BPHA1_RHOJR
ID BPHA1_RHOJR Reviewed; 460 AA.
AC Q53122;
DT 29-OCT-2014, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 145.
DE RecName: Full=Biphenyl 2,3-dioxygenase subunit alpha {ECO:0000305};
DE EC=1.14.12.18 {ECO:0000269|PubMed:17420585};
DE AltName: Full=Biphenyl dioxygenase system, oxygenase component subunit alpha {ECO:0000305};
DE Short=BDO, oxygenase component subunit alpha {ECO:0000305};
DE AltName: Full=Rieske dioxygenase {ECO:0000303|PubMed:15342255};
DE AltName: Full=Terminal oxygenase component of biphenyl dioxygenase, large subunit {ECO:0000303|PubMed:15342255};
GN Name=bphA1 {ECO:0000303|PubMed:7793929};
GN Synonyms=bphAa {ECO:0000312|EMBL:ABG99107.1};
GN OrderedLocusNames=RHA1_ro08060 {ECO:0000312|EMBL:ABG99107.1};
OS Rhodococcus jostii (strain RHA1).
OG Plasmid pRHL1 {ECO:0000312|EMBL:ABG99107.1}.
OC Bacteria; Actinobacteria; Corynebacteriales; Nocardiaceae; Rhodococcus.
OX NCBI_TaxID=101510;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, DISRUPTION PHENOTYPE, AND
RP PATHWAY.
RC STRAIN=RHA1;
RX PubMed=7793929; DOI=10.1128/aem.61.6.2079-2085.1995;
RA Masai E., Yamada A., Healy J.M., Hatta T., Kimbara K., Fukuda M., Yano K.;
RT "Characterization of biphenyl catabolic genes of gram-positive
RT polychlorinated biphenyl degrader Rhodococcus sp. strain RHA1.";
RL Appl. Environ. Microbiol. 61:2079-2085(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=RHA1;
RX PubMed=17030794; DOI=10.1073/pnas.0607048103;
RA McLeod M.P., Warren R.L., Hsiao W.W.L., Araki N., Myhre M., Fernandes C.,
RA Miyazawa D., Wong W., Lillquist A.L., Wang D., Dosanjh M., Hara H.,
RA Petrescu A., Morin R.D., Yang G., Stott J.M., Schein J.E., Shin H.,
RA Smailus D., Siddiqui A.S., Marra M.A., Jones S.J.M., Holt R.,
RA Brinkman F.S.L., Miyauchi K., Fukuda M., Davies J.E., Mohn W.W.,
RA Eltis L.D.;
RT "The complete genome of Rhodococcus sp. RHA1 provides insights into a
RT catabolic powerhouse.";
RL Proc. Natl. Acad. Sci. U.S.A. 103:15582-15587(2006).
RN [3]
RP INDUCTION.
RC STRAIN=RHA1;
RX PubMed=15028699; DOI=10.1128/jb.186.7.2134-2146.2004;
RA Takeda H., Yamada A., Miyauchi K., Masai E., Fukuda M.;
RT "Characterization of transcriptional regulatory genes for biphenyl
RT degradation in Rhodococcus sp. strain RHA1.";
RL J. Bacteriol. 186:2134-2146(2004).
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, AND SUBSTRATE SPECIFICITY.
RC STRAIN=RHA1;
RX PubMed=17420585; DOI=10.1271/bbb.60663;
RA Iwasaki T., Takeda H., Miyauchi K., Yamada T., Masai E., Fukuda M.;
RT "Characterization of two biphenyl dioxygenases for biphenyl/PCB degradation
RT in A PCB degrader, Rhodococcus sp. strain RHA1.";
RL Biosci. Biotechnol. Biochem. 71:993-1002(2007).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) IN COMPLEXES WITH BETA SUBUNIT;
RP BIPHENYL; IRON AND IRON-SULFUR (2FE-2S), AND COFACTOR.
RC STRAIN=RHA1;
RX PubMed=15342255; DOI=10.1016/j.jmb.2004.07.062;
RA Furusawa Y., Nagarajan V., Tanokura M., Masai E., Fukuda M., Senda T.;
RT "Crystal structure of the terminal oxygenase component of biphenyl
RT dioxygenase derived from Rhodococcus sp. strain RHA1.";
RL J. Mol. Biol. 342:1041-1052(2004).
CC -!- FUNCTION: Part of the oxygenase component of the biphenyl dioxygenase
CC system that catalyzes the stereospecific dihydroxylation of the
CC aromatic ring of biphenyl, yielding a dihydrodiol compound. Is
CC essential for biphenyl degradation and growth of Rhodococcus sp. strain
CC RHA1 on biphenyl as the sole source of carbon and energy. Can also use
CC naphtalene and 4-chlorobiphenyl (4-CB) as substrates, as well as some
CC polychlorinated biphenyls (PCB) such as 2,2'-dichlorobiphenyl, 2,3-
CC dichlorobiphenyl and 2,5,2'-trichlorobiphenyl. Exhibits weak activity
CC toward dibenzofuran and dibenzo-p-dioxin. Electrons are transferred
CC from NADH to the [2Fe-2S] cluster in BphA1 via FAD of BphA4 and [2Fe-
CC 2S] cluster of BphA3. {ECO:0000269|PubMed:17420585,
CC ECO:0000269|PubMed:7793929}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=biphenyl + H(+) + NADH + O2 = (2R,3S)-3-phenylcyclohexa-3,5-
CC diene-1,2-diol + NAD(+); Xref=Rhea:RHEA:18165, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:15379, ChEBI:CHEBI:17097, ChEBI:CHEBI:32922,
CC ChEBI:CHEBI:57540, ChEBI:CHEBI:57945; EC=1.14.12.18;
CC Evidence={ECO:0000269|PubMed:17420585};
CC -!- COFACTOR:
CC Name=[2Fe-2S] cluster; Xref=ChEBI:CHEBI:190135;
CC Evidence={ECO:0000269|PubMed:15342255};
CC Note=Binds 1 [2Fe-2S] cluster per subunit.
CC {ECO:0000269|PubMed:15342255};
CC -!- COFACTOR:
CC Name=Fe cation; Xref=ChEBI:CHEBI:24875;
CC Evidence={ECO:0000269|PubMed:15342255};
CC Note=Binds 1 Fe cation per subunit. {ECO:0000269|PubMed:15342255};
CC -!- PATHWAY: Xenobiotic degradation; biphenyl degradation; 2-hydroxy-2,4-
CC pentadienoate and benzoate from biphenyl: step 1/4.
CC {ECO:0000269|PubMed:7793929}.
CC -!- SUBUNIT: Heterohexamer consisting of three BphA1 subunits and three
CC BphA2 subunits. The multicomponent biphenyl dioxygenase system is
CC composed of a ferredoxin reductase (BphA4), a ferredoxin (BphA3), and a
CC terminal oxygenase (BphA1A2). {ECO:0000269|PubMed:15342255,
CC ECO:0000303|PubMed:17420585}.
CC -!- INTERACTION:
CC Q53122; Q53123: bphA2; NbExp=2; IntAct=EBI-1040100, EBI-1040088;
CC -!- INDUCTION: Transcription is up-regulated by aromatic compounds
CC including biphenyl, ethylbenzene, benzene, toluene, xylene, cumene,
CC cymene, and chlorinated benzenes. Is under the control of the BphST
CC two-component regulatory system. {ECO:0000269|PubMed:15028699}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene lose their ability to
CC grow on biphenyl. {ECO:0000269|PubMed:7793929}.
CC -!- SIMILARITY: Belongs to the bacterial ring-hydroxylating dioxygenase
CC alpha subunit family. {ECO:0000305}.
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DR EMBL; CP000432; ABG99107.1; -; Genomic_DNA.
DR EMBL; D32142; BAA06868.1; -; Genomic_DNA.
DR RefSeq; WP_011599002.1; NC_008269.1.
DR PDB; 1ULI; X-ray; 2.20 A; A/C/E=1-460.
DR PDB; 1ULJ; X-ray; 2.60 A; A/C/E=1-460.
DR PDBsum; 1ULI; -.
DR PDBsum; 1ULJ; -.
DR AlphaFoldDB; Q53122; -.
DR SMR; Q53122; -.
DR IntAct; Q53122; 1.
DR EnsemblBacteria; ABG99107; ABG99107; RHA1_ro08060.
DR KEGG; rha:RHA1_ro08060; -.
DR PATRIC; fig|101510.16.peg.7407; -.
DR HOGENOM; CLU_026244_4_0_11; -.
DR OMA; SEFMEGR; -.
DR UniPathway; UPA00155; UER00250.
DR EvolutionaryTrace; Q53122; -.
DR Proteomes; UP000008710; Plasmid pRHL1.
DR GO; GO:0051537; F:2 iron, 2 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0018687; F:biphenyl 2,3-dioxygenase activity; IEA:UniProtKB-EC.
DR GO; GO:0005506; F:iron ion binding; IEA:InterPro.
DR GO; GO:0004497; F:monooxygenase activity; IEA:UniProt.
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;
KW Reference proteome.
FT CHAIN 1..460
FT /note="Biphenyl 2,3-dioxygenase subunit alpha"
FT /id="PRO_0000430659"
FT DOMAIN 56..165
FT /note="Rieske"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00628"
FT BINDING 98
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000269|PubMed:15342255,
FT ECO:0000312|PDB:1ULI, ECO:0000312|PDB:1ULJ"
FT BINDING 100
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000269|PubMed:15342255,
FT ECO:0000312|PDB:1ULI, ECO:0000312|PDB:1ULJ"
FT BINDING 118
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000269|PubMed:15342255,
FT ECO:0000312|PDB:1ULI, ECO:0000312|PDB:1ULJ"
FT BINDING 121
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000269|PubMed:15342255,
FT ECO:0000312|PDB:1ULI, ECO:0000312|PDB:1ULJ"
FT BINDING 217..230
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:15342255"
FT BINDING 224
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000269|PubMed:15342255,
FT ECO:0000312|PDB:1ULI, ECO:0000312|PDB:1ULJ"
FT BINDING 230
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000269|PubMed:15342255,
FT ECO:0000312|PDB:1ULI, ECO:0000312|PDB:1ULJ"
FT BINDING 378
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000269|PubMed:15342255,
FT ECO:0000312|PDB:1ULI, ECO:0000312|PDB:1ULJ"
FT HELIX 19..23
FT /evidence="ECO:0007829|PDB:1ULI"
FT TURN 28..31
FT /evidence="ECO:0007829|PDB:1ULI"
FT HELIX 35..38
FT /evidence="ECO:0007829|PDB:1ULI"
FT HELIX 41..50
FT /evidence="ECO:0007829|PDB:1ULI"
FT TURN 51..54
FT /evidence="ECO:0007829|PDB:1ULI"
FT STRAND 57..61
FT /evidence="ECO:0007829|PDB:1ULI"
FT HELIX 62..64
FT /evidence="ECO:0007829|PDB:1ULI"
FT STRAND 70..76
FT /evidence="ECO:0007829|PDB:1ULI"
FT STRAND 79..85
FT /evidence="ECO:0007829|PDB:1ULI"
FT STRAND 91..96
FT /evidence="ECO:0007829|PDB:1ULI"
FT TURN 99..101
FT /evidence="ECO:0007829|PDB:1ULI"
FT STRAND 108..112
FT /evidence="ECO:0007829|PDB:1ULI"
FT TURN 119..121
FT /evidence="ECO:0007829|PDB:1ULI"
FT STRAND 131..133
FT /evidence="ECO:0007829|PDB:1ULI"
FT HELIX 137..140
FT /evidence="ECO:0007829|PDB:1ULI"
FT HELIX 146..148
FT /evidence="ECO:0007829|PDB:1ULI"
FT STRAND 153..159
FT /evidence="ECO:0007829|PDB:1ULI"
FT STRAND 162..166
FT /evidence="ECO:0007829|PDB:1ULI"
FT HELIX 174..178
FT /evidence="ECO:0007829|PDB:1ULI"
FT HELIX 181..189
FT /evidence="ECO:0007829|PDB:1ULI"
FT STRAND 196..198
FT /evidence="ECO:0007829|PDB:1ULI"
FT STRAND 203..207
FT /evidence="ECO:0007829|PDB:1ULI"
FT HELIX 211..220
FT /evidence="ECO:0007829|PDB:1ULI"
FT HELIX 222..226
FT /evidence="ECO:0007829|PDB:1ULI"
FT TURN 227..230
FT /evidence="ECO:0007829|PDB:1ULI"
FT HELIX 231..236
FT /evidence="ECO:0007829|PDB:1ULI"
FT STRAND 253..257
FT /evidence="ECO:0007829|PDB:1ULI"
FT STRAND 259..262
FT /evidence="ECO:0007829|PDB:1ULI"
FT STRAND 264..270
FT /evidence="ECO:0007829|PDB:1ULI"
FT HELIX 273..288
FT /evidence="ECO:0007829|PDB:1ULI"
FT HELIX 291..299
FT /evidence="ECO:0007829|PDB:1ULI"
FT HELIX 303..307
FT /evidence="ECO:0007829|PDB:1ULI"
FT STRAND 308..316
FT /evidence="ECO:0007829|PDB:1ULI"
FT TURN 317..319
FT /evidence="ECO:0007829|PDB:1ULI"
FT STRAND 320..322
FT /evidence="ECO:0007829|PDB:1ULI"
FT TURN 324..326
FT /evidence="ECO:0007829|PDB:1ULI"
FT STRAND 328..334
FT /evidence="ECO:0007829|PDB:1ULI"
FT STRAND 340..349
FT /evidence="ECO:0007829|PDB:1ULI"
FT HELIX 354..367
FT /evidence="ECO:0007829|PDB:1ULI"
FT HELIX 375..388
FT /evidence="ECO:0007829|PDB:1ULI"
FT HELIX 393..395
FT /evidence="ECO:0007829|PDB:1ULI"
FT TURN 403..406
FT /evidence="ECO:0007829|PDB:1ULI"
FT STRAND 408..410
FT /evidence="ECO:0007829|PDB:1ULJ"
FT STRAND 413..415
FT /evidence="ECO:0007829|PDB:1ULI"
FT STRAND 417..423
FT /evidence="ECO:0007829|PDB:1ULI"
FT HELIX 426..439
FT /evidence="ECO:0007829|PDB:1ULI"
FT HELIX 444..448
FT /evidence="ECO:0007829|PDB:1ULI"
SQ 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
