NDOC_PSEPU
ID NDOC_PSEPU Reviewed; 194 AA.
AC P0A112; P23095; Q52125;
DT 01-MAR-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2005, sequence version 1.
DT 03-AUG-2022, entry version 98.
DE RecName: Full=Naphthalene 1,2-dioxygenase system, small oxygenase component {ECO:0000305};
DE AltName: Full=Naphthalene 1,2-dioxygenase ISP beta {ECO:0000303|PubMed:6874638};
DE AltName: Full=Naphthalene 1,2-dioxygenase subunit beta {ECO:0000303|PubMed:6874638};
DE Short=ND subunit beta {ECO:0000303|PubMed:3243438};
DE Short=NDO subunit beta {ECO:0000303|PubMed:9634695};
GN Name=ndoC {ECO:0000303|PubMed:3243438};
GN Synonyms=nahAD {ECO:0000303|PubMed:8486285};
OS Pseudomonas putida (Arthrobacter siderocapsulatus).
OG Plasmid pDTG1, and Plasmid NAH7.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=303;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=DSM 8368 / NCIMB 9816 / PG;
RX PubMed=3243438; DOI=10.1016/0378-1119(88)90500-8;
RA Kurkela S., Lehvaeslaiho H., Palva E.T., Teeri T.H.;
RT "Cloning, nucleotide sequence and characterization of genes encoding
RT naphthalene dioxygenase of Pseudomonas putida strain NCIB9816.";
RL Gene 73:355-362(1988).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=NCIMB 9816-4; PLASMID=pDTG1;
RX PubMed=8973308; DOI=10.1016/s0378-1119(96)00462-3;
RA Parales J.V., Kumar A., Parales R.E., Gibson D.T.;
RT "Cloning and sequencing of the genes encoding 2-nitrotoluene dioxygenase
RT from Pseudomonas sp. JS42.";
RL Gene 181:57-61(1996).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 17485 / DSM 50208 / JCM 6158 / NCIMB 12092 / Stanier 111 /
RC Biotype A; PLASMID=NAH7;
RX PubMed=8486285; DOI=10.1016/0378-1119(93)90613-8;
RA Simon M.J., Osslund T.D., Saunders R., Ensley B.D., Suggs S.,
RA Harcourt A.A., Suen W.-C., Cruden D.L., Gibson D.T., Zylstra G.J.;
RT "Sequences of genes encoding naphthalene dioxygenase in Pseudomonas putida
RT strains G7 and NCIB 9816-4.";
RL Gene 127:31-37(1993).
RN [4]
RP FUNCTION, AND SUBUNIT.
RC STRAIN=DSM 8368 / NCIMB 9816 / PG;
RX PubMed=6874638; DOI=10.1128/jb.155.2.505-511.1983;
RA Ensley B.D., Gibson D.T.;
RT "Naphthalene dioxygenase: purification and properties of a terminal
RT oxygenase component.";
RL J. Bacteriol. 155:505-511(1983).
RN [5]
RP FUNCTION, SUBSTRATE SPECIFICITY, AND PATHWAY.
RC STRAIN=NCIMB 9816-4;
RX PubMed=10692370; DOI=10.1128/jb.182.6.1641-1649.2000;
RA Parales R.E., Lee K., Resnick S.M., Jiang H., Lessner D.J., Gibson D.T.;
RT "Substrate specificity of naphthalene dioxygenase: effect of specific amino
RT acids at the active site of the enzyme.";
RL J. Bacteriol. 182:1641-1649(2000).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS), AND SUBUNIT.
RC STRAIN=NCIMB 9816-4;
RX PubMed=9634695; DOI=10.1016/s0969-2126(98)00059-8;
RA Kauppi B., Lee K., Carredano E., Parales R.E., Gibson D.T., Eklund H.,
RA Ramaswamy S.;
RT "Structure of an aromatic-ring-hydroxylating dioxygenase-naphthalene 1,2-
RT dioxygenase.";
RL Structure 6:571-586(1998).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS).
RC STRAIN=NCIMB 9816-4;
RX PubMed=10669618; DOI=10.1006/jmbi.1999.3462;
RA Carredano E., Karlsson A., Kauppi B., Choudhury D., Parales R.E.,
RA Parales J.V., Lee K., Gibson D.T., Eklund H., Ramaswamy S.;
RT "Substrate binding site of naphthalene 1,2-dioxygenase: functional
RT implications of indole binding.";
RL J. Mol. Biol. 296:701-712(2000).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (1.40 ANGSTROMS), AND SUBUNIT.
RX PubMed=12586937; DOI=10.1126/science.1078020;
RA Karlsson A., Parales J.V., Parales R.E., Gibson D.T., Eklund H.,
RA Ramaswamy S.;
RT "Crystal structure of naphthalene dioxygenase: side-on binding of dioxygen
RT to iron.";
RL Science 299:1039-1042(2003).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS), AND SUBUNIT.
RX PubMed=15942729; DOI=10.1007/s00775-005-0657-1;
RA Karlsson A., Parales J.V., Parales R.E., Gibson D.T., Eklund H.,
RA Ramaswamy S.;
RT "NO binding to naphthalene dioxygenase.";
RL J. Biol. Inorg. Chem. 10:483-489(2005).
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 beta subunit seems to have a structural role in
CC the holoenzyme. Also able to catalyze the cis-dihydroxylation of
CC biphenyl and phenanthrene (PubMed:10692370).
CC {ECO:0000269|PubMed:10692370, ECO:0000269|PubMed:6874638}.
CC -!- PATHWAY: Aromatic compound metabolism; naphthalene degradation.
CC {ECO:0000305|PubMed:10692370}.
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 (NdoR) and a ferredoxin (NdoA),
CC and the dioxygenase component is formed of a heterohexamer (trimer of
CC heterodimers) of three large alpha subunits (NdoB) and three small beta
CC subunits (NdoC). {ECO:0000269|PubMed:12586937,
CC ECO:0000269|PubMed:15942729, ECO:0000269|PubMed:9634695,
CC ECO:0000305|PubMed:6874638}.
CC -!- INTERACTION:
CC P0A112; P0A110: ndoB; NbExp=7; IntAct=EBI-1029028, EBI-1029015;
CC -!- SIMILARITY: Belongs to the bacterial ring-hydroxylating dioxygenase
CC beta subunit family. {ECO:0000305}.
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DR EMBL; M23914; AAB47592.1; -; Genomic_DNA.
DR EMBL; U49496; AAA92142.1; -; Genomic_DNA.
DR EMBL; M83949; AAA25903.1; -; Genomic_DNA.
DR PIR; JN0645; JN0645.
DR PIR; JS0072; JS0072.
DR RefSeq; NP_863073.1; NC_004999.1.
DR RefSeq; WP_011117401.1; NC_004999.1.
DR RefSeq; YP_534823.1; NC_007926.1.
DR PDB; 1EG9; X-ray; 1.60 A; B=1-194.
DR PDB; 1NDO; X-ray; 2.25 A; B/D/F=1-194.
DR PDB; 1O7G; X-ray; 1.70 A; B=1-194.
DR PDB; 1O7H; X-ray; 2.20 A; B=1-194.
DR PDB; 1O7M; X-ray; 1.75 A; B=1-194.
DR PDB; 1O7N; X-ray; 1.40 A; B=1-194.
DR PDB; 1O7P; X-ray; 1.95 A; B=1-194.
DR PDB; 1O7W; X-ray; 1.90 A; B=1-194.
DR PDB; 1UUV; X-ray; 1.65 A; B=1-194.
DR PDB; 1UUW; X-ray; 2.30 A; B=1-194.
DR PDBsum; 1EG9; -.
DR PDBsum; 1NDO; -.
DR PDBsum; 1O7G; -.
DR PDBsum; 1O7H; -.
DR PDBsum; 1O7M; -.
DR PDBsum; 1O7N; -.
DR PDBsum; 1O7P; -.
DR PDBsum; 1O7W; -.
DR PDBsum; 1UUV; -.
DR PDBsum; 1UUW; -.
DR AlphaFoldDB; P0A112; -.
DR SMR; P0A112; -.
DR IntAct; P0A112; 1.
DR DrugBank; DB08264; (1R, 2S)-cis 1,2 dihydroxy-1,2-dihydronaphthalene.
DR BioCyc; MetaCyc:MON-12803; -.
DR BRENDA; 1.14.12.12; 5092.
DR UniPathway; UPA00082; -.
DR EvolutionaryTrace; P0A112; -.
DR GO; GO:0051213; F:dioxygenase activity; IEA:UniProtKB-KW.
DR GO; GO:0019439; P:aromatic compound catabolic process; IEA:UniProtKB-KW.
DR GO; GO:0071704; P:organic substance metabolic process; IEA:UniProt.
DR CDD; cd00667; ring_hydroxylating_dioxygenases_beta; 1.
DR InterPro; IPR032710; NTF2-like_dom_sf.
DR InterPro; IPR000391; Rng_hydr_dOase-bsu.
DR Pfam; PF00866; Ring_hydroxyl_B; 1.
DR SUPFAM; SSF54427; SSF54427; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Aromatic hydrocarbons catabolism; Dioxygenase;
KW Oxidoreductase; Plasmid.
FT CHAIN 1..194
FT /note="Naphthalene 1,2-dioxygenase system, small oxygenase
FT component"
FT /id="PRO_0000085072"
FT VARIANT 17
FT /note="E -> Q (in strain: G7)"
FT VARIANT 19
FT /note="I -> F (in strain: G7)"
FT VARIANT 28
FT /note="S -> A (in strain: G7)"
FT VARIANT 39..40
FT /note="TQ -> NR (in strain: G7)"
FT VARIANT 99
FT /note="V -> I (in strain: G7)"
FT VARIANT 109
FT /note="G -> S (in strain: G7)"
FT VARIANT 127
FT /note="M -> R (in strain: G7)"
FT VARIANT 130
FT /note="N -> D (in strain: G7)"
FT VARIANT 132
FT /note="K -> E (in strain: G7)"
FT TURN 5..7
FT /evidence="ECO:0007829|PDB:1O7N"
FT HELIX 13..23
FT /evidence="ECO:0007829|PDB:1O7N"
FT HELIX 28..46
FT /evidence="ECO:0007829|PDB:1O7N"
FT HELIX 50..57
FT /evidence="ECO:0007829|PDB:1O7N"
FT STRAND 58..69
FT /evidence="ECO:0007829|PDB:1O7N"
FT STRAND 84..90
FT /evidence="ECO:0007829|PDB:1O7N"
FT HELIX 92..103
FT /evidence="ECO:0007829|PDB:1O7N"
FT HELIX 108..110
FT /evidence="ECO:0007829|PDB:1O7N"
FT STRAND 115..127
FT /evidence="ECO:0007829|PDB:1O7N"
FT STRAND 134..147
FT /evidence="ECO:0007829|PDB:1O7N"
FT TURN 148..150
FT /evidence="ECO:0007829|PDB:1O7N"
FT STRAND 151..167
FT /evidence="ECO:0007829|PDB:1O7N"
FT STRAND 170..179
FT /evidence="ECO:0007829|PDB:1O7N"
FT STRAND 183..185
FT /evidence="ECO:0007829|PDB:1O7N"
SQ SEQUENCE 194 AA; 22935 MW; 168D2E1535E66416 CRC64;
MMINIQEDKL VSAHDAEEIL RFFNCHDSAL QQEATTLLTQ EAHLLDIQAY RAWLEHCVGS
EVQYQVISRE LRAASERRYK LNEAMNVYNE NFQQLKVRVE HQLDPQNWGN SPKLRFTRFI
TNVQAAMDVN DKELLHIRSN VILHRARRGN QVDVFYAARE DKWKRGEGGV RKLVQRFVDY
PERILQTHNL MVFL
