SELU_SALTY
ID SELU_SALTY Reviewed; 364 AA.
AC Q8ZR88;
DT 06-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2002, sequence version 1.
DT 03-AUG-2022, entry version 103.
DE RecName: Full=tRNA 2-selenouridine synthase {ECO:0000255|HAMAP-Rule:MF_01622, ECO:0000303|PubMed:7520175};
DE EC=2.9.1.3 {ECO:0000255|HAMAP-Rule:MF_01622, ECO:0000305|PubMed:27073879};
DE AltName: Full=Selenophosphate-dependent tRNA 2-selenouridine synthase;
GN Name=selU {ECO:0000255|HAMAP-Rule:MF_01622};
GN Synonyms=mnmH {ECO:0000303|PubMed:27073879}; OrderedLocusNames=STM0513;
OS Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Salmonella.
OX NCBI_TaxID=99287;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX PubMed=11677609; DOI=10.1038/35101614;
RA McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P.,
RA Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D.,
RA Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E.,
RA Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R.,
RA Wilson R.K.;
RT "Complete genome sequence of Salmonella enterica serovar Typhimurium LT2.";
RL Nature 413:852-856(2001).
RN [2]
RP FUNCTION, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=7520175; DOI=10.1073/pnas.91.17.8092;
RA Veres Z., Stadtman T.C.;
RT "A purified selenophosphate-dependent enzyme from Salmonella typhimurium
RT catalyzes the replacement of sulfur in 2-thiouridine residues in tRNAs with
RT selenium.";
RL Proc. Natl. Acad. Sci. U.S.A. 91:8092-8096(1994).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, PROPOSED REACTION MECHANISM, DOMAIN, AND
RP MUTAGENESIS OF ALA-63; LEU-66; GLY-67; ARG-79; ALA-82; CYS-97; ARG-129 AND
RP LYS-155.
RC STRAIN=LT2;
RX PubMed=27073879; DOI=10.1371/journal.pone.0153488;
RA Jaeger G., Chen P., Bjoerk G.R.;
RT "Transfer RNA bound to MnmH protein is enriched with geranylated tRNA--a
RT possible intermediate in its selenation?";
RL PLoS ONE 11:E0153488-E0153488(2016).
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:27073879, PubMed:7520175). Catalyzes the conversion
CC of 2-thiouridine (S2U-RNA) to 2-selenouridine (Se2U-RNA)
CC (PubMed:7520175, PubMed:27073879). Acts in a two-step process involving
CC geranylation of 2-thiouridine (S2U) to S-geranyl-2-thiouridine (geS2U)
CC and subsequent selenation of the latter derivative to 2-selenouridine
CC (Se2U) in the tRNA chain (Probable). {ECO:0000269|PubMed:27073879,
CC ECO:0000269|PubMed:7520175, ECO:0000305|PubMed:27073879}.
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:0000305|PubMed:27073879};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:42717;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01622};
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 PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:14086;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01622};
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 PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:60173;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01622};
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 PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:60177;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01622};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=17.1 uM for selenophosphate {ECO:0000269|PubMed:7520175};
CC -!- SUBUNIT: Monomer. {ECO:0000255|HAMAP-Rule:MF_01622}.
CC -!- DOMAIN: Composed of a rhodanese domain and a P-loop domain, which
CC probably binds geranyl diphosphate. The two activities are
CC mechanistically different, but the rhodanese domain is important for
CC both. {ECO:0000269|PubMed:27073879}.
CC -!- MISCELLANEOUS: It was also suggested that 2-thiourine geranylation and
CC 2-thiouridine selenation in the tRNA chain may occur independently, in
CC two distinc metabolic processes. {ECO:0000305|PubMed:27073879}.
CC -!- SIMILARITY: Belongs to the SelU family. {ECO:0000255|HAMAP-
CC Rule:MF_01622, ECO:0000305}.
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DR EMBL; AE006468; AAL19467.1; -; Genomic_DNA.
DR RefSeq; NP_459508.1; NC_003197.2.
DR RefSeq; WP_001154078.1; NC_003197.2.
DR AlphaFoldDB; Q8ZR88; -.
DR SMR; Q8ZR88; -.
DR STRING; 99287.STM0513; -.
DR PaxDb; Q8ZR88; -.
DR EnsemblBacteria; AAL19467; AAL19467; STM0513.
DR GeneID; 1252033; -.
DR KEGG; stm:STM0513; -.
DR PATRIC; fig|99287.12.peg.547; -.
DR HOGENOM; CLU_043456_1_0_6; -.
DR OMA; RPLVYCW; -.
DR PhylomeDB; Q8ZR88; -.
DR BioCyc; SENT99287:STM0513-MON; -.
DR BRENDA; 2.9.1.3; 5542.
DR Proteomes; UP000001014; 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; IBA:GO_Central.
DR GO; GO:0002098; P:tRNA wobble uridine modification; IBA:GO_Central.
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_0000210875"
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 BINDING 149
FT /ligand="(2E)-geranyl diphosphate"
FT /ligand_id="ChEBI:CHEBI:58057"
FT /evidence="ECO:0000305|PubMed:27073879"
FT MUTAGEN 63
FT /note="A->P: Increases geranylation activity."
FT /evidence="ECO:0000269|PubMed:27073879"
FT MUTAGEN 66
FT /note="L->P: Increases geranylation activity."
FT /evidence="ECO:0000269|PubMed:27073879"
FT MUTAGEN 67
FT /note="G->C,H,I,L,M,N,R,T,V: Increases geranylation
FT activity."
FT /evidence="ECO:0000269|PubMed:27073879"
FT MUTAGEN 67
FT /note="G->E: Increases geranylation activity. Lack of
FT geranylation activity; when associated with A-155."
FT /evidence="ECO:0000269|PubMed:27073879"
FT MUTAGEN 79
FT /note="R->W: Increases geranylation activity."
FT /evidence="ECO:0000269|PubMed:27073879"
FT MUTAGEN 82
FT /note="A->T: Increases geranylation activity."
FT /evidence="ECO:0000269|PubMed:27073879"
FT MUTAGEN 97
FT /note="C->A: Reduces the level of geranylation but does not
FT abolish it."
FT /evidence="ECO:0000269|PubMed:27073879"
FT MUTAGEN 97
FT /note="C->S: Reduces the level of geranylation but does not
FT abolish it."
FT /evidence="ECO:0000269|PubMed:27073879"
FT MUTAGEN 129
FT /note="R->C: Increases geranylation activity."
FT /evidence="ECO:0000269|PubMed:27073879"
FT MUTAGEN 155
FT /note="K->A: Lack of geranylation activity."
FT /evidence="ECO:0000269|PubMed:27073879"
SQ SEQUENCE 364 AA; 41328 MW; 2A21D240295B0C73 CRC64;
MQDRQKAQDY RALLLADTPL IDVRAPIEFE QGAMPGAINL PLMMDDERAA VGTCYKRQGA
DAALALGHRL VCGDIRQQRL EAWKAAYQRF PNGYLCCARG GQRSHIVQRW LQETGIDCPL
IEGGYKALRQ TAIQATWQLA QKPILLIGGC TGSGKTQLVR QQPNGVDLEG LARHRGSSFG
RTLNPQLSQA SFENKLAVEL LKINARQTLK RWVLEDEGRT IGANHLPECL RERMAQAPIA
VVEDPFALRL ERLREEYFIR MHHDFTHAYG DEAGWQAYSE YLHHGLFAIR RRLGLQRFAE
LTDTLDRALA EQLSSGSTDG HMAWLVPLLN EYYDPMYRYQ LEKKAANIVF RGTWQDVANW
LKAQ
