NDOB_PSEU8
ID NDOB_PSEU8 Reviewed; 449 AA.
AC P0A111; O07830; O33461; P23094; Q52124;
DT 01-MAR-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2005, sequence version 1.
DT 03-AUG-2022, entry version 74.
DE RecName: Full=Naphthalene 1,2-dioxygenase system, large oxygenase component {ECO:0000250|UniProtKB:P0A110};
DE EC=1.14.12.12 {ECO:0000250|UniProtKB:P0A110};
DE AltName: Full=ISP NAP {ECO:0000250|UniProtKB:P0A110};
DE AltName: Full=Naphthalene 1,2-dioxygenase ISP alpha {ECO:0000250|UniProtKB:P0A110};
DE AltName: Full=Naphthalene 1,2-dioxygenase subunit alpha {ECO:0000303|PubMed:8226631};
DE Short=ND subunit alpha {ECO:0000250|UniProtKB:P0A110};
DE Short=NDO subunit alpha {ECO:0000250|UniProtKB:P0A110};
GN Name=doxB {ECO:0000303|PubMed:8226631};
OS Pseudomonas sp. (strain C18).
OG Plasmid unnamed.
OC Bacteria; Proteobacteria.
OX NCBI_TaxID=69011;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, DISRUPTION PHENOTYPE, PATHWAY,
RP AND SUBUNIT.
RC STRAIN=C18; PLASMID=unnamed;
RX PubMed=8226631; DOI=10.1128/jb.175.21.6890-6901.1993;
RA Denome S.A., Stanley D.C., Olson E.S., Young K.D.;
RT "Metabolism of dibenzothiophene and naphthalene in Pseudomonas strains:
RT complete DNA sequence of an upper naphthalene catabolic pathway.";
RL J. Bacteriol. 175:6890-6901(1993).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS) OF WILD-TYPE AND MUTANT VAL-352 IN
RP COMPLEX WITH SUBSTRATE ANALOG; IRON ION AND IRON-SULFUR (2FE-2S), COFACTOR,
RP MUTAGENESIS OF PHE-352, AND SUBUNIT.
RX PubMed=16980501; DOI=10.1128/jb.00707-06;
RA Ferraro D.J., Okerlund A.L., Mowers J.C., Ramaswamy S.;
RT "Structural basis for regioselectivity and stereoselectivity of product
RT formation by naphthalene 1,2-dioxygenase.";
RL J. Bacteriol. 188:6986-6994(2006).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.30 ANGSTROMS) IN COMPLEX WITH IRON; IRON-SULFUR
RP (2FE-2S) AND SUBSTRATE ANALOGS, COFACTOR, AND SUBUNIT.
RA Ferraro D.J., Ramaswamy S.;
RT "Naphthalene 1,2-Dioxygenase bound to thioanisole.";
RL Submitted (OCT-2012) to the PDB data bank.
CC -!- FUNCTION: Component of the naphthalene dioxygenase (NDO) multicomponent
CC enzyme system which catalyzes the incorporation of both atoms of
CC molecular oxygen into naphthalene to form cis-(1R,2S)-dihydroxy-1,2-
CC dihydronaphthalene. The alpha subunit has a catalytic role in the
CC holoenzyme. {ECO:0000269|PubMed:8226631}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H(+) + NADH + naphthalene + O2 = (1R,2S)-1,2-
CC dihydronaphthalene-1,2-diol + NAD(+); Xref=Rhea:RHEA:19173,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:15379, ChEBI:CHEBI:16482,
CC ChEBI:CHEBI:44343, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945;
CC EC=1.14.12.12; Evidence={ECO:0000250|UniProtKB:P0A110};
CC -!- COFACTOR:
CC Name=[2Fe-2S] cluster; Xref=ChEBI:CHEBI:190135;
CC Evidence={ECO:0000269|PubMed:16980501, ECO:0000269|Ref.3};
CC Note=Binds 1 [2Fe-2S] cluster per subunit.
CC {ECO:0000269|PubMed:16980501, ECO:0000269|Ref.3};
CC -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000269|PubMed:16980501, ECO:0000269|Ref.3};
CC Note=Binds 1 Fe(2+) ion per subunit. {ECO:0000269|PubMed:16980501,
CC ECO:0000269|Ref.3};
CC -!- PATHWAY: Aromatic compound metabolism; naphthalene degradation.
CC {ECO:0000305|PubMed:8226631}.
CC -!- SUBUNIT: The naphthalene dioxygenase (NDO) multicomponent enzyme system
CC is composed of an electron transfer component and a dioxygenase
CC component (iron sulfur protein (ISP)). The electron transfer component
CC is composed of a ferredoxin reductase and a ferredoxin (DoxA), and the
CC dioxygenase component is formed of a heterohexamer (trimer of
CC heterodimers) of three large alpha subunits (DoxB) and three small beta
CC subunits (DoxD). {ECO:0000269|PubMed:16980501,
CC ECO:0000305|PubMed:8226631, ECO:0000305|Ref.3}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene are unable to degrade
CC naphthalene. {ECO:0000269|PubMed:8226631}.
CC -!- MISCELLANEOUS: Encoded on an unnamed 75 kb plasmid.
CC {ECO:0000305|PubMed:8226631}.
CC -!- SIMILARITY: Belongs to the bacterial ring-hydroxylating dioxygenase
CC alpha subunit family. {ECO:0000305}.
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DR EMBL; M60405; AAA16125.1; -; Genomic_DNA.
DR PIR; S27632; S27632.
DR PDB; 2HMJ; X-ray; 1.50 A; A=1-449.
DR PDB; 2HMK; X-ray; 1.65 A; A=1-449.
DR PDB; 2HML; X-ray; 1.80 A; A=1-449.
DR PDB; 2HMM; X-ray; 1.60 A; A=1-449.
DR PDB; 2HMN; X-ray; 1.70 A; A=1-449.
DR PDB; 2HMO; X-ray; 1.60 A; A=1-449.
DR PDB; 4HJL; X-ray; 1.50 A; A=1-446.
DR PDB; 4HKV; X-ray; 1.65 A; A=1-449.
DR PDB; 4HM0; X-ray; 1.80 A; A=1-449.
DR PDB; 4HM1; X-ray; 1.50 A; A=1-449.
DR PDB; 4HM2; X-ray; 1.60 A; A=1-449.
DR PDB; 4HM3; X-ray; 1.50 A; A=1-449.
DR PDB; 4HM4; X-ray; 1.50 A; A=1-449.
DR PDB; 4HM5; X-ray; 1.50 A; A=1-449.
DR PDB; 4HM6; X-ray; 1.50 A; A=1-449.
DR PDB; 4HM7; X-ray; 1.50 A; A=1-449.
DR PDB; 4HM8; X-ray; 1.30 A; A=1-449.
DR PDBsum; 2HMJ; -.
DR PDBsum; 2HMK; -.
DR PDBsum; 2HML; -.
DR PDBsum; 2HMM; -.
DR PDBsum; 2HMN; -.
DR PDBsum; 2HMO; -.
DR PDBsum; 4HJL; -.
DR PDBsum; 4HKV; -.
DR PDBsum; 4HM0; -.
DR PDBsum; 4HM1; -.
DR PDBsum; 4HM2; -.
DR PDBsum; 4HM3; -.
DR PDBsum; 4HM4; -.
DR PDBsum; 4HM5; -.
DR PDBsum; 4HM6; -.
DR PDBsum; 4HM7; -.
DR PDBsum; 4HM8; -.
DR AlphaFoldDB; P0A111; -.
DR SMR; P0A111; -.
DR BRENDA; 1.14.12.12; 5085.
DR UniPathway; UPA00082; -.
DR EvolutionaryTrace; P0A111; -.
DR GO; GO:0051537; F:2 iron, 2 sulfur cluster binding; IDA:UniProtKB.
DR GO; GO:0005506; F:iron ion binding; IDA:UniProtKB.
DR GO; GO:0018625; F:naphthalene 1,2-dioxygenase activity; ISS:UniProtKB.
DR GO; GO:0019439; P:aromatic compound catabolic process; IEA:UniProtKB-KW.
DR CDD; cd08881; RHO_alpha_C_NDO-like; 1.
DR Gene3D; 2.102.10.10; -; 1.
DR InterPro; IPR043266; RHO_NdoB-like_C.
DR InterPro; IPR017941; Rieske_2Fe-2S.
DR InterPro; IPR036922; Rieske_2Fe-2S_sf.
DR InterPro; IPR015881; Ring-hydroxy_dOase_2Fe2S_BS.
DR InterPro; IPR015879; Ring_hydroxy_dOase_asu_C_dom.
DR InterPro; IPR001663; Rng_hydr_dOase-A.
DR PANTHER; PTHR43756; PTHR43756; 1.
DR Pfam; PF00355; Rieske; 1.
DR Pfam; PF00848; Ring_hydroxyl_A; 1.
DR PRINTS; PR00090; RNGDIOXGNASE.
DR SUPFAM; SSF50022; SSF50022; 1.
DR PROSITE; PS51296; RIESKE; 1.
DR PROSITE; PS00570; RING_HYDROXYL_ALPHA; 1.
PE 1: Evidence at protein level;
KW 2Fe-2S; 3D-structure; Aromatic hydrocarbons catabolism; Dioxygenase; Iron;
KW Iron-sulfur; Metal-binding; NAD; Oxidoreductase; Plasmid.
FT CHAIN 1..449
FT /note="Naphthalene 1,2-dioxygenase system, large oxygenase
FT component"
FT /id="PRO_0000085054"
FT DOMAIN 39..137
FT /note="Rieske"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00628"
FT BINDING 81
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000269|PubMed:16980501, ECO:0000269|Ref.3,
FT ECO:0007744|PDB:2HMJ, ECO:0007744|PDB:2HMK,
FT ECO:0007744|PDB:2HML, ECO:0007744|PDB:2HMM,
FT ECO:0007744|PDB:2HMN, ECO:0007744|PDB:2HMO,
FT ECO:0007744|PDB:4HJL, ECO:0007744|PDB:4HKV,
FT ECO:0007744|PDB:4HM0, ECO:0007744|PDB:4HM1,
FT ECO:0007744|PDB:4HM2, ECO:0007744|PDB:4HM3,
FT ECO:0007744|PDB:4HM4, ECO:0007744|PDB:4HM5,
FT ECO:0007744|PDB:4HM6, ECO:0007744|PDB:4HM7,
FT ECO:0007744|PDB:4HM8"
FT BINDING 83
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000269|PubMed:16980501, ECO:0000269|Ref.3,
FT ECO:0007744|PDB:2HMJ, ECO:0007744|PDB:2HMK,
FT ECO:0007744|PDB:2HML, ECO:0007744|PDB:2HMM,
FT ECO:0007744|PDB:2HMN, ECO:0007744|PDB:2HMO,
FT ECO:0007744|PDB:4HJL, ECO:0007744|PDB:4HKV,
FT ECO:0007744|PDB:4HM0, ECO:0007744|PDB:4HM1,
FT ECO:0007744|PDB:4HM2, ECO:0007744|PDB:4HM3,
FT ECO:0007744|PDB:4HM4, ECO:0007744|PDB:4HM5,
FT ECO:0007744|PDB:4HM6, ECO:0007744|PDB:4HM7,
FT ECO:0007744|PDB:4HM8"
FT BINDING 101
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000269|PubMed:16980501, ECO:0000269|Ref.3,
FT ECO:0007744|PDB:2HMJ, ECO:0007744|PDB:2HMK,
FT ECO:0007744|PDB:2HML, ECO:0007744|PDB:2HMM,
FT ECO:0007744|PDB:2HMN, ECO:0007744|PDB:2HMO,
FT ECO:0007744|PDB:4HJL, ECO:0007744|PDB:4HKV,
FT ECO:0007744|PDB:4HM0, ECO:0007744|PDB:4HM1,
FT ECO:0007744|PDB:4HM2, ECO:0007744|PDB:4HM3,
FT ECO:0007744|PDB:4HM4, ECO:0007744|PDB:4HM5,
FT ECO:0007744|PDB:4HM6, ECO:0007744|PDB:4HM7,
FT ECO:0007744|PDB:4HM8"
FT BINDING 104
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000269|PubMed:16980501, ECO:0000269|Ref.3,
FT ECO:0007744|PDB:2HMJ, ECO:0007744|PDB:2HMK,
FT ECO:0007744|PDB:2HML, ECO:0007744|PDB:2HMM,
FT ECO:0007744|PDB:2HMN, ECO:0007744|PDB:2HMO,
FT ECO:0007744|PDB:4HJL, ECO:0007744|PDB:4HKV,
FT ECO:0007744|PDB:4HM0, ECO:0007744|PDB:4HM1,
FT ECO:0007744|PDB:4HM2, ECO:0007744|PDB:4HM3,
FT ECO:0007744|PDB:4HM4, ECO:0007744|PDB:4HM5,
FT ECO:0007744|PDB:4HM6, ECO:0007744|PDB:4HM7,
FT ECO:0007744|PDB:4HM8"
FT BINDING 208
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000269|PubMed:16980501, ECO:0000269|Ref.3,
FT ECO:0007744|PDB:2HMJ, ECO:0007744|PDB:2HMK,
FT ECO:0007744|PDB:2HML, ECO:0007744|PDB:2HMM,
FT ECO:0007744|PDB:2HMN, ECO:0007744|PDB:2HMO,
FT ECO:0007744|PDB:4HJL, ECO:0007744|PDB:4HKV,
FT ECO:0007744|PDB:4HM0, ECO:0007744|PDB:4HM1,
FT ECO:0007744|PDB:4HM2, ECO:0007744|PDB:4HM3,
FT ECO:0007744|PDB:4HM4, ECO:0007744|PDB:4HM5,
FT ECO:0007744|PDB:4HM6, ECO:0007744|PDB:4HM7,
FT ECO:0007744|PDB:4HM8"
FT BINDING 213
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000269|PubMed:16980501, ECO:0000269|Ref.3,
FT ECO:0007744|PDB:2HMJ, ECO:0007744|PDB:2HMK,
FT ECO:0007744|PDB:2HML, ECO:0007744|PDB:2HMM,
FT ECO:0007744|PDB:2HMN, ECO:0007744|PDB:2HMO,
FT ECO:0007744|PDB:4HJL, ECO:0007744|PDB:4HKV,
FT ECO:0007744|PDB:4HM0, ECO:0007744|PDB:4HM1,
FT ECO:0007744|PDB:4HM2, ECO:0007744|PDB:4HM3,
FT ECO:0007744|PDB:4HM4, ECO:0007744|PDB:4HM5,
FT ECO:0007744|PDB:4HM6, ECO:0007744|PDB:4HM7,
FT ECO:0007744|PDB:4HM8"
FT BINDING 362
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000269|PubMed:16980501, ECO:0000269|Ref.3,
FT ECO:0007744|PDB:2HMJ, ECO:0007744|PDB:2HMK,
FT ECO:0007744|PDB:2HML, ECO:0007744|PDB:2HMM,
FT ECO:0007744|PDB:2HMN, ECO:0007744|PDB:2HMO,
FT ECO:0007744|PDB:4HJL, ECO:0007744|PDB:4HKV,
FT ECO:0007744|PDB:4HM0, ECO:0007744|PDB:4HM1,
FT ECO:0007744|PDB:4HM2, ECO:0007744|PDB:4HM3,
FT ECO:0007744|PDB:4HM4, ECO:0007744|PDB:4HM5,
FT ECO:0007744|PDB:4HM6, ECO:0007744|PDB:4HM7,
FT ECO:0007744|PDB:4HM8"
FT MUTAGEN 352
FT /note="F->V: Changes the regioselectivity of the product
FT for naphthalene, phenanthrene and biphenyl."
FT /evidence="ECO:0000269|PubMed:16980501"
FT TURN 3..5
FT /evidence="ECO:0007829|PDB:4HM8"
FT HELIX 11..13
FT /evidence="ECO:0007829|PDB:4HM8"
FT STRAND 15..17
FT /evidence="ECO:0007829|PDB:4HM8"
FT HELIX 18..21
FT /evidence="ECO:0007829|PDB:4HM8"
FT HELIX 24..33
FT /evidence="ECO:0007829|PDB:4HM8"
FT TURN 34..37
FT /evidence="ECO:0007829|PDB:4HM8"
FT STRAND 40..44
FT /evidence="ECO:0007829|PDB:4HM8"
FT HELIX 45..47
FT /evidence="ECO:0007829|PDB:4HM8"
FT STRAND 53..59
FT /evidence="ECO:0007829|PDB:4HM8"
FT STRAND 62..68
FT /evidence="ECO:0007829|PDB:4HM8"
FT STRAND 74..80
FT /evidence="ECO:0007829|PDB:4HM8"
FT TURN 82..84
FT /evidence="ECO:0007829|PDB:4HM8"
FT STRAND 91..95
FT /evidence="ECO:0007829|PDB:4HM8"
FT STRAND 97..100
FT /evidence="ECO:0007829|PDB:4HM8"
FT TURN 102..104
FT /evidence="ECO:0007829|PDB:4HM8"
FT STRAND 107..109
FT /evidence="ECO:0007829|PDB:4HM8"
FT STRAND 114..116
FT /evidence="ECO:0007829|PDB:4HM8"
FT HELIX 120..123
FT /evidence="ECO:0007829|PDB:4HM8"
FT TURN 124..126
FT /evidence="ECO:0007829|PDB:4HM8"
FT HELIX 130..132
FT /evidence="ECO:0007829|PDB:4HM8"
FT STRAND 139..144
FT /evidence="ECO:0007829|PDB:4HM8"
FT STRAND 147..152
FT /evidence="ECO:0007829|PDB:4HM8"
FT HELIX 159..163
FT /evidence="ECO:0007829|PDB:4HM8"
FT HELIX 166..174
FT /evidence="ECO:0007829|PDB:4HM8"
FT TURN 175..177
FT /evidence="ECO:0007829|PDB:4HM8"
FT STRAND 180..193
FT /evidence="ECO:0007829|PDB:4HM8"
FT HELIX 196..204
FT /evidence="ECO:0007829|PDB:4HM8"
FT HELIX 209..212
FT /evidence="ECO:0007829|PDB:4HM8"
FT HELIX 214..220
FT /evidence="ECO:0007829|PDB:4HM8"
FT HELIX 225..230
FT /evidence="ECO:0007829|PDB:4HM8"
FT STRAND 238..243
FT /evidence="ECO:0007829|PDB:4HM8"
FT STRAND 249..253
FT /evidence="ECO:0007829|PDB:4HM8"
FT TURN 257..260
FT /evidence="ECO:0007829|PDB:4HM8"
FT TURN 263..265
FT /evidence="ECO:0007829|PDB:4HM8"
FT HELIX 266..284
FT /evidence="ECO:0007829|PDB:4HM8"
FT HELIX 286..292
FT /evidence="ECO:0007829|PDB:4HM8"
FT STRAND 294..300
FT /evidence="ECO:0007829|PDB:4HM8"
FT TURN 301..303
FT /evidence="ECO:0007829|PDB:4HM8"
FT STRAND 304..307
FT /evidence="ECO:0007829|PDB:4HM8"
FT TURN 308..311
FT /evidence="ECO:0007829|PDB:4HM8"
FT STRAND 312..320
FT /evidence="ECO:0007829|PDB:4HM8"
FT STRAND 323..333
FT /evidence="ECO:0007829|PDB:4HM8"
FT HELIX 338..352
FT /evidence="ECO:0007829|PDB:4HM8"
FT HELIX 357..372
FT /evidence="ECO:0007829|PDB:4HM8"
FT TURN 376..380
FT /evidence="ECO:0007829|PDB:4HM8"
FT STRAND 382..384
FT /evidence="ECO:0007829|PDB:4HM8"
FT TURN 387..390
FT /evidence="ECO:0007829|PDB:4HM8"
FT STRAND 393..395
FT /evidence="ECO:0007829|PDB:4HM8"
FT STRAND 397..399
FT /evidence="ECO:0007829|PDB:4HM8"
FT STRAND 401..410
FT /evidence="ECO:0007829|PDB:4HM8"
FT HELIX 411..424
FT /evidence="ECO:0007829|PDB:4HM8"
FT HELIX 429..434
FT /evidence="ECO:0007829|PDB:4HM8"
FT TURN 435..438
FT /evidence="ECO:0007829|PDB:4HM8"
FT HELIX 439..444
FT /evidence="ECO:0007829|PDB:4HM8"
SQ SEQUENCE 449 AA; 49608 MW; 1FD2F42296B4F7A8 CRC64;
MNYNNKILVS ESGLSQKHLI HGDEELFQHE LKTIFARNWL FLTHDSLIPA PGDYVTAKMG
IDEVIVSRQN DGSIRAFLNV CRHRGKTLVS VEAGNAKGFV CSYHGWGFGS NGELQSVPFE
KDLYGESLNK KCLGLKEVAR VESFHGFIYG CFDQEAPPLM DYLGDAAWYL EPMFKHSGGL
ELVGPPGKVV IKANWKAPAE NFVGDAYHVG WTHASSLRSG ESIFSSLAGN AALPPEGAGL
QMTSKYGSGM GVLWDGYSGV HSADLVPELM AFGGAKQERL NKEIGDVRAR IYRSHLNCTV
FPNNSMLTCS GVFKVWNPID ANTTEVWTYA IVEKDMPEDL KRRLADSVQR TFGPAGFWES
DDNDNMETAS QNGKKYQSRD SDLLSNLGFG EDVYGDAVYP GVVGKSAIGE TSYRGFYRAY
QAHVSSSNWA EFEHASSTWH TELTKTTDR
