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Biphenyl 2,3-dioxygenase subunit alpha (EC 1.14.12.18) (Biphenyl dioxygenase system, oxygenase component subunit alpha) (BDO, oxygenase component subunit alpha) (Rieske dioxygenase) (Terminal oxygenase component of biphenyl dioxygenase, large subunit)

 BPHA1_RHOJR             Reviewed;         460 AA.
Q53122;
29-OCT-2014, integrated into UniProtKB/Swiss-Prot.
01-NOV-1996, sequence version 1.
25-OCT-2017, entry version 113.
RecName: Full=Biphenyl 2,3-dioxygenase subunit alpha {ECO:0000305};
EC=1.14.12.18 {ECO:0000269|PubMed:17420585};
AltName: Full=Biphenyl dioxygenase system, oxygenase component subunit alpha {ECO:0000305};
Short=BDO, oxygenase component subunit alpha {ECO:0000305};
AltName: Full=Rieske dioxygenase {ECO:0000303|PubMed:15342255};
AltName: Full=Terminal oxygenase component of biphenyl dioxygenase, large subunit {ECO:0000303|PubMed:15342255};
Name=bphA1 {ECO:0000303|PubMed:7793929};
Synonyms=bphAa {ECO:0000312|EMBL:ABG99107.1};
OrderedLocusNames=RHA1_ro08060 {ECO:0000312|EMBL:ABG99107.1};
Rhodococcus jostii (strain RHA1).
Plasmid pRHL1 {ECO:0000312, ECO:0000312|EMBL:ABG99107.1}.
Bacteria; Actinobacteria; Corynebacteriales; Nocardiaceae;
Rhodococcus.
NCBI_TaxID=101510;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, DISRUPTION PHENOTYPE, AND
PATHWAY.
STRAIN=RHA1;
PubMed=7793929;
Masai E., Yamada A., Healy J.M., Hatta T., Kimbara K., Fukuda M.,
Yano K.;
"Characterization of biphenyl catabolic genes of gram-positive
polychlorinated biphenyl degrader Rhodococcus sp. strain RHA1.";
Appl. Environ. Microbiol. 61:2079-2085(1995).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=RHA1;
PubMed=17030794; DOI=10.1073/pnas.0607048103;
McLeod M.P., Warren R.L., Hsiao W.W.L., Araki N., Myhre M.,
Fernandes C., Miyazawa D., Wong W., Lillquist A.L., Wang D.,
Dosanjh M., Hara H., Petrescu A., Morin R.D., Yang G., Stott J.M.,
Schein J.E., Shin H., Smailus D., Siddiqui A.S., Marra M.A.,
Jones S.J.M., Holt R., Brinkman F.S.L., Miyauchi K., Fukuda M.,
Davies J.E., Mohn W.W., Eltis L.D.;
"The complete genome of Rhodococcus sp. RHA1 provides insights into a
catabolic powerhouse.";
Proc. Natl. Acad. Sci. U.S.A. 103:15582-15587(2006).
[3]
INDUCTION.
STRAIN=RHA1;
PubMed=15028699; DOI=10.1128/JB.186.7.2134-2146.2004;
Takeda H., Yamada A., Miyauchi K., Masai E., Fukuda M.;
"Characterization of transcriptional regulatory genes for biphenyl
degradation in Rhodococcus sp. strain RHA1.";
J. Bacteriol. 186:2134-2146(2004).
[4]
FUNCTION, CATALYTIC ACTIVITY, AND SUBSTRATE SPECIFICITY.
STRAIN=RHA1;
PubMed=17420585; DOI=10.1271/bbb.60663;
Iwasaki T., Takeda H., Miyauchi K., Yamada T., Masai E., Fukuda M.;
"Characterization of two biphenyl dioxygenases for biphenyl/PCB
degradation in A PCB degrader, Rhodococcus sp. strain RHA1.";
Biosci. Biotechnol. Biochem. 71:993-1002(2007).
[5]
X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) IN COMPLEXES WITH BETA SUBUNIT;
BIPHENYL; IRON AND IRON-SULFUR (2FE-2S), AND COFACTOR.
STRAIN=RHA1;
PubMed=15342255; DOI=10.1016/j.jmb.2004.07.062;
Furusawa Y., Nagarajan V., Tanokura M., Masai E., Fukuda M., Senda T.;
"Crystal structure of the terminal oxygenase component of biphenyl
dioxygenase derived from Rhodococcus sp. strain RHA1.";
J. Mol. Biol. 342:1041-1052(2004).
-!- FUNCTION: Part of the oxygenase component of the biphenyl
dioxygenase system that catalyzes the stereospecific
dihydroxylation of the aromatic ring of biphenyl, yielding a
dihydrodiol compound. Is essential for biphenyl degradation and
growth of Rhodococcus sp. strain RHA1 on biphenyl as the sole
source of carbon and energy. Can also use naphtalene and 4-
chlorobiphenyl (4-CB) as substrates, as well as some
polychlorinated biphenyls (PCB) such as 2,2'-dichlorobiphenyl,
2,3-dichlorobiphenyl and 2,5,2'-trichlorobiphenyl. Exhibits weak
activity toward dibenzofuran and dibenzo-p-dioxin. Electrons are
transferred from NADH to the [2Fe-2S] cluster in BphA1 via FAD of
BphA4 and [2Fe-2S] cluster of BphA3. {ECO:0000269|PubMed:17420585,
ECO:0000269|PubMed:7793929}.
-!- CATALYTIC ACTIVITY: Biphenyl + NADH + O(2) = (1S,2R)-3-
phenylcyclohexa-3,5-diene-1,2-diol + NAD(+).
{ECO:0000269|PubMed:17420585}.
-!- COFACTOR:
Name=[2Fe-2S] cluster; Xref=ChEBI:CHEBI:49601;
Evidence={ECO:0000269|PubMed:15342255};
Note=Binds 1 [2Fe-2S] cluster per subunit.
{ECO:0000269|PubMed:15342255};
-!- COFACTOR:
Name=Fe cation; Xref=ChEBI:CHEBI:24875;
Evidence={ECO:0000269|PubMed:15342255};
Note=Binds 1 Fe cation per subunit. {ECO:0000269|PubMed:15342255};
-!- PATHWAY: Xenobiotic degradation; biphenyl degradation; 2-hydroxy-
2,4-pentadienoate and benzoate from biphenyl: step 1/4.
{ECO:0000269|PubMed:7793929}.
-!- SUBUNIT: Heterohexamer consisting of three BphA1 subunits and
three BphA2 subunits. The multicomponent biphenyl dioxygenase
system is composed of a ferredoxin reductase (BphA4), a ferredoxin
(BphA3), and a terminal oxygenase (BphA1A2).
{ECO:0000269|PubMed:15342255, ECO:0000303|PubMed:17420585}.
-!- INTERACTION:
Q53123:bphA2; NbExp=2; IntAct=EBI-1040100, EBI-1040088;
-!- INDUCTION: Transcription is up-regulated by aromatic compounds
including biphenyl, ethylbenzene, benzene, toluene, xylene,
cumene, cymene, and chlorinated benzenes. Is under the control of
the BphST two-component regulatory system.
{ECO:0000269|PubMed:15028699}.
-!- DISRUPTION PHENOTYPE: Cells lacking this gene lose their ability
to grow on biphenyl. {ECO:0000269|PubMed:7793929}.
-!- SIMILARITY: Belongs to the bacterial ring-hydroxylating
dioxygenase alpha subunit family. {ECO:0000305}.
-----------------------------------------------------------------------
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Distributed under the Creative Commons Attribution-NoDerivs License
-----------------------------------------------------------------------
EMBL; CP000432; ABG99107.1; -; Genomic_DNA.
EMBL; D32142; BAA06868.1; -; Genomic_DNA.
RefSeq; WP_011599002.1; NC_008269.1.
PDB; 1ULI; X-ray; 2.20 A; A/C/E=1-460.
PDB; 1ULJ; X-ray; 2.60 A; A/C/E=1-460.
PDBsum; 1ULI; -.
PDBsum; 1ULJ; -.
ProteinModelPortal; Q53122; -.
SMR; Q53122; -.
IntAct; Q53122; 1.
PRIDE; Q53122; -.
EnsemblBacteria; ABG99107; ABG99107; RHA1_ro08060.
GeneID; 4225185; -.
KEGG; rha:RHA1_ro08060; -.
PATRIC; fig|101510.16.peg.7407; -.
HOGENOM; HOG000105925; -.
KO; K08689; -.
OMA; SASHKGH; -.
OrthoDB; POG091H0936; -.
UniPathway; UPA00155; UER00250.
EvolutionaryTrace; Q53122; -.
Proteomes; UP000008710; Plasmid pRHL1.
GO; GO:0051537; F:2 iron, 2 sulfur cluster binding; IEA:UniProtKB-KW.
GO; GO:0018687; F:biphenyl 2,3-dioxygenase activity; IEA:UniProtKB-EC.
GO; GO:0005506; F:iron ion binding; IEA:InterPro.
GO; GO:0019439; P:aromatic compound catabolic process; IEA:UniProtKB-KW.
Gene3D; 2.102.10.10; -; 1.
InterPro; IPR017941; Rieske_2Fe-2S.
InterPro; IPR036922; Rieske_2Fe-2S_sf.
InterPro; IPR015881; Ring-hydroxy_dOase_2Fe2S_BS.
InterPro; IPR015879; Ring_hydroxy_dOase_asu_C_dom.
InterPro; IPR001663; Rng_hydr_dOase-A.
Pfam; PF00355; Rieske; 1.
Pfam; PF00848; Ring_hydroxyl_A; 1.
PRINTS; PR00090; RNGDIOXGNASE.
SUPFAM; SSF50022; SSF50022; 1.
PROSITE; PS51296; RIESKE; 1.
PROSITE; PS00570; RING_HYDROXYL_ALPHA; 1.
1: Evidence at protein level;
2Fe-2S; 3D-structure; Aromatic hydrocarbons catabolism;
Complete proteome; Dioxygenase; Iron; Iron-sulfur; Metal-binding; NAD;
Oxidoreductase; Plasmid; Reference proteome.
CHAIN 1 460 Biphenyl 2,3-dioxygenase subunit alpha.
/FTId=PRO_0000430659.
DOMAIN 56 165 Rieske. {ECO:0000255|PROSITE-
ProRule:PRU00628}.
REGION 217 230 Substrate binding.
{ECO:0000269|PubMed:15342255}.
METAL 98 98 Iron-sulfur (2Fe-2S).
{ECO:0000269|PubMed:15342255,
ECO:0000312|PDB:1ULI,
ECO:0000312|PDB:1ULJ}.
METAL 100 100 Iron-sulfur (2Fe-2S); via pros nitrogen.
{ECO:0000269|PubMed:15342255,
ECO:0000312|PDB:1ULI,
ECO:0000312|PDB:1ULJ}.
METAL 118 118 Iron-sulfur (2Fe-2S).
{ECO:0000269|PubMed:15342255,
ECO:0000312|PDB:1ULI,
ECO:0000312|PDB:1ULJ}.
METAL 121 121 Iron-sulfur (2Fe-2S); via pros nitrogen.
{ECO:0000269|PubMed:15342255,
ECO:0000312|PDB:1ULI,
ECO:0000312|PDB:1ULJ}.
METAL 224 224 Iron; via tele nitrogen.
{ECO:0000269|PubMed:15342255,
ECO:0000312|PDB:1ULI,
ECO:0000312|PDB:1ULJ}.
METAL 230 230 Iron; via tele nitrogen.
{ECO:0000269|PubMed:15342255,
ECO:0000312|PDB:1ULI,
ECO:0000312|PDB:1ULJ}.
METAL 378 378 Iron. {ECO:0000269|PubMed:15342255,
ECO:0000312|PDB:1ULI,
ECO:0000312|PDB:1ULJ}.
HELIX 19 23 {ECO:0000244|PDB:1ULI}.
TURN 28 31 {ECO:0000244|PDB:1ULI}.
HELIX 35 38 {ECO:0000244|PDB:1ULI}.
HELIX 41 50 {ECO:0000244|PDB:1ULI}.
TURN 51 54 {ECO:0000244|PDB:1ULI}.
STRAND 57 61 {ECO:0000244|PDB:1ULI}.
HELIX 62 64 {ECO:0000244|PDB:1ULI}.
STRAND 70 76 {ECO:0000244|PDB:1ULI}.
STRAND 79 85 {ECO:0000244|PDB:1ULI}.
STRAND 91 96 {ECO:0000244|PDB:1ULI}.
TURN 99 101 {ECO:0000244|PDB:1ULI}.
STRAND 108 112 {ECO:0000244|PDB:1ULI}.
TURN 119 121 {ECO:0000244|PDB:1ULI}.
STRAND 131 133 {ECO:0000244|PDB:1ULI}.
HELIX 137 140 {ECO:0000244|PDB:1ULI}.
HELIX 146 148 {ECO:0000244|PDB:1ULI}.
STRAND 153 159 {ECO:0000244|PDB:1ULI}.
STRAND 162 166 {ECO:0000244|PDB:1ULI}.
HELIX 174 178 {ECO:0000244|PDB:1ULI}.
HELIX 181 189 {ECO:0000244|PDB:1ULI}.
STRAND 196 198 {ECO:0000244|PDB:1ULI}.
STRAND 203 207 {ECO:0000244|PDB:1ULI}.
HELIX 211 220 {ECO:0000244|PDB:1ULI}.
HELIX 222 226 {ECO:0000244|PDB:1ULI}.
TURN 227 230 {ECO:0000244|PDB:1ULI}.
HELIX 231 236 {ECO:0000244|PDB:1ULI}.
STRAND 253 257 {ECO:0000244|PDB:1ULI}.
STRAND 259 262 {ECO:0000244|PDB:1ULI}.
STRAND 264 270 {ECO:0000244|PDB:1ULI}.
HELIX 273 288 {ECO:0000244|PDB:1ULI}.
HELIX 291 299 {ECO:0000244|PDB:1ULI}.
HELIX 303 307 {ECO:0000244|PDB:1ULI}.
STRAND 308 316 {ECO:0000244|PDB:1ULI}.
TURN 317 319 {ECO:0000244|PDB:1ULI}.
STRAND 320 322 {ECO:0000244|PDB:1ULI}.
TURN 324 326 {ECO:0000244|PDB:1ULI}.
STRAND 328 334 {ECO:0000244|PDB:1ULI}.
STRAND 340 349 {ECO:0000244|PDB:1ULI}.
HELIX 354 367 {ECO:0000244|PDB:1ULI}.
HELIX 375 388 {ECO:0000244|PDB:1ULI}.
HELIX 393 395 {ECO:0000244|PDB:1ULI}.
TURN 403 406 {ECO:0000244|PDB:1ULI}.
STRAND 408 410 {ECO:0000244|PDB:1ULJ}.
STRAND 413 415 {ECO:0000244|PDB:1ULI}.
STRAND 417 423 {ECO:0000244|PDB:1ULI}.
HELIX 426 439 {ECO:0000244|PDB:1ULI}.
HELIX 444 448 {ECO:0000244|PDB:1ULI}.
SEQUENCE 460 AA; 51592 MW; 28D86F926FA4E9A0 CRC64;
MTDVQCEPAL AGRKPKWADA DIAELVDERT GRLDPRIYTD EALYEQELER IFGRSWLLMG
HETQIPKAGD FMTNYMGEDP VMVVRQKNGE IRVFLNQCRH RGMRICRADG GNAKSFTCSY
HGWAYDTGGN LVSVPFEEQA FPGLRKEDWG PLQARVETYK GLIFANWDAD APDLDTYLGE
AKFYMDHMLD RTEAGTEAIP GIQKWVIPCN WKFAAEQFCS DMYHAGTTSH LSGILAGLPD
GVDLSELAPP TEGIQYRATW GGHGSGFYIG DPNLLLAIMG PKVTEYWTQG PAAEKASERL
GSTERGQQLM AQHMTIFPTC SFLPGINTIR AWHPRGPNEI EVWAFTVVDA DAPEEMKEEY
RQQTLRTFSA GGVFEQDDGE NWVEIQQVLR GHKARSRPFN AEMGLGQTDS DNPDYPGTIS
YVYSEEAARG LYTQWVRMMT SPDWAALDAT RPAVSESTHT


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