SELU_ECOLI
ID SELU_ECOLI Reviewed; 364 AA.
AC P33667; P77709; Q2MBS5;
DT 01-FEB-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 2.
DT 03-AUG-2022, entry version 145.
DE RecName: Full=tRNA 2-selenouridine synthase {ECO:0000255|HAMAP-Rule:MF_01622, ECO:0000303|PubMed:14594807, ECO:0000303|PubMed:29862510};
DE EC=2.9.1.3 {ECO:0000255|HAMAP-Rule:MF_01622, ECO:0000269|PubMed:24971911, ECO:0000269|PubMed:29862510};
DE AltName: Full=Selenophosphate-dependent tRNA 2-selenouridine synthase {ECO:0000303|PubMed:14594807};
GN Name=selU {ECO:0000255|HAMAP-Rule:MF_01622, ECO:0000303|PubMed:22983156};
GN Synonyms=ybbB; OrderedLocusNames=b0503, JW0491;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RA Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M.,
RA Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D.,
RA Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.;
RT "Sequence of minutes 4-25 of Escherichia coli.";
RL Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 268-364.
RC STRAIN=K12;
RX PubMed=1766878; DOI=10.1093/nar/19.25.7177;
RA Sadosky A.B., Gray J.A., Hill C.W.;
RT "The RhsD-E subfamily of Escherichia coli K-12.";
RL Nucleic Acids Res. 19:7177-7183(1991).
RN [5]
RP FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, DISRUPTION PHENOTYPE, AND
RP MUTAGENESIS OF CYS-96 AND CYS-97.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=14594807; DOI=10.1074/jbc.m310442200;
RA Wolfe M.D., Ahmed F., Lacourciere G.M., Lauhon C.T., Stadtman T.C.,
RA Larson T.J.;
RT "Functional diversity of the rhodanese homology domain: the Escherichia
RT coli ybbB gene encodes a selenophosphate-dependent tRNA 2-selenouridine
RT synthase.";
RL J. Biol. Chem. 279:1801-1809(2004).
RN [6]
RP FUNCTION IN TRNA GERANYLATION, AND DISRUPTION PHENOTYPE.
RX PubMed=22983156; DOI=10.1038/nchembio.1070;
RA Dumelin C.E., Chen Y., Leconte A.M., Chen Y.G., Liu D.R.;
RT "Discovery and biological characterization of geranylated RNA in
RT bacteria.";
RL Nat. Chem. Biol. 8:913-919(2012).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, AND PROPOSED REACTION MECHANISM.
RX PubMed=24971911; DOI=10.1016/j.bioorg.2014.05.012;
RA Bartos P., Maciaszek A., Rosinska A., Sochacka E., Nawrot B.;
RT "Transformation of a wobble 2-thiouridine to 2-selenouridine via S-geranyl-
RT 2-thiouridine as a possible cellular pathway.";
RL Bioorg. Chem. 56:49-53(2014).
RN [8]
RP FUNCTION, CATALYTIC ACTIVITY, REACTION MECHANISM, AND BIOPHYSICOCHEMICAL
RP PROPERTIES.
RX PubMed=29862510; DOI=10.1002/1873-3468.13124;
RA Sierant M., Leszczynska G., Sadowska K., Komar P., Radzikowska-Cieciura E.,
RA Sochacka E., Nawrot B.;
RT "Escherichia coli tRNA 2-selenouridine synthase (SelU) converts S2U-RNA to
RT Se2U-RNA via S-geranylated-intermediate.";
RL FEBS Lett. 592:2248-2258(2018).
CC -!- FUNCTION: Involved in the post-transcriptional modification of the
CC uridine at the wobble position (U34) of tRNA(Lys), tRNA(Glu) and
CC tRNA(Gln) (PubMed:14594807, PubMed:22983156, PubMed:24971911,
CC PubMed:29862510). Catalyzes the conversion of 2-thiouridine (S2U-RNA)
CC to 2-selenouridine (Se2U-RNA) (PubMed:14594807, PubMed:24971911,
CC PubMed:29862510). Acts in a two-step process involving geranylation of
CC 2-thiouridine (S2U) to S-geranyl-2-thiouridine (geS2U) and subsequent
CC selenation of the latter derivative to 2-selenouridine (Se2U) in the
CC tRNA chain (PubMed:24971911, PubMed:29862510).
CC {ECO:0000269|PubMed:14594807, ECO:0000269|PubMed:22983156,
CC ECO:0000269|PubMed:24971911, ECO:0000269|PubMed:29862510}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2E)-geranyl diphosphate + 5-methylaminomethyl-2-
CC thiouridine(34) in tRNA + H(+) + H2O + selenophosphate = (2E)-
CC thiogeraniol + 5-methylaminomethyl-2-selenouridine(34) in tRNA +
CC diphosphate + phosphate; Xref=Rhea:RHEA:42716, Rhea:RHEA-COMP:10195,
CC Rhea:RHEA-COMP:10196, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16144, ChEBI:CHEBI:33019, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:58057, ChEBI:CHEBI:74455, ChEBI:CHEBI:82743,
CC ChEBI:CHEBI:143703; EC=2.9.1.3; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_01622, ECO:0000269|PubMed:24971911,
CC ECO:0000269|PubMed:29862510};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:42717;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01622,
CC ECO:0000269|PubMed:24971911, ECO:0000269|PubMed:29862510};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2E)-geranyl diphosphate + 5-methylaminomethyl-2-
CC thiouridine(34) in tRNA = 5-methylaminomethyl-S-(2E)-geranyl-
CC thiouridine(34) in tRNA + diphosphate; Xref=Rhea:RHEA:14085,
CC Rhea:RHEA-COMP:10195, Rhea:RHEA-COMP:14654, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:58057, ChEBI:CHEBI:74455, ChEBI:CHEBI:140632;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01622,
CC ECO:0000269|PubMed:29862510};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:14086;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01622,
CC ECO:0000269|PubMed:29862510};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5-methylaminomethyl-S-(2E)-geranyl-thiouridine(34) in tRNA +
CC H(+) + selenophosphate = (2E)-thiogeraniol + 5-methylaminomethyl-2-
CC (Se-phospho)selenouridine(34) in tRNA; Xref=Rhea:RHEA:60172,
CC Rhea:RHEA-COMP:14654, Rhea:RHEA-COMP:15523, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16144, ChEBI:CHEBI:140632, ChEBI:CHEBI:143702,
CC ChEBI:CHEBI:143703; Evidence={ECO:0000255|HAMAP-Rule:MF_01622,
CC ECO:0000269|PubMed:29862510};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:60173;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01622,
CC ECO:0000269|PubMed:29862510};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5-methylaminomethyl-2-(Se-phospho)selenouridine(34) in tRNA +
CC H2O = 5-methylaminomethyl-2-selenouridine(34) in tRNA + phosphate;
CC Xref=Rhea:RHEA:60176, Rhea:RHEA-COMP:10196, Rhea:RHEA-COMP:15523,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:43474, ChEBI:CHEBI:82743,
CC ChEBI:CHEBI:143702; Evidence={ECO:0000255|HAMAP-Rule:MF_01622,
CC ECO:0000269|PubMed:29862510};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:60177;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01622,
CC ECO:0000269|PubMed:29862510};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Absorption:
CC Abs(max)=258 nm {ECO:0000269|PubMed:14594807};
CC Kinetic parameters:
CC KM=1.23 uM for S2U-RNA {ECO:0000269|PubMed:29862510};
CC KM=2.49 uM for geS2U-RNA {ECO:0000269|PubMed:29862510};
CC Note=kcat is 0.00014 min(-1) for the geranylation reaction. kcat is
CC 0.53 min(-1) for the selenation reaction.
CC {ECO:0000269|PubMed:29862510};
CC -!- SUBUNIT: Monomer. {ECO:0000255|HAMAP-Rule:MF_01622,
CC ECO:0000269|PubMed:14594807}.
CC -!- DISRUPTION PHENOTYPE: Disruption mutant is incapable of incorporating
CC selenium into tRNA. Disruption does not affect 2 thiouridine generation
CC (PubMed:14594807). Mutant cannot produce geranylated RNA
CC (PubMed:22983156). {ECO:0000269|PubMed:14594807,
CC ECO:0000269|PubMed:22983156}.
CC -!- SIMILARITY: Belongs to the SelU family. {ECO:0000255|HAMAP-
CC Rule:MF_01622, ECO:0000305}.
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DR EMBL; U82664; AAB40256.1; -; Genomic_DNA.
DR EMBL; U00096; AAC73605.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76281.1; -; Genomic_DNA.
DR EMBL; X60999; CAA43313.1; -; Genomic_DNA.
DR PIR; F64781; F64781.
DR RefSeq; NP_415036.1; NC_000913.3.
DR RefSeq; WP_001157938.1; NZ_SSZK01000024.1.
DR AlphaFoldDB; P33667; -.
DR SMR; P33667; -.
DR BioGRID; 4259870; 6.
DR IntAct; P33667; 2.
DR STRING; 511145.b0503; -.
DR jPOST; P33667; -.
DR PaxDb; P33667; -.
DR PRIDE; P33667; -.
DR EnsemblBacteria; AAC73605; AAC73605; b0503.
DR EnsemblBacteria; BAE76281; BAE76281; BAE76281.
DR GeneID; 947063; -.
DR KEGG; ecj:JW0491; -.
DR KEGG; eco:b0503; -.
DR PATRIC; fig|511145.12.peg.524; -.
DR EchoBASE; EB1718; -.
DR eggNOG; COG2603; Bacteria.
DR HOGENOM; CLU_043456_1_0_6; -.
DR InParanoid; P33667; -.
DR OMA; RPLVYCW; -.
DR PhylomeDB; P33667; -.
DR BioCyc; EcoCyc:EG11768-MON; -.
DR BioCyc; MetaCyc:EG11768-MON; -.
DR BRENDA; 2.9.1.3; 2026.
DR PRO; PR:P33667; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0016765; F:transferase activity, transferring alkyl or aryl (other than methyl) groups; IEA:UniProtKB-UniRule.
DR GO; GO:0043828; F:tRNA 2-selenouridine synthase activity; IDA:EcoCyc.
DR GO; GO:0070329; P:tRNA seleno-modification; IMP:EcoCyc.
DR GO; GO:0002098; P:tRNA wobble uridine modification; IMP:EcoCyc.
DR Gene3D; 3.40.250.10; -; 1.
DR HAMAP; MF_01622; tRNA_sel_U_synth; 1.
DR InterPro; IPR001763; Rhodanese-like_dom.
DR InterPro; IPR036873; Rhodanese-like_dom_sf.
DR InterPro; IPR017582; SelU.
DR SMART; SM00450; RHOD; 1.
DR SUPFAM; SSF52821; SSF52821; 1.
DR TIGRFAMs; TIGR03167; tRNA_sel_U_synt; 1.
DR PROSITE; PS50206; RHODANESE_3; 1.
PE 1: Evidence at protein level;
KW Reference proteome; Selenium; Transferase.
FT CHAIN 1..364
FT /note="tRNA 2-selenouridine synthase"
FT /id="PRO_0000210859"
FT DOMAIN 14..137
FT /note="Rhodanese"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01622,
FT ECO:0000255|PROSITE-ProRule:PRU00173"
FT ACT_SITE 97
FT /note="S-selanylcysteine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01622,
FT ECO:0000255|PROSITE-ProRule:PRU00173"
FT MUTAGEN 96
FT /note="C->S: No change in selenation activity."
FT /evidence="ECO:0000269|PubMed:14594807"
FT MUTAGEN 97
FT /note="C->S: In vivo, abolishes 2-selenouridine synthase
FT activity. In vitro, reduces activity by only 50%."
FT /evidence="ECO:0000269|PubMed:14594807"
SQ SEQUENCE 364 AA; 41111 MW; 8C0F244BA86B6C4A CRC64;
MQERHTEQDY RALLIADTPI IDVRAPIEFE HGAMPAAINL PLMNNDERAA VGTCYKQQGS
DAALALGHKL VAGEIRQQRM DAWRAACLQN PQGILCCARG GQRSHIVQSW LHAAGIDYPL
VEGGYKALRQ TAIQATIELA QKPIVLIGGC TGSGKTLLVQ QQPNGVDLEG LARHRGSAFG
RTLQPQLSQA SFENLLAAEM LKTDARQNLR LWVLEDESRM IGSNHLPECL RERMTQAAIA
VVEDPFEIRL ERLNEEYFLR MHHDFTHAYG DEQGWQEYCE YLHHGLSAIK RRLGLQRYNE
LAARLDAALT TQLTTGSTDG HLAWLVPLLE EYYDPMYRYQ LEKKAEKVVF RGEWAEVAEW
VKAR
