MIAE_PSEPK
ID MIAE_PSEPK Reviewed; 205 AA.
AC Q88KV1;
DT 23-FEB-2022, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 113.
DE RecName: Full=tRNA 2-(methylsulfanyl)-N(6)-isopentenyladenosine(37) hydroxylase {ECO:0000305};
DE EC=1.14.99.69 {ECO:0000269|PubMed:32785618};
DE AltName: Full=2-methylthio-N6-isopentenyladenosine(37)-tRNA monooxygenase {ECO:0000250|UniProtKB:Q08015};
DE AltName: Full=tRNA-(ms[2]io[6]A37)-hydroxylase {ECO:0000250|UniProtKB:Q08015};
GN Name=miaE {ECO:0000303|PubMed:32785618};
GN OrderedLocusNames=PP_2188 {ECO:0000312|EMBL:AAN67801.1};
OS Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950
OS / KT2440).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=160488;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440;
RX PubMed=12534463; DOI=10.1046/j.1462-2920.2002.00366.x;
RA Nelson K.E., Weinel C., Paulsen I.T., Dodson R.J., Hilbert H.,
RA Martins dos Santos V.A.P., Fouts D.E., Gill S.R., Pop M., Holmes M.,
RA Brinkac L.M., Beanan M.J., DeBoy R.T., Daugherty S.C., Kolonay J.F.,
RA Madupu R., Nelson W.C., White O., Peterson J.D., Khouri H.M., Hance I.,
RA Chris Lee P., Holtzapple E.K., Scanlan D., Tran K., Moazzez A.,
RA Utterback T.R., Rizzo M., Lee K., Kosack D., Moestl D., Wedler H.,
RA Lauber J., Stjepandic D., Hoheisel J., Straetz M., Heim S., Kiewitz C.,
RA Eisen J.A., Timmis K.N., Duesterhoeft A., Tuemmler B., Fraser C.M.;
RT "Complete genome sequence and comparative analysis of the metabolically
RT versatile Pseudomonas putida KT2440.";
RL Environ. Microbiol. 4:799-808(2002).
RN [2] {ECO:0007744|PDB:2ITB}
RP X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) IN COMPLEX WITH IRON.
RC STRAIN=ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440;
RG Joint Center for Structural Genomics (JCSG);
RT "Crystal structure of putative tRNA-(ms(2)io(6)a)-hydroxylase (NP_744337.1)
RT from Pseudomonas Putida KT2440 at 2.05 A resolution.";
RL Submitted (OCT-2006) to the PDB data bank.
RN [3] {ECO:0007744|PDB:6ZMA, ECO:0007744|PDB:6ZMB, ECO:0007744|PDB:6ZMC}
RP X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) OF 3-201, FUNCTION, CATALYTIC
RP ACTIVITY, COFACTOR, PATHWAY, SUBUNIT, AND MUTAGENESIS OF LYS-40 AND
RP ARG-100.
RC STRAIN=ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440;
RX PubMed=32785618; DOI=10.1093/nar/gkaa667;
RA Carpentier P., Lepretre C., Basset C., Douki T., Torelli S., Duarte V.,
RA Hamdane D., Fontecave M., Atta M.;
RT "Structural, biochemical and functional analyses of tRNA-monooxygenase
RT enzyme MiaE from Pseudomonas putida provide insights into tRNA/MiaE
RT interaction.";
RL Nucleic Acids Res. 48:9918-9930(2020).
CC -!- FUNCTION: Involved in specific tRNA modification. Catalyzes the oxygen-
CC dependent hydroxylation of 2-methylthio-N-6-isopentenyl adenosine
CC (ms2i6A) to produce 2-methylthio-N-6-(cis-hydroxy)isopentenyl adenosine
CC (ms2io6A) at position 37 in tRNAs. {ECO:0000269|PubMed:32785618}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-methylsulfanyl-N(6)-dimethylallyladenosine(37) in tRNA + AH2
CC + O2 = A + H2O + N(6)-[(2E)-4-hydroxy-3-methylbut-2-en-1-yl]-2-
CC (methylsulfanyl)adenosine(37) in tRNA; Xref=Rhea:RHEA:65812,
CC Rhea:RHEA-COMP:10376, Rhea:RHEA-COMP:17048, ChEBI:CHEBI:13193,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15379, ChEBI:CHEBI:17499,
CC ChEBI:CHEBI:74417, ChEBI:CHEBI:157739; EC=1.14.99.69;
CC Evidence={ECO:0000269|PubMed:32785618};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:65813;
CC Evidence={ECO:0000269|PubMed:32785618};
CC -!- COFACTOR:
CC Name=Fe cation; Xref=ChEBI:CHEBI:24875;
CC Evidence={ECO:0000269|PubMed:32785618};
CC Note=Contains a nonheme dinuclear iron cluster.
CC {ECO:0000269|PubMed:32785618};
CC -!- PATHWAY: tRNA modification; 2-methylthio-N-6-(cis-hydroxy)isopentenyl
CC adenosine-tRNA biosynthesis. {ECO:0000269|PubMed:32785618}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:32785618}.
CC -!- SIMILARITY: Belongs to the MiaE family. {ECO:0000305}.
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DR EMBL; AE015451; AAN67801.1; -; Genomic_DNA.
DR RefSeq; NP_744337.1; NC_002947.4.
DR RefSeq; WP_010953173.1; NC_002947.4.
DR PDB; 2ITB; X-ray; 2.05 A; A/B=1-205.
DR PDB; 6ZMA; X-ray; 2.15 A; B/C=3-201.
DR PDB; 6ZMB; X-ray; 1.70 A; B/C=3-201.
DR PDB; 6ZMC; X-ray; 2.50 A; B/C=3-201.
DR PDBsum; 2ITB; -.
DR PDBsum; 6ZMA; -.
DR PDBsum; 6ZMB; -.
DR PDBsum; 6ZMC; -.
DR SMR; Q88KV1; -.
DR STRING; 160488.PP_2188; -.
DR DNASU; 1045049; -.
DR EnsemblBacteria; AAN67801; AAN67801; PP_2188.
DR KEGG; ppu:PP_2188; -.
DR PATRIC; fig|160488.4.peg.2307; -.
DR eggNOG; COG4445; Bacteria.
DR HOGENOM; CLU_056571_0_0_6; -.
DR OMA; CEFKAAS; -.
DR PhylomeDB; Q88KV1; -.
DR BioCyc; PPUT160488:G1G01-2329-MON; -.
DR BRENDA; 1.14.99.69; 5092.
DR UniPathway; UPA00729; -.
DR EvolutionaryTrace; Q88KV1; -.
DR Proteomes; UP000000556; Chromosome.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004497; F:monooxygenase activity; IEA:UniProtKB-KW.
DR GO; GO:0045301; F:tRNA-(2-methylthio-N-6-(cis-hydroxy)isopentenyl adenosine)-hydroxylase activity; IEA:InterPro.
DR CDD; cd07910; MiaE; 1.
DR Gene3D; 1.20.1260.10; -; 1.
DR InterPro; IPR012347; Ferritin-like.
DR InterPro; IPR009078; Ferritin-like_SF.
DR InterPro; IPR010386; tRNA-Hydrxlase_MiaE.
DR PANTHER; PTHR42637; PTHR42637; 2.
DR Pfam; PF06175; MiaE; 2.
DR PIRSF; PIRSF020736; MiaE; 1.
DR SUPFAM; SSF47240; SSF47240; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Iron; Metal-binding; Monooxygenase; Oxidoreductase;
KW Reference proteome; tRNA processing.
FT CHAIN 1..205
FT /note="tRNA 2-(methylsulfanyl)-N(6)-
FT isopentenyladenosine(37) hydroxylase"
FT /id="PRO_0000454384"
FT BINDING 38
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:32785618, ECO:0000269|Ref.2,
FT ECO:0007744|PDB:2ITB, ECO:0007744|PDB:6ZMA,
FT ECO:0007744|PDB:6ZMB, ECO:0007744|PDB:6ZMC"
FT BINDING 69
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:32785618, ECO:0000269|Ref.2,
FT ECO:0007744|PDB:2ITB, ECO:0007744|PDB:6ZMA,
FT ECO:0007744|PDB:6ZMB, ECO:0007744|PDB:6ZMC"
FT BINDING 69
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:32785618, ECO:0000269|Ref.2,
FT ECO:0007744|PDB:2ITB, ECO:0007744|PDB:6ZMA,
FT ECO:0007744|PDB:6ZMB, ECO:0007744|PDB:6ZMC"
FT BINDING 72
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:32785618, ECO:0000269|Ref.2,
FT ECO:0007744|PDB:2ITB, ECO:0007744|PDB:6ZMA,
FT ECO:0007744|PDB:6ZMB, ECO:0007744|PDB:6ZMC"
FT BINDING 122
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:32785618, ECO:0000269|Ref.2,
FT ECO:0007744|PDB:2ITB, ECO:0007744|PDB:6ZMA,
FT ECO:0007744|PDB:6ZMB, ECO:0007744|PDB:6ZMC"
FT BINDING 151
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:32785618,
FT ECO:0007744|PDB:6ZMA, ECO:0007744|PDB:6ZMB,
FT ECO:0007744|PDB:6ZMC"
FT BINDING 154
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:32785618, ECO:0000269|Ref.2,
FT ECO:0007744|PDB:2ITB, ECO:0007744|PDB:6ZMA,
FT ECO:0007744|PDB:6ZMB, ECO:0007744|PDB:6ZMC"
FT MUTAGEN 40
FT /note="K->D: Loss of activity."
FT /evidence="ECO:0000269|PubMed:32785618"
FT MUTAGEN 100
FT /note="R->E: Loss of activity."
FT /evidence="ECO:0000269|PubMed:32785618"
FT HELIX 7..10
FT /evidence="ECO:0007829|PDB:2ITB"
FT STRAND 11..13
FT /evidence="ECO:0007829|PDB:2ITB"
FT HELIX 17..24
FT /evidence="ECO:0007829|PDB:2ITB"
FT HELIX 27..51
FT /evidence="ECO:0007829|PDB:2ITB"
FT TURN 52..54
FT /evidence="ECO:0007829|PDB:2ITB"
FT HELIX 56..82
FT /evidence="ECO:0007829|PDB:2ITB"
FT HELIX 95..100
FT /evidence="ECO:0007829|PDB:2ITB"
FT HELIX 109..132
FT /evidence="ECO:0007829|PDB:2ITB"
FT HELIX 133..135
FT /evidence="ECO:0007829|PDB:2ITB"
FT HELIX 138..165
FT /evidence="ECO:0007829|PDB:2ITB"
FT HELIX 168..187
FT /evidence="ECO:0007829|PDB:2ITB"
FT STRAND 188..192
FT /evidence="ECO:0007829|PDB:2ITB"
SQ SEQUENCE 205 AA; 23031 MW; DA044B40D55EA197 CRC64;
MSLIPEIDAF LGCPTPDAWI EAALADQETL LIDHKNCEFK AASTALSLIA KYNTHLDLIN
MMSRLAREEL VHHEQVLRLM KRRGVPLRPV SAGRYASGLR RLVRAHEPVK LVDTLVVGAF
IEARSCERFA ALVPHLDEEL GRFYHGLLKS EARHYQGYLK LAHNYGDEAD IARCVELVRA
AEMELIQSPD QELRFHSGIP QALAA
