URDA_SHEON
ID URDA_SHEON Reviewed; 582 AA.
AC Q8CVD0;
DT 03-APR-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2003, sequence version 1.
DT 03-AUG-2022, entry version 114.
DE RecName: Full=Urocanate reductase;
DE EC=1.3.99.33;
DE Flags: Precursor;
GN Name=urdA; OrderedLocusNames=SO_4620;
OS Shewanella oneidensis (strain MR-1).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales;
OC Shewanellaceae; Shewanella.
OX NCBI_TaxID=211586;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MR-1;
RX PubMed=12368813; DOI=10.1038/nbt749;
RA Heidelberg J.F., Paulsen I.T., Nelson K.E., Gaidos E.J., Nelson W.C.,
RA Read T.D., Eisen J.A., Seshadri R., Ward N.L., Methe B.A., Clayton R.A.,
RA Meyer T., Tsapin A., Scott J., Beanan M.J., Brinkac L.M., Daugherty S.C.,
RA DeBoy R.T., Dodson R.J., Durkin A.S., Haft D.H., Kolonay J.F., Madupu R.,
RA Peterson J.D., Umayam L.A., White O., Wolf A.M., Vamathevan J.J.,
RA Weidman J.F., Impraim M., Lee K., Berry K.J., Lee C., Mueller J.,
RA Khouri H.M., Gill J., Utterback T.R., McDonald L.A., Feldblyum T.V.,
RA Smith H.O., Venter J.C., Nealson K.H., Fraser C.M.;
RT "Genome sequence of the dissimilatory metal ion-reducing bacterium
RT Shewanella oneidensis.";
RL Nat. Biotechnol. 20:1118-1123(2002).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, KINETIC PARAMETERS, SUBSTRATE
RP SPECIFICITY, GENE NAME, INDUCTION, SUBCELLULAR LOCATION, AND DISRUPTION
RP PHENOTYPE.
RC STRAIN=MR-1;
RX PubMed=23078170; DOI=10.1111/mmi.12067;
RA Bogachev A.V., Bertsova Y.V., Bloch D.A., Verkhovsky M.I.;
RT "Urocanate reductase: identification of a novel anaerobic respiratory
RT pathway in Shewanella oneidensis MR-1.";
RL Mol. Microbiol. 86:1452-1463(2012).
CC -!- FUNCTION: Catalyzes the two-electron reduction of urocanate to
CC dihydrourocanate (also named imidazole propionate or deamino-
CC histidine). The physiological electron donor is unknown; it might be
CC the membrane-bound tetraheme cytochrome c (CymA). Enables anaerobic
CC growth with urocanate as a sole terminal electron acceptor, and thus
CC can provide the cells with a niche where no other bacteria can compete
CC and survive. Is unable to reduce cinnamate and other unsaturated
CC organic acids such as acrylic, crotonic, fumaric and orotic acids. Has
CC no fumarate reductase or succinate dehydrogenase activity.
CC {ECO:0000269|PubMed:23078170}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=A + dihydrourocanate = AH2 + urocanate; Xref=Rhea:RHEA:36059,
CC ChEBI:CHEBI:13193, ChEBI:CHEBI:17499, ChEBI:CHEBI:27247,
CC ChEBI:CHEBI:72991; EC=1.3.99.33;
CC Evidence={ECO:0000269|PubMed:23078170};
CC -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692;
CC Evidence={ECO:0000269|PubMed:23078170};
CC Note=Binds 1 FAD per subunit. {ECO:0000269|PubMed:23078170};
CC -!- COFACTOR:
CC Name=FMN; Xref=ChEBI:CHEBI:58210;
CC Evidence={ECO:0000269|PubMed:23078170};
CC Note=Binds 1 FMN covalently per subunit. {ECO:0000269|PubMed:23078170};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC Note=KM for urocanate is inferior to 10 uM and kcat is 360 sec(-1)
CC (at pH 7.0). {ECO:0000269|PubMed:23078170};
CC -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000305|PubMed:23078170};
CC Lipid-anchor {ECO:0000305|PubMed:23078170}; Periplasmic side
CC {ECO:0000305|PubMed:23078170}. Note=Is associated, but not too tight,
CC with the membrane.
CC -!- INDUCTION: By urocanate under anaerobic conditions.
CC {ECO:0000269|PubMed:23078170}.
CC -!- DISRUPTION PHENOTYPE: In the urdA-deficient strain, the urocanate
CC reductase activity measured in the crude extract from cells
CC anaerobically grown on a mixture of urocanate and fumarate (or
CC urocanate and nitrate) is about 20-fold lower than in the wild-type.
CC This strain is not affected in its ability to grow in the presence of
CC fumarate, but fails to grow anaerobically on urocanate.
CC {ECO:0000269|PubMed:23078170}.
CC -!- SIMILARITY: Belongs to the FAD-dependent oxidoreductase 2 family.
CC FRD/SDH subfamily. {ECO:0000305}.
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DR EMBL; AE014299; AAN57580.1; -; Genomic_DNA.
DR RefSeq; NP_720136.1; NC_004347.2.
DR RefSeq; WP_011074216.1; NZ_CP053946.1.
DR PDB; 6T85; X-ray; 1.10 A; A=130-582.
DR PDB; 6T86; X-ray; 2.56 A; A=130-582.
DR PDB; 6T87; X-ray; 1.56 A; A=130-582.
DR PDB; 6T88; X-ray; 1.40 A; A=130-582.
DR PDBsum; 6T85; -.
DR PDBsum; 6T86; -.
DR PDBsum; 6T87; -.
DR PDBsum; 6T88; -.
DR AlphaFoldDB; Q8CVD0; -.
DR SMR; Q8CVD0; -.
DR STRING; 211586.SO_4620; -.
DR PaxDb; Q8CVD0; -.
DR KEGG; son:SO_4620; -.
DR PATRIC; fig|211586.12.peg.4477; -.
DR eggNOG; COG1053; Bacteria.
DR eggNOG; COG3976; Bacteria.
DR HOGENOM; CLU_011398_4_0_6; -.
DR OMA; MAWAHGA; -.
DR OrthoDB; 153138at2; -.
DR PhylomeDB; Q8CVD0; -.
DR BioCyc; MetaCyc:MON-17916; -.
DR BioCyc; SONE211586:G1GMP-4269-MON; -.
DR BRENDA; 1.3.99.33; 5706.
DR Proteomes; UP000008186; Chromosome.
DR GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0010181; F:FMN binding; IEA:InterPro.
DR GO; GO:0016491; F:oxidoreductase activity; IEA:UniProtKB-KW.
DR GO; GO:0008152; P:metabolic process; IEA:UniProt.
DR Gene3D; 3.50.50.60; -; 1.
DR Gene3D; 3.90.700.10; -; 1.
DR InterPro; IPR003953; FAD-binding_2.
DR InterPro; IPR036188; FAD/NAD-bd_sf.
DR InterPro; IPR010960; Flavocytochrome_c.
DR InterPro; IPR007329; FMN-bd.
DR InterPro; IPR027477; Succ_DH/fumarate_Rdtase_cat_sf.
DR Pfam; PF00890; FAD_binding_2; 1.
DR Pfam; PF04205; FMN_bind; 1.
DR SMART; SM00900; FMN_bind; 1.
DR SUPFAM; SSF51905; SSF51905; 1.
DR SUPFAM; SSF56425; SSF56425; 1.
DR TIGRFAMs; TIGR01813; flavo_cyto_c; 1.
DR PROSITE; PS51257; PROKAR_LIPOPROTEIN; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cell membrane; FAD; Flavoprotein; FMN; Lipoprotein; Membrane;
KW Oxidoreductase; Palmitate; Phosphoprotein; Reference proteome; Signal.
FT SIGNAL 1..20
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00303"
FT CHAIN 21..582
FT /note="Urocanate reductase"
FT /id="PRO_0000421946"
FT ACT_SITE 411
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:P0C278"
FT BINDING 143
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P83223"
FT BINDING 162..163
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P83223"
FT BINDING 170..177
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P83223"
FT BINDING 550
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P83223"
FT BINDING 565..566
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:P83223"
FT LIPID 21
FT /note="N-palmitoyl cysteine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00303"
FT LIPID 21
FT /note="S-diacylglycerol cysteine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00303"
FT STRAND 130..138
FT /evidence="ECO:0007829|PDB:6T85"
FT HELIX 142..153
FT /evidence="ECO:0007829|PDB:6T85"
FT STRAND 158..161
FT /evidence="ECO:0007829|PDB:6T85"
FT STRAND 163..167
FT /evidence="ECO:0007829|PDB:6T85"
FT HELIX 169..173
FT /evidence="ECO:0007829|PDB:6T85"
FT HELIX 184..189
FT /evidence="ECO:0007829|PDB:6T85"
FT HELIX 195..205
FT /evidence="ECO:0007829|PDB:6T85"
FT TURN 206..208
FT /evidence="ECO:0007829|PDB:6T85"
FT HELIX 212..231
FT /evidence="ECO:0007829|PDB:6T85"
FT STRAND 237..243
FT /evidence="ECO:0007829|PDB:6T88"
FT STRAND 253..256
FT /evidence="ECO:0007829|PDB:6T88"
FT HELIX 257..259
FT /evidence="ECO:0007829|PDB:6T85"
FT HELIX 262..275
FT /evidence="ECO:0007829|PDB:6T85"
FT STRAND 284..290
FT /evidence="ECO:0007829|PDB:6T85"
FT STRAND 296..303
FT /evidence="ECO:0007829|PDB:6T85"
FT STRAND 306..318
FT /evidence="ECO:0007829|PDB:6T85"
FT HELIX 327..333
FT /evidence="ECO:0007829|PDB:6T85"
FT STRAND 343..345
FT /evidence="ECO:0007829|PDB:6T88"
FT HELIX 352..359
FT /evidence="ECO:0007829|PDB:6T85"
FT STRAND 370..376
FT /evidence="ECO:0007829|PDB:6T85"
FT TURN 378..380
FT /evidence="ECO:0007829|PDB:6T85"
FT HELIX 385..392
FT /evidence="ECO:0007829|PDB:6T85"
FT STRAND 395..397
FT /evidence="ECO:0007829|PDB:6T85"
FT HELIX 411..419
FT /evidence="ECO:0007829|PDB:6T85"
FT HELIX 422..424
FT /evidence="ECO:0007829|PDB:6T85"
FT STRAND 426..431
FT /evidence="ECO:0007829|PDB:6T85"
FT HELIX 432..438
FT /evidence="ECO:0007829|PDB:6T85"
FT HELIX 440..443
FT /evidence="ECO:0007829|PDB:6T85"
FT HELIX 445..453
FT /evidence="ECO:0007829|PDB:6T85"
FT STRAND 456..462
FT /evidence="ECO:0007829|PDB:6T85"
FT HELIX 463..469
FT /evidence="ECO:0007829|PDB:6T85"
FT HELIX 474..490
FT /evidence="ECO:0007829|PDB:6T85"
FT TURN 494..496
FT /evidence="ECO:0007829|PDB:6T85"
FT STRAND 510..522
FT /evidence="ECO:0007829|PDB:6T85"
FT STRAND 533..536
FT /evidence="ECO:0007829|PDB:6T85"
FT STRAND 541..547
FT /evidence="ECO:0007829|PDB:6T85"
FT STRAND 554..556
FT /evidence="ECO:0007829|PDB:6T85"
FT HELIX 564..582
FT /evidence="ECO:0007829|PDB:6T85"
SQ SEQUENCE 582 AA; 62235 MW; FDFB3DEB620EF361 CRC64;
MHYKKSIIGI AVTATAIIAG CQVTHQIVKS QGTAQGKHGE VQVETTFKDG HIVAIDVLKQ
KENKVLAGAV FKDVKQAIID NNSIEVDGIA GATVTSKALK EAVGKSIEAA GVTLVATASA
KKSEALTPAE YTYDVVIIGS GGAGFSAGLE AIAAGRSAVI IEKMPIIGGN SLISGAEMNV
AGSWVQKNMG ITDSKELFIS DTLKGGDFKG DPEMVKTMVD NAVGAAEWLR DYVKVEFYPD
QLFQFGGHSV KRALIPKGHT GAEVISKFSI KADEVGLPIH TNTKAEKLIQ DQTGRIVGVE
AAHNGKTITY HAKRGVVIAT GGFSSNMEMR KKYNPELDER YGSTGHAGGT GDGIVMAEKI
HAAAKNMGYI QSYPICSPTS GAIALIADSR FFGAVLINQK GERFVEELER RDVISHAILA
QPGRYTYVLW NQDIENVAHT VEMHQGELKE FTKDGLMYKV DTLEEAAKVF NIPEDKLLST
IKDVNHYAAT GKDEAFNHRS GLVDLSKGPY WILKATPSVH HTMGGLVVDT RTRVLDEQGK
VIPGLFAAGE VTGLTHGTNR LGGNAYTDII VYGRIAGQEA AK
