S
TitlePseudo-symmetry characterization and refinement of a trigonal crystal form of naphthalene 1,2-dioxygenase.
[9]
PubMed ID10692370
JournalJ Bacteriol
Year2000
Volume182
Pages1641-9
AuthorsParales RE, Lee K, Resnick SM, Jiang H, Lessner DJ, Gibson DT
TitleSubstrate specificity of naphthalene dioxygenase: effect of specific amino acids at the active site of the enzyme.
[10]
PubMed ID10986254
JournalJ Bacteriol
Year2000
Volume182
Pages5495-504
AuthorsParales RE, Resnick SM, Yu CL, Boyd DR, Sharma ND, Gibson DT
TitleRegioselectivity and enantioselectivity of naphthalene dioxygenase during arene cis-dihydroxylation: control by phenylalanine 352 in the alpha subunit.
[11]
CommentsX-ray crystallography
PubMed ID10669618
JournalJ Mol Biol
Year2000
Volume296
Pages701-12
AuthorsCarredano E, Karlsson A, Kauppi B, Choudhury D, Parales RE, Parales JV, Lee K, Gibson DT, Eklund H, Ramaswamy S
TitleSubstrate binding site of naphthalene 1,2-dioxygenase: functional implications of indole binding.
Related PDB1eg9
[12]
PubMed ID10919518
JournalRes Microbiol
Year2000
Volume151
Pages383-91
AuthorsGennaro PD, Galli E, Orsini F, Pelizzoni F, Sello G, Bestetti G
TitleDevelopment of biocatalysts carrying naphthalene dioxygenase and dihydrodiol dehydrogenase genes inducible in aerobic and anaerobic conditions.
[13]
PubMed ID11849939
JournalCurr Opin Biotechnol
Year2001
Volume12
Pages564-73
AuthorsBoyd DR, Sharma ND, Allen CC
TitleAromatic dioxygenases: molecular biocatalysis and applications.
[14]
PubMed ID11056161
JournalJ Biol Chem
Year2001
Volume276
Pages1945-53
AuthorsWolfe MD, Parales JV, Gibson DT, Lipscomb JD
TitleSingle turnover chemistry and regulation of O2 activation by the oxygenase component of naphthalene 1,2-dioxygenase.
[15]
PubMed ID11641767
JournalJ Ind Microbiol Biotechnol
Year2001
Volume27
Pages94-103
AuthorsYu CL, Parales RE, Gibson DT
TitleMultiple mutations at the active site of naphthalene dioxygenase affect regioselectivity and enantioselectivity.
[16]
PubMed ID12189839
JournalChem Commun (Camb)
Year2002
Volume(14)
Pages1452-3
AuthorsBoyd DR, Sharma ND, Kennedy MA, Shepherd SD, Malone JF, Alves-Areias A, Holt R, Allenmark SG, Lemurell MA, Dalton H, Luckarift H
TitleEnzyme-catalysed oxygenation and deoxygenation routes to chiral thiosulfinates.
[17]
PubMed ID12783560
JournalJ Am Chem Soc
Year2003
Volume125
Pages7056-66
AuthorsYang TC, Wolfe MD, Neibergall MB, Mekmouche Y, Lipscomb JD, Hoffman BM
TitleSubstrate binding to NO-ferro-naphthalene 1,2-dioxygenase studied by high-resolution Q-band pulsed 2H-ENDOR spectroscopy.
[18]
PubMed ID12695887
JournalJ Ind Microbiol Biotechnol
Year2003
Volume30
Pages271-8
AuthorsParales RE
TitleThe role of active-site residues in naphthalene dioxygenase.
[19]
CommentsX-ray crystallography
PubMed ID12586937
JournalScience
Year2003
Volume299
Pages1039-42
AuthorsKarlsson A, Parales JV, Parales RE, Gibson DT, Eklund H, Ramaswamy S
TitleCrystal structure of naphthalene dioxygenase: side-on binding of dioxygen to iron.
Related PDB1ndo,1o7g,1o7h,1o7m,1o7n,1o7p,1o7w
[20]
PubMed ID12586930
JournalScience
Year2003
Volume299
Pages1024-5
AuthorsKovacs JA
TitleBiochemistry. How iron activates O2.
[21]
PubMed ID15042436
JournalJ Biol Inorg Chem
Year2004
Volume9
Pages439-52
AuthorsBassan A, Blomberg MR, Siegbahn PE
TitleA theoretical study of the cis-dihydroxylation mechanism in naphthalene 1,2-dioxygenase.
[22]
PubMed ID15942729
JournalJ Biol Inorg Chem
Year2005
Volume10
Pages483-9
AuthorsKarlsson A, Parales JV, Parales RE, Gibson DT, Eklund H, Ramaswamy S
TitleNO binding to naphthalene dioxygenase.
Related PDB1uuv,1uuw

comments
This enzyme belongs to a large family of bacterial Rieske non-heme iron oxygenases. This enzyme is a part of naphthalene 1,2-dioxygenase system (NDOS).
Although NADH and NAD+ are included as a substrate and a product, respectively, they do not interact directly with this enzyme. According to the literature [4], [7], [14] and [18], the reaction proceeds as follows:
(#) Ferredoxin-NAD+ reductase (cf. D00071 in EzCatDB) of NDOS catalyzes electron transfer from NADH to Ferredoxin of NDOS.
(A) Electron transfer from Ferredoxin to the FE2S2 (Iron-sulfur) of the oxidized form of this enzyme.
(A1) Indirect transfer through Trp211 from the adjacent alpha-subunit and Val100, to Cys101, which is bound to FE2S2 (see [4]).
(B) Electron transfer from the FE2S2 to the mononuclear iron center of the adjacent subunit of this enzyme.
(B1) Indirect transfer through His104 bound to the FE2S2, the sidechain of Asp205 from the adjacent alpha-subunit, and His208 bound to the mononuclear iron center from the adjacent alpha-subunit (see [4] and [7]).
(C) Oxygenation of naphthalene at the mononuclear iron center.

createdupdated
2005-05-312018-04-23
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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